Documentation

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Description
 
File Info
Date
IEM Nextera Quick Ref Card (15037155)
Instructions for using IEM with the Nextera sample prep kits.
iControlDB Download Client User Guide (11297399)
Instructions for installing the download client and downloading data from iControlDB.
TruSight Enrichment DNA Sample Prep Experienced User Card

Intended for the experienced user, this document summarizes instructions for using the TruSight Enrichment DNA Sample Prep Kit to prepare up to 96 indexed paired-end libraries, followed by enrichment using the TruSight Content Set CSO (custom selected oligos).

Infinium LCG Quad Assay Lab Tracking Form (15025911)

Lab tracking form for the Infinium LCG Quad assay.

HiSeq 2500 User Guide (15035786)

This guide contains an overview of instrument components and instructions for operating and maintaining the HiSeq 2500. Workflows include high output and rapid run.

RRBS for Methylation Analysis Guide (15021647)

Instructions for RRBS for Methylation Analysis.

MiSeq System Site Preparation Guide

This guide provides requirements for preparing your lab for a MiSeq System: lab space requirements, electrical requirements, bench recommendations, UPS recommendations, and user-supplied consumables.

TruSeq DNA Sample Preparation Low Sample Experienced User Card

Experienced-level instructions for using the TruSeq DNA sample prep LS protocol.

TruSight One Consumables and Equipment

This document provides a list of all of the necessary user-supplied consumables and equipment.

Frequently Asked Questions (FAQs) - Certificate of Analysis (CofA)

Frequently Asked Questions (FAQs) for the Certificate of Analysis (CofA)

Denaturing and Diluting Libraries for the NextSeq 500

This guide contains instructions for denaturing and diluting libraries before sequencing on the NextSeq 500, and instructions for preparing a PhiX control. This procedure is required for most library types.

TruSight Enrichment DNA Sample Prep Guide

Instructions for using the TruSight Enrichment DNA Sample Prep Kit to prepare up to 96 indexed paired-end libraries, followed by enrichment using the TruSight Content Set CSO (custom selected oligos).

TruSeq ChIP Sample Prep EUC and LTF

Experienced-level instructions for using the TruSeq ChIP Sample Prep Kit to prepare samples for sequencing.

Infinium HD Gemini Assay Experienced User Card, Automated Protocol (11311023)

Experienced-level instructions for performing the Infinium HD Gemini assay.

Excerpt (Troubleshooting) from HiScanSQ System User Guide (15015392)

Instructions for troubleshooting problems on the HiScanSQ.

TruSeq Synthetic Long-Read DNA Library Prep User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq Synthetic Long-Read DNA Library Prep Guide.

Sequencing Analysis Viewer User Guide

This guide includes instructions for installing and using Sequencing Analysis Viewer (SAV) software to view metrics generated by the real-time analysis software on Illumina sequencing systems.

CytoSNP-850K Protocol Guide (15046690)

Instructions for performing the CytoSNP-850K Assay Protocol.

TruSeq Synthetic Long-Read DNA Library Prep Guide

Instructions for preparing libraries using the TruSeq Synthetic Long-Read DNA Library Prep and TruSeq Synthetic Long-Read DNA Barcode kits.

Preparing Samples for ChIP Sequencing of DNA

Instructions for preparing samples using the ChIP-Seq sample prep Kit.

Infinium HD Assay Gemini Protocol Guide (11311007)

Instructions for performing the Infinium HD Gemini assay.

Using the Paired-End Cluster Generation Kit v2 on the Cluster Station and Paired-End Module (1005629)

Instructions for using the Paired-End Cluster Generation Kit v2 on the Cluster Station and Paired-End Module.

MiSeq System User Guide

This guide includes information about instrument components, MiSeq Control Software (MCS), and required consumables, and instructions for performing a sequencing run and maintaining the instrument.

NextSeq 500 System User Guide

This guide contains an overview of instrument components and instructions for operating and maintaining the NextSeq 500.

TruSeq Enrichment Guide

Instructions for performing the TruSeq Enrichment protocol.

MCS3 Expiration Date Change

Product Quality Notification for Recent DASL Purchases.

cBot User Guide

This guide contains instructions for using the cBot for cluster generation on flow cells for the HiSeq X, HiSeq high output runs, HiSeq rapid runs, Genome Analyzer.

TruSeq Nano DNA Sample Preparation High Sample Experienced User Card and Lab Tracking Form

Experienced-level instructions for preparing samples using the high sample protocol for the TruSeq Nano DNA Sample Prep Kit.

Nextera XT Sample Preparation Lab Tracking Form

Interactive form for recording sample preparation steps using the Nextera XT sample prep Kit.

GoldenGate Indexing Assay Automated Experienced User Card (15006938)

Experienced-level instructions for performing the GoldenGate Indexing assay.

IEM TruSeq Synthetic Long-Read DNA Quick Reference Card

Instructions for using IEM with the TruSeq Synthetic Long-Read DNA Library Prep and TruSeq Synthetic Long-Read DNA Barcode kits.

CASAVA v1.8 Quick Reference Booklet (15011197 B)

This download contains the quick reference booklet for CASAVA v1.8 sequencing analysis software.

Thermocycler Control Software User Guide (15004310)

Instructions for using the Thermocycler Control Software.

TruSeq RNA Sample Preparation High Throughput Lab Tracking Form

Instructions for using the TruSeq RNA sample prep HT protocol.

IEM TruSeq Small RNA Quick Ref Card (15037153)

Instructions for using IEM with the TruSeq Small RNA Sample Prep Kit.

TruSeq DNA PCR-Free Sample Prep Dual Index Product Insert

This document outlines dual index sequencing workflows and requirements with the TruSeq DNA PCR-Free HT Sample Prep Kit.

GoldenGate Assay for Methylation Experienced User Card, Multi-Use, Manual Protocol (11233117)

Experienced-level instructions for performing the GoldenGate assay for Methylation.

Hybridization Oven System Guide (11317134)

Instructions for performing the Hybridization Oven with Infinium assays.

GoldenGate Genotyping Assay Guide (15004065)

Instructions for performing the GoldenGate Genotyping assay

Using eQTL Demo Data (970-2009-011)

This download contains documentation explaining how to use eQTL Demo Data in GenomeStudio.

Infinium Multi-User LCG Assay Protocol Guide (15023284)

Instructions for performing the Infinium protocol using the manual method or the automated method.

KaryoStudio Software v1.4 Release Notes (11328870 D)

This download contains the release notes for version 1.4 of the KaryoStudio Software.

GoldenGate Genotyping Assay for VeraCode Experienced User Card, Manual Protocol (11312755)

Instructions for performing the GoldenGate Genotyping assay for VeraCode.

MiSeq System Safety and Compliance Guide

This guide contains safety information and product compliance markings for the MiSeq System.

TruSeq Nano DNA Sample Preparation Guide

Instructions for preparing samples using the TruSeq Nano DNA Sample Prep Kit.

TruSeq Stranded Total RNA Sample Prep HS EUC and LTF

Experienced-level instructions for preparing samples using the HS protocol for the TruSeq Stranded Total RNA Sample Prep Kit.

HiSeq X Safety and Compliance Guide

The safety and compliance guide describes safety considerations and lists product compliance markings for the HiSeq X.

TruSeq Stranded Total RNA Sample Preparation User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq Stranded Total RNA Sample Preparation Guide.

MicroRNA Expression Profiling Assay for SAMs Experienced User Card (11317311)

Experienced-level instructions for performing the MicroRNA Expression Profiling assay.

TruSeq RNA Sample Preparation Guide

This download contains the guide for the TruSeq RNA Sample Preparation protocol for sequencing.

BaseSpace Onsite User Guide

This guide contains instructions for using the BaseSpace Onsite System, a genomics analysis platform that is a directly integrated end-to-end solution.

Automated GoldenGate Genotyping Assay Lab Track Sheet (11295203)

Automated GoldenGate Genotyping Assay Lab Track Sheet (11295203)

Infinium LCG Assay Automated Protocol Experienced User Card (15023141)

Experienced-level instructions for performing the Infinium LCG assay automated protocol.

Human_mtDNA_D_Loop_Hypervariable_Region Guide (15034858)

Instructions for Human mtDNA D-Loop Hypervariable Region sample preparation.

TruSeq Stranded mRNA Dual Index Product Insert

Instructions for dual-indexing with TruSeq Stranded mRNA HT Sample Prep.

MicroRNA SAM Lab Track Form (11317337)

Lab tracking form for the microRNA Expression Profiling assay for SAMs.

BeadXpress Reader System Manual

This download contains the IVD (U.S.A. only) and RUO versions of the system manual for the BeadXpress Reader and VeraScan software v2.0.

Inf LCG Quad Manual EUC (15025909)

Experienced-level instructions for using the Infinium LCG Quad.

TruSeq DNA Sample Preparation (v1) High Throughput Experienced User Card

Instructions for using TruSeq DNA sample prep HT protocol.

GenomeStudio Protein Analysis Module v1.0 User Guide (11319148)

Instructions for using the GenomeStudio Polyploid Clustering Module to identify clusters for samples for which the standard diploid clustering algorithm is not appropriate or otherwise useful, such as for polyploid organisms like wheat and potato.

TruSight DNA Amplicon Library Preparation Experienced User Card and Lab Tracking Form

Experienced user level instructions for preparing samples using the TruSight DNA Amplicon Library Preparation Kit.

TruSeq Stranded mRNA Sample Prep LS EUC and LTF

Experienced-level instructions for preparing samples using the LS protocol for the TruSeq Stranded mRNA Sample Prep Kit.

VeraCode Assay Guide

This download contains the user guide for performing multiple assays using VeraCode technology on the BeadXpress platform.

GenomeStudio DNA Sequencing Module v1.0 User Guide (11319092)

Instructions for using the GenomeStudio DNA Sequencing Module to visualize and analyze sequencing data.

GoldenGate Genotyping Assay for VeraCode Automated Protocol Experienced User Card (11312763)

Experienced-level instructions for performing the GoldenGate Genotyping assay for VeraCode.

Denaturing and Diluting Libraries for the HiSeq and GAIIx

This guide contains instructions for denaturing and diluting libraries for sequencing on the HiSeq and GAIIx, and instructions for preparing a PhiX control.

Infinium Multi-Use LCG Assay Lab Tracking Form (15023287)

Lab tracking form for the Infinium Multi-Use LCG assay.

bcl2fastq v1.8.4 Conversion User Guide

This guide includes instructions for using the bcl2fastq 1.8.4 conversion software to convert MiSeq or HiSeq output to standard FASTQ file formats for downstream analysis using third-party analysis solutions.

DASL Gene Expression Assay for VeraCode Manual Protocol (11312780)

Experienced-level instructions for performing the DASL Gene Expression assay for VeraCode.

Nextera DNA Sample Preparation Product Insert

This download contains the product insert listing the necessary sample preparation kits, software, and documentation for Nextera DNA Sample Preparation as well as pooling guidelines and requirements for enabling dual indexing.

Illumina Infinium HD FFPE Assay Automated Protocol Experienced User Card (15021524)

Experienced-level instructions for performing the Infinium HD FFPE assay automated protocol.

Infinium HD FFPE Assay Protocol Guide (15021525)

Instructions for performing the Infinium HD FFPE assay.

MiSeq Workflow Quick Reference Cards

Each quick reference card provides a graphical representation of the MiSeq analysis workflow for the experienced user. Workflows include Assembly, Enrichment, Library QC, Metagenomics, PCR Amplicon, Resequencing, Small RNA, and TruSeq Amplicon.

DASL Assay Automation Experienced User Card (11195173)

Experienced-level instructions for performing the DASL assay.

Illumina Sequencers Support - Configuring Virus Scanner Software Download

Explains how to set up virus scanners on instrument control computers for HiSeq, HiScanSQ, MiSeq and Genome Analyzer, such that they do not degrade or harm system performance

GoldenGate Genotyping Assay for Universal BeadChip Lab Tracking Form (15004071)

Lab tracking form for GoldenGate Genotyping assay for Universal BeadChip.

TruSeq SBS Kit v3 Reagent Prep Guide

This guide contains instructions for preparing SBS reagents provided in TruSeq SBS Kit v3 for the HiSeq.

HiSeq Safety and Compliance Guide

This guide contains safety information and product compliance statements for the HiSeq.

TruSeq DNA PCR-Free Sample Preparation High Sample Experienced User Card and Lab Tracking Form

Experienced-level instructions for preparing samples using the high sample protocol for the TruSeq DNA PCR-Free Sample Preparation Kit.

Mate Pair Library v2 Sample Preparation Guide for 2-5 kb Libraries (15008135)

Instructions for preparing samples using the Mate Pair Library Kit v2.

TruSight One Sequencing Panel Library Prep Guide

Instructions for using the TruSight One Sequencing Panel Library Prep Kit to prepare up to 36 indexed paired-end libraries, followed by enrichment using the TruSight One Content Set.

Nextera Rapid Capture Enrichment Sequencing Product Insert

This document outlines the sequencing workflows and requirements with the Nextera Rapid Capture Exome, Expanded Exome, and Custom Enrichment Kits.

Running TruSight Tumor Analysis on HiSeq 2500

This guide includes instructions for generating, sequencing, and analyzing TruSight Tumor libraries with the HiSeq 2500.

Preparing Samples for Paired-End Sequencing (1005063)

Instructions for preparing samples using the Paired-End sample prep Kit.

GenomeStudio Genotyping Module Workflow for the GoldenGate Indexing Assay (15009829)

Instructions for performing GenomeStudio Genotyping Module for the GoldenGate Indexing assay.

Genomic DNA Sample Prep Guide - Oligo Only Kit (1003492)

This download contains the sample preparation guide for sequencing genomic DNA (Oligo Only Kit).

Directional mRNA-Seq Sample Prep Guide (15018460)

Instructions for performing the Directional mRNA-Seq sample prep assay.

TruSeq Amplicon - Cancer Panel Lab Tracking Form

Interactive form for recording sample preparation steps using the TruSeq Amplicon - Cancer Panel kit.

Infinium HD FFPE Lab Tracking Form (15021527)

Lab tracking form for the Infinium HD FFPE.

MiSeqDx Cystic Fibrosis 139-Variant Assay Reference Guide

This guide contains best practices and instructions for preparing libraries using the MiSeqDx Cystic Fibrosis 139-Variant Assay.

TruSeq Custom Amplicon Library Preparation Guide

Instructions for preparing samples using the TruSeq Custom Amplicon Library Preparation Kit.

Whole-Genome Gene Expression DASL Assay (11322347)

Instructions for performing the Whole-Genome Gene Expression DASL assay.

TruSeq Stranded mRNA Sample Preparation User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq Stranded mRNA Sample Preparation Guide.

TruSeq Rapid Cluster Kit Documentation

This guide contains instructions for preparing reagents provided in the TruSeq Rapid Cluster Kit for rapid runs on the HiSeq 2500 and HiSeq 1500.

Infinium II Assay HC Two-Sample Manual Experienced User Card (11280802)

Experienced-level instructions for performing the Infinium II assay HC Two-Sample protocol.

Performing Rapid Run Primer Rehybridization

Instructions for performing rapid run primer rehybridization on the HiSeq 2500 and HiSeq 1500.

Illumina Experiment Manager Guide (15031335)

Instructions for using the Illumina Experiment Manager.

Introduction to MiSeq Reporter Analysis Workflows Quick Ref

This document provides a brief description of each available MiSeq Reporter workflow and file formats of analysis output files.

NextSeq 500 Safety and Compliance Guides

The safety and compliance guide contains safety considerations and product compliance markings for the NextSeq 500.

The RFID Reader guide contains compliance information for the RFID reader, an internal component of the NextSeq 500.

TruSeq DNA Sample Preparation High Sample Lab Tracking Form

Lab tracking form for the TruSeq DNA sample prep HS protocol.

Infinium HD Super Assay Protocol Guide ( 11322427)

Instructions for performing the Infinium HD Super assay.

MiSeq Reporter Amplicon - DS Workflow Reference Guide

This guide provides an overview of the MiSeq Reporter Amplicon - DS analysis workflow, including installation instructions, workflow requirements, and descriptions of analysis output files.

Autoloader Single BeadArray Reader Configuration Quick Reference Card (11219892)

Instructions for setting up and configuring the Autoloader Single BeadArray Reader.

MiSeqDx Cystic Fibrosis 139-Variant Assay Package Insert

This document includes information about the intended use, instructions for use, and performance characteristics of the MiSeqDx Cystic Fibrosis 139-Variant Assay.

Lab tracking form for the Whole-Genome Gene Expression DASL HT assay (11233109).

Experienced-level instructions for performing the GoldenGate Methylation assay.

Staggering Runs on the HiSeq 2000 or 2500

This quick reference covers how to start and stop experiments independently on sides A and B and run staggered runs continuously on the HiSeq 2000 or HiSeq 2500.

cBot Lab Tracking Form for the Rapid IAL Workflow

This download contains the interactive lab tracking form for the Rapid Individual Addressable Lane (IAL) workflow on the cBot.

Lab Tracking Form Single-Read Cluster Station v5 (15019439)

Lab Tracking Form Single-Read Cluster Station v5 (15019439)

TruSeq Amplicon - Cancer Panel Library Preparation Guide

Instructions for preparing samples using the TruSeq Amplicon - Cancer Panel Library Preparation Kit.

MicroRNA Expression Profiling Assay for BeadChips Experienced User Card

Experienced-level instructions for performing the MicroRNA Expression Profiling assay for BeadChips.

TruSeq Stranded mRNA Sample Prep HS EUC and LTF

Experienced-level instructions for preparing samples using the HS protocol for the TruSeq Stranded mRNA Sample Prep Kit.

VeraCode ADME Core Panel Assay Lab Tracking Form (15009588)

Lab tracking form for the VeraCode ADME Core Panel assay.

AutoLoader 2.x User Guide (15015394)

Instructions for using the AutoLoader 2.x.

HiSeq Analysis Software User Guide

HiSeq Analysis Software User Guide

TruSight One Sequencing Panel Quick Reference Cards

These application workflow cards provide guidance for planning, running, and analyzing a TruSight One Sequencing Panel project.

NextSeq 500 System Site Preparation Guide

This guide contains lab specifications and requirements for NextSeq 500 installation and operation.

Infinium HD FFPE Methylation Assay Manual Protocol Experienced User Card (15027310)

Experienced-level instructions for performing the Infinium HD FFPE assay.

MiSeqDx Instrument Package Insert

This document includes information about the intended use, instructions for use, and performance characteristics of the MiSeqDx Instrument.

Nextera Enrichment Sample Preparation Experienced User Card

Experienced-level instructions for preparing samples using the Nextera Enrichment Kit.

BeadStation 500G System Manual (11165222 B)

This download contains the user guide for BeadStation 500G.

TruSeq DNA Sample Preparation High Sample Experienced User Card

Experienced-level instructions for using the TruSeq DNA sample prep HS protocol.

Infinium Multi-Use LCG Assay Manual Protocol Experienced User Card (15023285)

Experienced-level instructions for performing Infinium Multi-Use LCG assay.

HiScanSQ System Sequencing Best Practices (15029252)

Best practices poster for the HiScanSQ system.

HiSeq Sequencing System Site Preparation Guide (15006407)

This guide contains lab specifications and requirements for HiSeq installation and operation.

Nextera DNA Sample Preparation Guide

Instructions for preparing samples using the Nextera DNA sample preparation Kit.

GoldenGate Indexing Assay Guide (15006937)

Instructions for performing the GoldenGate Indexing assay.

GoldenGate Assay for Methylation Multi-Use Automated Experienced User Guide (11233096)

Experienced-level instructions for performing the GoldenGate assay for methylation.

MiSeq Reporter Workflows in BaseSpace Customer Release Notes

Release notes for MiSeq Reporter workflows in BaseSpace.

TruSeq Sample Prep Best Practices Guide

Overview of the best practices for the TruSeq sample prep protocol.

Nextera DNA Sample Preparation Experienced User Card

Experienced-level instructions for preparing samples using the Nextera DNA sample preparation Kit.

Golden Gate Meth for Vera Code Lab Tracking Form (11312739)

Lab tracking form for the Golden Gate Meth for Vera Code.

CASAVA Software Version 1.7 User Guide (15011196 A)

This download contains the user guide for the CASAVA v1.7 sequencing analysis software.

Preparing Samples for Sequencing Genomic DNA (1003806)

Instructions for preparing samples using the Genomic DNA kit.

Infinium II Assay HC Two-Sample Automated Experienced User Card (11280811)

Experienced-level instructions for performing the Infinium II assay.

GenomeStudio Gene Expression Module v1.0 User Guide (11319121)

Instructions for using the GenomeStudio Gene Expression Module to view analysis data.

MiSeqDx Cystic Fibrosis Clinical Sequencing Assay Physician Insert

This guide contains physician information for the MiSeqDx Cystic Fibrosis Clinical Sequencing Assay.

TruSeq RNA Sample Preparation High Throughput Experienced User Card

Instructions for using the TruSeq RNA sample prep HT protocol.

TruSeq DNA Sample Preparation (v1) Low Throughput Experienced User Card

Instructions for using the TruSeq DNA sample prep LT protocol.

Preparing Samples for Analysis of Small RNA Using the Oligo Only Kit (1003651)

Instructions for preparing samples using the Small RNA Oligo Only Kit.

TruSeq Targeted RNA Expression Guide

Instructions for preparing samples using the TruSeq Targeted RNA Expression Kit.

TruSeq DNA PCR-Free Sample Preparation Guide

Instructions for preparing samples using the TruSeq DNA PCR-Free Sample Preparation Kit.

Nextera Mate Pair Sample Preparation Guide

This guide explains how to prepare samples using the Nextera Mate Pair Sample Preparation Kit.

MiSeqDx Cystic Fibrosis Clinical Sequencing Assay Package Insert

This document includes information about the intended use, instructions for use, and performance characteristics of the MiSeqDx Cystic Fibrosis Clinical Sequencing Assay.

TruSeq Enrichment User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq Enrichment Guide.

MiSeqDx Cystic Fibrosis Clinical Sequencing Assay Lab Tracking Form

This document summarizes the steps in the MiSeqDx Cystic Fibrosis Clinical Sequencing Assay and includes fields for recording reagent lot numbers, as well as start and stop times for various steps.

VeraCode and BeadXpress Equipment Materials and Reagents Checklist ( 11275659)

List of equipment, materials, and reagents required for VeraCode and BeadXpress.

Infinium HD FFPE Restore Protocol Guide (15014614)

Instructions for performing the Infinium HD FFPE Restore protocol.

Illumina Infinium HD Methylation Assay Automated Protocol Experienced User Card (15019521)

Experienced-level instructions for performing the Infinium HD Methylation assay.

GoldenGate Genotyping Assay for Universal Array Matrix Lab Tracking Form (15005077)

Lab tracking form for the GoldenGate Genotyping assay for Universal Array.

MiSeq Reporter v2.1 Theory of Operation (15038604)

Summary of concepts and workflows in the MiSeq Reporter software.

GenomeStudio Software 2009.1 Release Notes (11319658 B)

This download contains the release notes for GenomeStudio Software 2009.1.

TruSight Tumor Sample Prep Experienced User Card

Intended for the experienced user, this document summarizes instructions for using the TruSight Tumor Sample Prep Kit. Sufficient reagents are supplied for 48 samples and indexes provided enable sample indexing of 4 samples per sequencing run.

MiSeq Software Release Notes

MiSeq software release notes describe features and changes introduced in the latest versions of MiSeq Control Software (MCS) and related software components, including MiSeq Reporter.

Illumina LIMS Project Manager Guide (15000396)

Instructions for using Illumina LIMS to manage projects and tasks, generate reports, and track history.

TruSeq Stranded Total RNA Sample Prep Guide

Instructions for preparing samples using the TruSeq Stranded Total RNA Sample Prep Kit.

CASAVA User Guide (15011196 D)

This download contains the user guide for the CASAVA sequencing analysis software.

VeraCode Bead Kitting System User Guide (11248028)

Instructions for kitting and storing VeraCode beads, as well as cleaning the bead kitting system.

TruSeq Synthetic Long-Read DNA Library Prep Sequencing and Analysis Product Insert

This document outlines sequencing and analysis workflows with the TruSeq Synthetic Long-Read DNA Library Prep and TruSeq Synthetic Long-Read DNA Barcode kits.

MiSeqDx Instrument Site Preparation Guide

This guide provides requirements for preparing a lab for the MiSeqDx Platform: lab space requirements, electrical requirements, bench recommendations, UPS recommendations, and user-supplied consumables.

CytoSNP-850K Assay Experienced User Card (15046993)

Experienced-level instructions for performing the CytoSNP-850K assay protocol.

Infinium LCG Quad Assay Automated Protocol Experienced User Card (15025910)

Experienced-level instructions for performing the Infinium LCG Quad assay.

TruSeq Nano DNA Sample Prep Dual Index Product Insert

This document outlines dual index sequencing workflows and requirements for the TruSeq Nano DNA HT Sample Prep Kit.

HiSeq SBS Kit v4 Reference Guide

This guide contains instructions for preparing reagents provided in the HiSeq SBS Kit v4 for use with HiSeq v4 high output mode.

Release Notes for BaseSpace Onsite

Release Notes for BaseSpace Onsite v1.1

GoldenGate GT for VeraCode Lab Tracking Form (11312721)

Lab tracking form for the GoldenGate GT for VeraCode.

GTS LIMS User Guide (11295182 A)

This download contains the user guide for the Genotyping System Lab Information Management System (GTS LIMS).

IEM TruSeq Targeted RNA Expression Quick Reference Card

Instructions for using IEM with the TruSeq Targeted RNA Expression kits.

HiSeq X HD Reagent Kit Reference Guide

The kit reference guide contains an overview of kit components and instructions for preparing the reagents and the flow cell for a sequencing run on the HiSeq X.

Illumina Infinium LCG Assay Manual Protocol Experienced User Card (15023140)

Experienced-level instructions for performing the Infinium LCG assay manual protocol.

Infinium II Multi-Sample Assay Experienced User Card, Manual Protocol (11208000)

Experienced-level instructions for performing the Infinium II Multi-Sample assay.

Whole-Genome Gene Expression Direct Hybridization Assay (11322187)

Experienced-level instructions for performing the Whole-Genome Gene Expression Direct Hybridization assay.

TruSeq Amplicon - Cancer Panel Resources (15033227)

Links to documentation, accessories, and product files for the TruSeq Amplicon - Cancel Panel.

HiSeq System Upgrade Information Sheet

This document describes key upgrade features, upgrade components, software upgrade features, and new chemistry features.

TruSeq Stranded mRNA Sample Prep Guide

Instructions for using the TruSeq Stranded mRNA sample prep protocol.

Infinium Karyomapping Lab Tracking Form (15052711)

Lab tracking form for the Infinium Karyomapping Assay.

GoldenGate Methylation Single-Use DNA Auto EUC (11233088 A)

This download contains the experienced user card for performing the GoldenGate Methylation Assay with Single-Use DNA, using the automated protocol.

TruSeq DNA PCR-Free Sample Preparation Low Sample Experienced User Card and Lab Tracking Form

Experienced-level instructions for preparing samples using the low sample protocol for the TruSeq DNA PCR-Free Sample Preparation Kit.

VeraCode Vortex Incubator User Guide (11251876 A)

This download contains the Vortex Incubator User Guide for use with VeraCode Assays.

iScan Control Software Release Notes (15022764 C)

Summary of changes introduced in iScan Control Software (ICS) v3.3.29.

TruSeq ChIP Sample Preparation User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq ChIP Sample Preparation Guide.

TruSeq RNA Sample Preparation Low Throughput Lab Tracking Form

Lab tracking form for the TruSeq RNA sample prep LT protocol.

GoldenGate Methylation Assay for VeraCode Experienced User Card, Manual Protocol (11312771)

Instructions for performing the GoldenGate Methylation assay for VeraCode.

Nextera XT PCR Amplicon Quick Reference Cards

These application workflow cards provide guidance for planning, running, and analyzing a Nextera XT PCR Amplicon project.

Nextera DNA Resequencing Quick Reference Cards

These application workflow cards provide guidance for planning, running, and analyzing a Nextera DNA Resequencing project.

Infinium Assay Lab Setup and Procedures (11322460)

Lab requirements and preparation instructions for performing Infinium assays.

KaryoStudio Software v1.3 Release Notes (11328870 C)

This download contains the release notes for version 1.3 of the KaryoStudio Software.

TruSeq DNA Sample Preparation (v1) Guide

Instructions for using the TruSeq DNA sample prep (v1) protocol.

HiScanSQ System User Guide (15015392)

Instructions for using the HiScanSQ.

Infinium Plate Heat Sealing Best Practices Video

This video demonstrates the updated heat sealing technique for the Infinium assay. This heat sealing technique is required for the Infinium Multi-Use assay and recommended for all Infinium assays.

GoldenGate Methylation Lab Tracking Worksheet (11237396 A)

This download contains the GoldenGate Methylation Lab Tracking Worksheet.

TruSeq DNA Sample Preparation (v1) High Throughput Lab Tracking Form

Lab tracking form for the TruSeq DNA sample prep HT assay.

Infinium HD Assay Ultra Manual Experienced User Card (11328095)

Experienced-level instructions for performing the Infinium HD assay ultra manual protocol.

mRNA-Seq Sample Prep Guide (1004898 D)

This download contains the sample preparation guide for mRNA sequencing.

GenomeStudio Software 2011.1 Release Notes

Summary of new features and known issues in the GenomeStudio Software 2011.1 release.

MiSeqDx Universal Kit 1.0 Reference Guide

This guide contains best practices and instructions for preparing libraries using the MiSeqDx Universal Kit 1.0.

Infinium HD FFPE QC Assay Protocol Guide (15020981)

Instructions for determining whether DNA samples are candidates for the Infinium HD FFPE genotyping or methylation assay.

Infinium Multi-User LCG Assay Automated Protocol Experienced User Card (15023286)

Experienced-level instructions for performing the Infinium Multi-User LCG assay.

TruSight Enrichment DNA Sample Prep Kit Lab Tracking Form

This download contains the lab tracking form for the TruSight Enrichment DNA Sample Prep Kit.

GenomeStudio 2009.1 Release Notes (11319658)

Summary of changes introduced in GenomeStudio 2009.1 software.

WGDASL HT Assay Guide (15018210)

Instructions for performing the WGDASL HT assay.

CASAVA v1.8 Changes

Summary of changes introduced in CASAVA v1.8.

TruSeq Sample Preparation Pooling Guide

Instructions for pooling samples using the TruSeq LT, HT, Small RNA, or ChIP sample prep kits.

Whole-Genome Gene Expression Direct Hybridization Assay Lab Tracking Form (11327279)

Interactive form for recording steps during the Whole-Genome Gene Expression Direct Hybridization assay.

TruSeq Cluster Kit v2 (cBot-GA) Reagent Prep Guide

This guide contains descriptions of kit components and instructions for preparing reagents provided in TruSeq Cluster Kit v2.

GenomeStudio GT Module v1.0 UG (11319113 A)

This download contains the GenomeStudio GT Module v1.0 user guide. The GenomeStudio release notes, available separately for download, describe updates to this module since v1.0.

TruSeq DNA Sample Preparation (v1) Low Throughput Lab Tracking Form

Lab tracking form for the TruSeq DNA sample prep protocol.

Beeline Software User Guide (15016340)

Instructions for using Beeline software.

IEM TruSeq DNA, RNA, or ChIP Quick Reference Card (15037152)

Instructions for using IEM with the TruSeq DNA, RNA, or ChIP sample prep kits.

Preparing Libraries for Sequencing on the MiSeq

This guide provides instructions for denaturing and diluting libraries after sample preparation and before sequencing on the MiSeq, and instructions for preparing a PhiX control. This procedure is required for most library types. It is not required for TruSeq Custom Amplicon libraries, TruSeq Amplicon - Cancer Panel libraries, or Nextera XT libraries.

GoldenGate Genotyping Assay Automated Protocol Experienced User Card (11295191)

Experienced-level instructions for performing the GoldenGate Genotyping assay.

GenomeStudio Software v2011.1 Release Notes

Summary of changes introduced GenomeStudio Software v2011.1.

NuPCR Assay Guide

This download contains the assay guide for the NuPCR assay.

FastTrack Services Long Reads Pipeline User Guide

This document provides an overview of the Long Read Sequencing Service informatics pipeline. It provides details of the source and contents of the main files that Illumina sequencing services creates when assembling long read data sets. Additionally it provides information about the algorithms used for assembling the synthetic long reads. The aim of this document is to help you understand the Long Read Sequencing Service data package that you received from Illumina.

TruSeq Enrichment Lab Tracking Form

Lab tracking form for the TruSeq Enrichment protocol.

New TeFlow Components in the Infinium LCG Assay (15024058)

Ordering information for the TeFlow components used in the Infinium LCG assay.

WGDASL HT Experienced User Card (15018211)

Experienced-level instructions for using the WGDASL HT.

IEM TruSeq Amplicon Quick Ref Card (15037154)

Instructions for using IEM with the TruSeq Amplicon kits.

TruSeq Targeted RNA Expression Experienced User Card and Lab Tracking Form

Experienced-level instructions for preparing samples using the TruSeq Targeted RNA Expression Kit.

MiSeq Run Folder Quick Reference Card

Quick reference overview of the MiSeq Output and Analysis Folders.

TruSeq DNA PCR-Free Sample Preparation User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq DNA PCR-Free Sample Preparation Guide.

GoldenGate Auto EUC for Universal Array Matrix (15005076 A)

This download contains the experienced user card for performing the GoldenGate Genotyping Assay on Universal Array Matrices (UAMs) using the automated protocol.

VeraCode ADME Software Release Notes (15036802)

Summary of instructions for using the VeraCode ADME Software.

Nextera Mate Pair Gel-Plus Experienced User Card

Intended for the experienced user, this document summarizes the steps for preparing samples using the Nextera Mate Pair Gel-Plus protocol.

Nextera DNA Assembly Quick Reference Cards

These application workflow cards provide guidance for planning, running, and analyzing a Nextera DNA Assembly project.

Frequently Asked Questions (FAQs) for the Master Lot Sheet (MLS)

Frequently Asked Questions (FAQs) for the Master Lot Sheet (MLS)

TruSeq Rapid SBS Kit Reagent Preparation Guide for HiSeq 1500 and HiSeq 2500.

This guide contains instructions for preparing SBS reagents provided in the TruSeq Rapid SBS Kit for rapid runs on the HiSeq 1500 and 2500.

Infinium HD Ultra Lab Tracking Form (11328116)

Lab tracking form for the Infinium HD Ultra.

TruSight Tumor Sample Prep Guide

Instructions for using the TruSight Tumor Sample Prep protocol.

AutoLoader Dual BeadArray Reader Configuration Quick Reference Card (11219905)

Instructions for configuring the AutoLoader Dual BeadArray Reader.

Nextera Rapid Capture Enrichment User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the Nextera Rapid Capture Enrichment Guide.

iScan System Safety and Compliance Guide (15022905)

Safety information and product compliance statements for the iScan.

GGGT Auto EUC (15004069)

Experienced-level instructions for performing the GoldenGate Genotyping assay, Automated.

Nextera Rapid Capture Guide

Instructions for preparing samples using the Nextera Rapid Capture Enrichment Kit.

Using the Illumina FFPE QC Kit with the TruSeq Amplicon - Cancer Panel

Instructions for using the FFPE QC kit with the TruSeq Amplicon - Cancer Panel.

CASAVA 1.8.2 Quick Reference Guide (15011197)

Reference Guide for CASAVA v1.8.2 software.

HiSeq Lab Tracking Form (15011200)

This download contains the interactive lab tracking form for high output runs on the HiSeq.

MiSeqDx Instrument Reference Guide

This guide includes information about instrument components, MiSeq Operating Software, and instructions for performing a sequencing run and maintaining the MiSeqDx instrument.

Infinium LCG Assay Lab Tracking Form (15023142)

Lab tracking form for the Infinium LCG assay.

TruSeq RNA Sample Prep v2 Guide

Instructions for preparing samples using the TruSeq RNA Sample Preparation Kit v2.

Lab tracking form for the Infinium HD assay Super.

Infinium HD Assay Super Lab Tracking Form (11327261)

Infinium II Assay Two-Sample HC Protocols (11280749)

Instructions for performing the Infinium II Two-Sample assay.

HiSeq X Lab Tracking Form

The lab tracking form is an interactive form for recording run details, reagent weights, and priming volumes.

Infinium HD Methylation Assay Manual Protocol Experienced User Card (15019522)

Experienced-level instructions for performing the Infinium HD Methylation assay.

TruSeq Enrichment Analysis Guide (15029648)

Instructions for TruSeq Enrichment Analysis.

Infinium Assay Glass Cleaning Protocol (11316641)

Infinium Assay Glass Cleaning Protocol (11316641)

MiSeq Sample Sheet Quick Reference Guide

This guide provides guidance for setting up sample sheets for sequencing on the MiSeq.

Nextera XT DNA Sample Preparation Guide

Instructions for preparing samples using the Nextera XT DNA sample preparation Kit.

Infinium Workflow Settings and Specifications (370-2010-014)

Summary of workflow requirements and estimated scan times for Infinium BeadChips.

Off-Line Basecaller v1.9.4 User Guide (15009920)

Instructions for using OLB v1.9.4 for basecalling and converting *.bcl files to *qseq.txt files.

iScan System Quick Reference Guide (15020712)

Instructions for using the iScan.

VeraCode ADME Kit Mod Release Notes (15031141)

Summary of instructions for using the VeraCode ADME Kit Module Software.

TruSeq RNA Sample Preparation v2 Low Sample Experienced User Card and Lab Tracking Form

Experienced-level instructions for preparing samples using the low sample protocol for the TruSeq RNA Sample Preparation v2 Kit.

Infinium Karyomapping Protocol Guide (15052711)

Instructions for performing the Infinium Karyomapping Protocol.

MiSeqDx Universal Kit 1.0 Package Insert

This document includes information about the intended use, instructions for use, and performance characteristics of the MiSeqDx Universal Kit.

MiSeqDx Cystic Fibrosis 139-Variant Assay Physician Insert

This guide contains physician information for the MiSeqDx Cystic Fibrosis 139-Variant Assay.

Human mtDNA Genome Guide (15037958)

Instructions for Human mtDNA Genome sample preparation.

FastTrack Phasing Services User Guide

This document provides an overview of the Phasing Analysis sequencing service informatics pipeline. It provides details of the source and contents of the main files that Illumina sequencing services creates when analyzing phasing data sets. Additionally it provides information about the algorithms used for phasing. The aim of this document is to help you understand the Phasing Analysis Sequencing Service data package that you received from Illumina.

Genome Analyzer IIx Site Prep Guide

This guide contains lab specifications and requirements for installing and operating the Genome Analyzer.

Analysis Visual Controller v1.7 User Guide

Analysis Visual Controller (AVC) v1.7 User Guide

Performing a Read 2 Rehybridization on a HiSeq Flow Cell (15033400)

Instructions for performing a Read 2 rehybridization on a HiSeq flow cell.

Ultra Low mRNA-Seq Sample Prep Guide (11322751)

Instructions for Ultra Low mRNA-Seq sample preparation.

Infinium HD Super Assay Experienced User Card, Automated Protocol (11322291)

Experienced-level instructions for performing the Infinium HD Super assay.

User-supplied consumables and equipment excerpt from the TruSeq RNA Sample Preparation v2 Guide.

Consumables and equipment excerpt from the TruSeq RNA Sample Preparation v2 Guide.

Multiplexing Sample Prep Guide (1005361)

Instructions for performing the Multiplexing sample prep assay.

TruSeq Stranded Total RNA Dual Index Product Insert

Instructions for dual-indexing with TruSeq Stranded Total RNA HT Sample Prep.

GoldenGate Indexing Assay Lab Tracking Form for Universal BeadChip, 8x192 or 4x384 Index (15009926)

Interactive form for recording steps during the GoldenGate Indexing assay.

TruSeq Small RNA Sample Preparation User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq Small RNA Sample Preparation Guide.

Nextera Rapid Capture Experienced User Card and Lab Tracking Form

Experienced-level instructions for preparing samples using the Nextera Rapid Capture Enrichment Kit.

WGDASL HT Lab Tracking Form (15018212)

Lab tracking form for the Whole-Genome Gene Expression DASL HT assay.

MiSeq Reporter User Guide (15028784)

This guide provides an overview of the MiSeq Reporter interface and instructions for using the MiSeq Reporter. For information about analysis workflows, see the MiSeq Reporter Workflow Reference Guides.

Important Customer Information about the Infinium LCG Assay (15024057)

Summary of guidelines and requirements for performing the Infinium LCG assay.

MiSeq Reporter Software Reference Guide (15038356)

This guide describes the MiSeq Reporter user interface, defines concepts and terms, and explains the folders, files, and data generated from the Amplicon workflow used to analyze MiSeqDx Cystic Fibrosis Assays and Universal Kit 1.0.

Small RNA Sample Prep Guide (1004239)

Instructions for performing the Small RNA sample prep assay.

GenomeStudio Protein Analysis Module v1.0 User Guide (11319148)

Instructions for using the GenomeStudio Protein Analysis Module v1.0 to view analysis data.

TruSeq Synthetic Long-Read DNA Library Prep Experienced User Card and Lab Tracking Form

Experienced-level instructions for preparing libraries using the TruSeq Synthetic Long-Read DNA Library Prep and TruSeq Synthetic Long-Read DNA Barcode kits.

Best Practices for Infinium Assays (370-2009-010)

Best practices for performing Infinium assays.

TruSeq RNA Sample Preparation Low Throughput Experienced User Card

Experienced-level instructions for using the TruSeq RNA sample prep LT protocol.

Infinium Karyomapping Technical Guide (15052496)

An introduction to the Infinium Karyomapping Protocol.

MiSeqDx Cystic Fibrosis Clinical Sequencing Assay Reference Guide

This guide contains best practices and instructions for preparing libraries using the MiSeqDx Cystic Fibrosis Clinical Sequencing Assay.

Using Custom Primers on the MiSeq

This guide provides instructions for using custom primers for sequencing on the MiSeq.

Sequencing Dual-Indexed Libraries on the HiSeq System User Guide (15032071)

This guide contains instructions for sequencing dual-indexed libraries on the HiSeq.

MiSeq Enhancements Customer Letter

This customer letter describes enhancements and components associated with the MiSeq upgrade, and how upgrades are schedule.

Nextera XT DNA Sample Preparation Insert

Summary of the Nextera XT DNA sample preparation.

TruSeq RNA Sample Preparation v2 High Sample Experienced User Card and Lab Tracking Form

Experienced-level instructions for preparing samples using the high sample protocol for the TruSeq RNA Sample Preparation v2 Kit.

Small RNA v1.5 Sample Prep Guide (15002615)

Instructions for using the Small RNA v1.5 sample prep.

MiSeqDx Instrument Safety and Compliance Guide

This guide contains safety information and product compliance markings for the MiSeqDx instrument.

Inf HD Gemini Lab Tracking Form (11311031)

Lab tracking form for the Inf HD Gemini assay.

GenomeStudio Methylation Module v1.8 User Guide (11319130)

Instructions for using the GenomeStudio Methylation Module v1.8 software.

iScan System Quick Reference Card (11313555)

Instructions for starting up and shutting down the iScan.

TruSeq Small RNA Sample Prep Guide

Instructions for using the TruSeq Small RNA sample prep protocol.

Sequencing Mixed Libraries on a HiSeq or GA Flow Cell

Summary of guidelines and requirements for sequencing mixed libraries on the same flow cell.

MiSeq Sequencing Welcome Card

This quick reference card is a graphical introduction to the MiSeq instrument. It covers information such as MiSeq appllications, MiSeq publications, Sample Preparation, navigating through the support website, and MiSeq community resources.

MiSeqDx Library Prep Check Kit Quick Reference Card

This document includes information regarding the use of the MiSeqDx Library Prep Check Kit.

cBot Safety and Compliance Guide

This guide contains safety information and product compliance markings for the cBot Cluster Generation System.

VeraCode ADME Assay Guide (15007510)

Instructions for performing the VeraCode ADME assay.

Performing Read 1 Primer Rehyb on the cBot

This insert contains instructions for performing a Read 1 rehyb on the cBot using cBot Rehyb Kit.

GoldenGate Automation DASL Assay for BeadStation Addendum (11194357)

Instructions for performing the GoldenGate DASL assay performing the automated method.

Infinium HD Assay Gemini Manual Protocol (11311015)

Experienced-level instructions for performing the Infinium HD assay.

Whole-Genome Gene Expression DASL Assay Lab Tracking Form (11327210)

Lab tracking form for the Whole-Genome Gene Expression DASL assay.

TruSeq Nano DNA Sample Preparation User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq Nano DNA Sample Preparation Guide.

iScan System User Guide (11313539)

Instructions for using the iScan.

Universal BC Booklet ( 11325425)

Instructions for performing the MicroRNA GoldenGate Methylation and DASL Gene Expression assays.

TruSeq DNA Sample Preparation Guide

Instructions for preparing samples using the TruSeq DNA Sample Prep Kit.

TruSeq Small RNA Sample Preparation Experienced User Card and Lab Tracking Form

Experienced-level instructions for the TruSeq Small RNA Sample Prep Kit.

DASL Assay Manual Protocols Experienced User Card (11175148)

Experienced-level instructions for performing the DASL assay.

BeadLab System Guide with GoldenGate Assay (11295174 A)

This download contains the BeadLab System Guide, which describes how to perform the GoldenGate Genotyping Assay on BeadLab equipment.

Genome Analyzer PE Lab Tracking Form (15014599)

This download contains the interactive lab tracking form for the Genome Analyzer.

CASAVA Software Version 1.8 User Guide (15011196 B)

This download contains the user guide for the CASAVA v1.8 sequencing analysis software.

VariantStudio Release Notes

Summary of changes introduced in VariantStudio software.

TruSeq Custom Amplicon Library Preparation Experienced User Card and Lab Tracking Form

Experienced user level instructions for preparing samples using the TruSeq Custom Amplicon Library Preparation Kit.

GoldenGate Automation DASL Assay Production Tracking Worksheet (11194390)

Production tracking form for GoldenGate Automation DASL assay.

BeadStation 500G Manual Experienced User Card (11171817)

Experienced-level instructions for using the BeadStation 500G.

GenomeStudio ChIP Sequencing Module v1.0 User Guide (11319084)

Instructions for using the GenomeStudio ChIP Sequencing Module.

New 12-sample miRNA Universal BeadChip Information (11326920)

Information about changes to the miRNA Universal BeadChip protocol.

Nextera XT Sample Preparation Experienced User Card

Experienced-level instructions for preparing samples using the Nextera XT sample prep Kit.

TruSeq Nano DNA Sample Preparation Low Sample Experienced User Card and Lab Tracking Form

Experienced-level instructions for preparing samples using the low sample protocol for the TruSeq Nano DNA Sample Prep Kit.

DesignStudio Customer Release Notes

DesignStudio release notes describe features and changes introduced in the latest versions of DesignStudio.

TruSeq Rapid Duo Sample Loading Kit Reagent Preparation Guide (for cbot - HiSeq 1500/2500) (15036504)

Instructions for preparing reagents in the TruSeq Rapid Duo Sample Loading Kit for the cBot.

MicroRNA Expression Profiling Assay Guide (11317302)

Instructions for performing the MicroRNA Expression Profiling assay.

Bead Array Reader User Guide (11179510)

Instructions for using the Bead Array Reader.

DASL for VeraCode Lab Track Form (11312747)

Lab tracking form for DASL for VeraCode.

TruSeq Cluster Kit v5 (CS-GA) Reagent Prep Guide

This guide contains descriptions of kit components and reagent preparation instructions for the Cluster Station.

Small RNA Quick Reference Cards

These application workflow cards provide guidance for planning, running, and analyzing a Small RNA project.

VariantStudio User Guide

This guide provides an overview of the Illumina VariantStudio desktop application and instructions for importing, annotating, and filtering variants.

Infinium HD Ultra Assay Experienced User Card, Automated Protocol (11328108)

Experienced-level instructions for performing the Infinium HD Ultra assay automated protocol.

TruSeq Cluster Kit v3 (cBot-HiSeq) Reagent Prep Guide

This guide contains instructions for preparing reagents provided in the TruSeq Cluster Kit v3 and the TruSeq Dual Index Sequencing Primer Box.

TruSeq Targeted RNA Expression User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq Targeted RNA Expression Guide.

Infinium HD Assay Ultra Protocol Guide (11328087)

Instructions for performing the Infinium HD Ultra assay.

MiSeq Reporter Analysis Workflow Reference Guides

Each workflow reference guide contains an overview of the analysis workflow and descriptions of analysis output files. For information about the MiSeq Reporter interface and instructions for instructions for installing, using, and troubleshooting the software, see the MiSeq Reporter User Guide.

Evaluation of Infinium Genotyping Assay Controls Training Guide

This download contains the training guide that accompanies that Evaluation of Infinium Genotyping Assay Controls online training course.

Infinium LCG Workflows Overview Video Version 2

This short video describes the new Infinium LCG assay workflows by reviewing changes in the new workflows compared to the existing Infinium HD assay workflows.

GenomeStudio RNA Sequencing Module v1.0 User Guide (11319105)

Instructions for using the GenomeStudio RNA Sequencing Module v1.0 to view sequencing data.

Infinium HD FFPE Methylation Assay Automated Protocol Experienced User Card (15027309)

Experienced-level instructions for performing the Infinium HD FFPE assay.

New 12-sample DASL Universal BeadChip Information (11326911)

Overview of changes introduced with the DASL Universal BeadChip.

TruSight Rapid Capture Sample Prep Experienced User Card

Intended for the experienced user, this document summarizes instructions for using the TruSight Rapid Capture Sample Prep Kit to prepare up to 96 indexed paired-end libraries, followed by enrichment using the TruSight Content Set CSO (custom selected oligos).

HiSeq 1500 User Guide

This guide contains an overview of instrument components and instructions for operating and maintaining the HiSeq 1500. Workflows include high output and rapid run.

HiSeq 1000 System User Guide (15023355)

Instructions for using the HiSeq 1000 system for sequencing.

TruSeq Amplicon - Cancer Panel Library Preparation Experienced User Card

Experienced-level instructions for preparing samples using the TruSeq Amplicon - Cancer Panel Library Preparation Kit.

Infinium II Assay Multi-Sample Lab Tracking Form (11237695 A)

This download contains the lab tracking form for the multi-sample Infinium II Assay.

MiSeqDx Universal Kit 1.0 Lab Tracking Form

This document summarizes the steps in the MiSeqDx Universal Kit 1.0 and includes fields for recording reagent lot numbers, as well as start and stop times for various steps.

HiSeq v4 System Upgrade Information Sheet

This document describes key upgrade features, upgrade components, software upgrade features, and new chemistry features for the v4 upgrade.

Sequencing Kit v4 Reagent Preparation Guide (15002739)

Instructions for using the Reagent Preparation for the Genome Analyzer - Sequencing Kit v4

Nextera DNA Sample Preparation Lab Tracking Form

Interactive form for recording sample preparation steps using the Nextera DNA sample prep Kit.

HiSeq v4 System Upgrade FAQ

This document describes key upgrade features, upgrade components, software upgrade features, and new chemistry features.

IEM TruSight Quick Reference Card

Instructions for using IEM with TruSight One, TruSight Enrichment, or TruSight Rapid Capture kits.

Infinium HD FFPE Assay Experienced User Card, Manual Protocol (15021526)

Experienced-level instructions for performing the Infinium HD FFPE assay manual protocol.

Infinium II Assay Experienced User Card, Multi-Sample, Automated Protocol (11208018)

Experienced-level instructions for performing the Infinium II Multi-Sample assay automated protocol.

MiSeq Reagent Kit Reagent Preparation Guide

Reagent prep guides contain an overview of kit contents and instructions for preparing the reagent cartridge for a sequencing run on the MiSeq.

Infinium HD Assay Super Manual Protocol Experienced User Card (11322312)

Experienced-level Lab tracking form for the Infinium HD assay.

DASL Assay System Manual Errata (11216069)

Instructions for performing the DASL assay.

HiScanSQ Pausing a Sequencing Run to Scan BeadChips (15023459 A)

Instructions for pausing a sequencing run on the HiScanSQ.

Infinium HD Assay Methylation Protocol Guide (15019519)

Instructions for performing the Infinium protocol using the manual method or the automated method.

cBot Lab Tracking Form

This download contains the interactive lab tracking form for the cBot.

GoldenGate Assay for Methylation System Guide (11228975)

Instructions for performing the GoldenGate assay for methylation protocol performing the manual method or the automated method.

TruSeq DNA Sample Preparation User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq DNA Sample Preparation Guide.

DesignStudio Update for Nextera Rapid Capture Custom Enrichment

Instructions for transferring existing TruSeq and Nextera Custom Enrichment DesignStudio projects to a new Nextera Rapid Capture Custom Enrichment DesignStudio project.

TruSeq Enrichment EUC

Experienced-level instructions for using the TruSeq Enrichment protocol.

GoldenGate Workflow Information (370-2010-015)

Summary of workflow requirements and estimated scan times for GoldenGate assays.

Read 1 Primer Rehybridization on a HiSeq X Flow Cell

Intructions for performing Read 1 primer rehybridization on a HiSeq X flow cell using the cBot.

Sequencing Library qPCR Quantification Guide

This download contains the protocol guide for SBS library qPCR quantification.

Nextera Enrichment Sample Preparation Lab Tracking Form

Interactive form for recording sample preparation steps using the Nextera Enrichment sample prep Kit.

GoldenGate Genotyping Assay Experienced User Card, Manual Protocol for Universal Array Matrix (15005074)

Experienced-level instructions for performing the GoldenGate Genotyping assay.

Infinium II Assay Two-Sample Lab Tracking Worksheet (11237708)

Interactive form for recording steps during the Infinium II assay.

TruSeq DNA Dual Index Product Insert

Summary of instructions for using the TruSeq DNA Dual Index.

KaryoStudio v1.4 User Guide (11328837)

Instructions for using KaryoStudio Software v1.4 to analyze detected regions, match results to known variants, and generate a cytogenetics report.

HiSeq Primer Rehybridization Reference Guide

This guide contains instructions for performing primer rehybridization on the HiSeq using the HiSeq Multi-Primer Rehyb Kit v4.

KaryoStudio Software v1.3 Release Notes (11328870)

Summary of changes introduced in KaryoStudio Software v1.3.

Illumina LIMS User Guide (15000395)

Instructions for using Illumina LIMS to manage projects and tasks, generate reports, and track history.

MiSeq Reagent Kit What's New Insert

Overview of changes introduced with the MiSeq reagent kit versions, related documentation, and software requirements.

Infinium LCG Assay Protocol Guide (15023139)

Instructions for performing the Infinium protocol using the manual method or the automated method.

Whole?genome Bisulfite Sequencing for Methylation Analysis Guide (15021861)

Instructions for WGBS for Methylation Analysis.

MicroRNA Expression Profiling Assay for BeadChips Lab Tracking Form (11317345)

Lab tracking form for the MicroRNA Expression Profiling assay for BeadChips.

HiSeq Lab Tracking Form for Rapid Run Mode

This download contains the interactive lab tracking form for rapid runs on the HiSeq 2500 and HiSeq 1500.

Ship Schedule Form

Shipping schedule change request form.

GoldenGate Indexing Site Prep Guide (15013485 A)

This download contains lab requirements and specifications for the GoldenGate Indexing assay.

TruSeq DNA Sample Preparation Low Sample Lab Tracking Form

Lab tracking form for the TruSeq DNA sample prep LS protocol.

GGGT Manual EUC (15004070)

Instructions for using the GGGT protocol.

MiSeqDx Cystic Fibrosis 139-Variant Assay Lab Tracking Form

This document summarizes the steps in the MiSeqDx Cystic Fibrosis 139-Variant Assay and includes fields for recording reagent lot numbers, as well as start and stop times for various steps.

Genome Analyzer IIx Run Rescue Protocols (15019044)

Instructions for restoring failed runs on the Genome Analyzer.

GoldenGate Indexing Assay Lab Tracking Form for Universal BeadChip, 16x96 Index (15006939)

Interactive form for recording steps during the GoldenGate Indexing assay.

New 12-sample Universal BeadChip Information (11326938)

Summary of changes to the 12-Sample Universal BeadChip.

Cluster Station Support - Decontamination Procedure Download

This download contains instructions on how to prepare a Cluster Station for shipping.

Paired-End Sample Preparation User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the Paired-End Sample Preparation Guide.

Genome Analyzer IIx (SCS v2.10) Quick Reference Guide (15030967)

This guide contains instructions for the experienced user for sequencing on the Genome Analyzer.

Paired-End Cluster Generation Lab Tracking Form (15009438)

This download contains the interactive lab tracking form for paired-end cluster generation on the Cluster Station.

Infinium HD Assay for Methylation Lab Tracking Form (15020316)

Instructions for performing the Infinium protocol using the manual method or the automated method.

TruSight DNA Amplicon Library Preparation Guide

Instructions for preparing samples using the TruSight DNA Amplicon Library Preparation Kit.

Genome Analyzer IIx User Guide (for SCS v2.10) (15030966)

This guide contains an overview of instrument components and instructions for operating and maintaining the Genome Analyzer.

HiSeq Upgrade Welcome Letter

This is the welcome letter that was sent to customers about their HiSeq upgrade.

cBot Site Prep and Installation Guide

This guide contains specifications for preparing your lab for installation and operation of the cBot.

CASAVA v1.8.2 Quick Reference Guide (15011197 C)

This download contains the quick reference guide for CASAVA v1.8.2 sequencing analysis software.

Infinium II Assay Multi-Sample Protocol Guide (11230143)

Instructions for performing the Infinium II Multi-Sample assay.

Whole-Genome Gene Expression Direct Hybridization Assay Guide ( 11322355)

Instructions for performing the Whole-Genome Gene Expression Direct Hybridization assay.

HiSeq v4 System Upgrade Welcome Letter

This letter was sent to customers about their HiSeq v4 system upgrade.

DASL Assay Laboratory Process Flow (11175130)

Overview of Gene Expression workflow using Sentrix arrays.

TruSight One Sequencing Panel Sample Prep Experienced User Card

Intended for the experienced user, this document summarizes the steps for preparing samples using the TruSight One Sequencing Panel Sample Prep protocol.

AutoLoader User Guide (11219711 A)

This download contains the user guide for AutoLoader, which works in conjunction with the BeadArray Reader.

Custom Protocol Selector

The Custom Protocol Selector enables you to generate your own customized documentation, specifically tailored to your experiment on the MiSeq, HiSeq 2000, HiSeq 2500, or NextSeq 500. You select the products and workflow options, then the Custom Protocol Selector generates a PDF with only the instructions that you need.

DASL Assay System Manual (11175105)

Instructions for performing the DASL assay.

TruSeq Stranded Total RNA Sample Preparation LS EUC and LTF

Experienced-level instructions for preparing samples using the LS protocol for the TruSeq Stranded Total RNA Sample Prep Kit.

Installing MiSeq Reporter on an Off-Instrument Computer (15031742)

Instructions for installing MiSeq Reporter software off-instrument.

TruSight Rapid Capture Sample Prep Guide

Instructions for using the TruSight Rapid Capture Sample Prep Kit to prepare up to 96 indexed paired-end libraries, followed by enrichment using the TruSight Content Set CSO (custom selected oligos).

Nextera Mate Pair Gel-Free Experienced User Card

Intended for the experienced user, this document summarizes the steps for preparing samples using the Nextera Mate Pair Gel-Free protocol.

GenomeStudio 2008.1 Framework UG (11318815)

Overview of the GenomeStudio interface used by all GenomeStudio software modules.

HiSeq 2000 System User Guide (15011190)

This guide contains an overview of instrument components and instructions for operating and maintaining the HiSeq 2000.

Cluster Station Support - User Guide Download

Instructions for using the Cluster Station for cluster generation.

GoldenGate Genotyping Assay Lab Setup and Procedures Guide

Lab requirements and preparation instructions for performing the GoldenGate Genotyping assay.

Nextera Enrichment Sample Preparation Guide

Instructions for preparing samples using the Nextera Enrichment sample prep Kit.

Illumina AutoLoader2 Quick Reference Card (11308641)

Overview of scanning process using AutoLoader2 with iScan.

Inf LCG Quad Assay Guide (15025908)

Instructions for performing the Inf LCG Quad assay.

WG-DASL Assay Guide (11322443 B)

This download contains the user guide for performing the Whole-Genome Gene Expression DASL Assay.

TruSeq ChIP Sample Prep Guide

Instructions for using the TruSeq ChIP Sample Prep Kit to prepare samples for sequencing.

16S Metagenomic Sequencing Library Preparation

Includes the 16S Illumina Demonstrated Library Prep Guide and links to an example 16S dataset from libraries generated with the protocol and run on the MiSeq with v3 reagents.

VeriSeq PGS Library Preparation Guide
Instructions for preparing samples using the VeriSeq PGS Library Preparation Kit.
SurePlex Summary Protocol Experienced User Card
Experienced-level instructions for preparing samples using the SurePlex DNA Amplification kit.
VeriSeq PGS Library Preparation Experienced User Card and Lab Tracking Form
Experienced-level instructions for preparing samples using the VeriSeq PGS Library Preparation Kit.
BlueFuse Multi Software Installation Guide (15053614)
This guide describes the key steps required to install BlueFuse Multi v3.0, or later, for the first time or to upgrade BlueFuse Multi from an earlier release. This document also describes how to install BlueFuse Server v1.5 for the first time and how to upgrade BlueFuse Server from an earlier release.
BlueFuse Multi Software Reference Guide (15053620)
This guide details functions, algorithms, and more advanced features of BlueFuse Multi. This guide has been written for BlueFuse Multi v4.1 and BlueFuse Server v1.5.
MiSeq Run Workflow Quick Reference Cards

Each quick reference card provides a graphical representation of the MiSeq analysis workflow for the experienced user. Workflows include Assembly, Enrichment, Library QC, Metagenomics, PCR Amplicon, Resequencing, Small RNA, and TruSeq Amplicon.

NextSeq 500 Quick Reference Cards

 

These application workflow cards provide guidance for planning, running, and analyzing a NextSeq 500 project.

Languages: Chinese, Korean, German, Spanish, French, and Italian.

 

HiSeq X System User Guide

The system user guide describes instrument components, on-instrument software, the sequencing workflow, and maintenance procedures.

HiSeq X System Site Preparation Guide

The lab setup and site prep guide guide provides important information about setting up a lab for the HiSeq X Ten system, including instrument dimensions, lab space requirements, electrical requirements, user-supplied consumables, and storage space.

Indexed Sequencing Overview Guide

This guide provides an overview of the indexed sequencing process for the single-indexing and dual-indexing workflows on the NextSeq 500, MiSeq, and HiSeq Platforms.

TruSeq RNA Access Library Prep Experienced User Card and Lab Tracking Form

Experienced-level instructions for preparing libraries using the TruSeq RNA Access Library Prep Kit.

TruSeq RNA Access Library Prep User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq RNA Access Library Prep Guide, 15049525 A

TruSeq RNA Access Library Prep Guide

Instructions for preparing libraries using the TruSeq RNA Access Library Prep Kit.

BaseSpace Core Apps Release Notes

BaseSpace Core Apps software release notes describe features and changes introduced in the latest versions.

BaseSpace User Guide

Instructions for using BaseSpace.

TruSeq SBS Kit v5 Reagent Preparation Guide (for the Genome Analyzer) (15013595)

Instructions for preparing TruSeq SBS v5 reagents for the Genome Analyzer.

Infinium HTS Restore Protocol Guide (15014614)

Instructions for performing the Infinium HTS assay Protocol.

Infinium HTS assay Experienced User Card, Manual Protocol (15021526)

Experienced-level instructions for performing the Infinium HTS assay manual protocol.

Infinium HTS Assay Lab Tracking Form (15021527)

Automated lab tracking form for the Infinium HTS assay.

Infinium HTS Assay Experienced User Card, Automated Protocol (11311023)

Experienced-level instructions for performing the Infinium HTS assay.

Infinium HTS Lab Tracking Form (15021527)

Manual lab tracking form for the Infinium HTS assay.

MiSeq Reagent Kit v3-PGS Reagent Preparation Guide

 

Reagent prep guides contain an overview of kit contents and instructions for preparing the reagent cartridge for a sequencing run on the MiSeq. This guide is for VeriSeq-PGS customers only.

 

BaseSpace Core App User Guides

Instructions for using the BaseSpace Core Apps: 

  • BWA Whole-Genome Sequencing App
  • BWA Enrichment App
  • Tumor Normal App
  • TopHat and Cufflinks RNA-seq Apps
  • Isaac Whole-Genome Sequencing v2 App
  • Isaac Enrichment App
  • RNA Express App
  • 16S Metagenomics App
  • TruSeq Amplicon App
  • TruSeq Long-Reads Assembly App
  • TruSeq Phasing App

Adapter Sequence Letter for Illumina Customers

 

This letter contains Illumina oligonucleotide (oligo) sequences, including adapter and primer sequences. TruSeq and Nextera PCR sequencing primer sequences and concentrations are proprietary information and not made publicly available. This letter is provided for use only with Illumina instruments: MiSeq, NextSeq, HiSeq, Genome Analyzer, and HiScanSQ.

 

BlueFuse Workflow Manager Quick Reference Card

 

Instructions for using the BlueFuse Workflow Manager.

 

BaseSpace Core App End-User License Agreements.

 

End-User License Agreements (EULAs) for BaseSpace Core App.

 

NextSeq 500 Kit Reference Guide

This guide contains an overview of kit contents and instructions for preparing the NextSeq 500 reagent cartridge and flow cell.

Nextera XT Small Genomes Assembly Workflow Cards

 

These application workflow cards provide guidance for planning, running, and analyzing a Nextera XT small genomes assembly project.

Languages: Chinese, Korean, German, Spanish, French, and Italian.

 

Nextera XT DNA Quick Reference Cards

 

These application workflow cards provide guidance for planning, running, and analyzing a Nextera XT Small Genomes Resequencing project.

Languages: Chinese, Korean, German, Spanish, French, and Italian.

 

TruSeq Custom Amplicon Workflow Cards

 

These application workflow cards provide guidance for planning, running, and analyzing a TruSeq Custom Amplicon project.

Languages: Chinese, Korean, German, Spanish, French, and Italian.

 

TruSeq Amplicon - Cancer Panel Quick Workflow Cards

 

These application workflow cards provide guidance for planning, running, and analyzing a TruSeq Amplicon - Cancer Panel project.

Languages: Chinese, Korean, German, Spanish, French, and Italian.