Product Documentation

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Description
 
File Info
Date
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.
A Technical Guide to Karyomapping (15052496 A)
An introduction to the Infinium Karyomapping Protocol.
Analysis Visual Controller v1.7 User Guide
Analysis Visual Controller (AVC) v1.7 User Guide
AutoLoader 2.x User Guide (15015394 A)
Instructions for using the AutoLoader 2.x.
AutoLoader Dual-Reader Quick Ref Card (11219905 A)
Instructions for configuring the AutoLoader Dual BeadArray Reader.
AutoLoader Single-Reader Quick Ref Card (11219892 A)
Instructions for setting up and configuring the Autoloader Single BeadArray Reader.
AutoLoader User Guide (11219711 A)
This download contains the user guide for AutoLoader, which works in conjunction with the BeadArray Reader.
AutoLoader2 Quick Reference Card (11313547 A)
Overview of scanning process using AutoLoader2 with iScan.
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
BaseSpace Core Apps Release Notes

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

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.
BaseSpace Onsite v1.1 Release Notes

Release Notes for BaseSpace Onsite v1.1

BaseSpace User Guide
Instructions for using BaseSpace.
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.

BeadArray Reader User Guide (11179510 B)
Instructions for using the Bead Array Reader.
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.
BeadStation 500G Manual EUC (11171817 A)
Experienced-level instructions for using the BeadStation 500G.
BeadStation 500G System Manual (11165222 B)
This download contains the user guide for BeadStation 500G.
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.
Beeline v1.0 User Guide (15016340 A)
Instructions for using Beeline software.
CASAVA 1.8 Changes
Summary of changes introduced in CASAVA v1.8.
CASAVA Software Version 1.7 User Guide (15011196 A)
This download contains the user guide for the CASAVA v1.7 sequencing analysis software.
CASAVA Software Version 1.8 User Guide (15011196 B)
This download contains the user guide for the CASAVA v1.8 sequencing analysis software.
CASAVA User Guide (15011196 D)
This download contains the user guide for the CASAVA sequencing analysis software.
CASAVA v1.7 Quick Reference Booklet (15011197 A)
Reference Guide for CASAVA v1.8.2 software.
CASAVA v1.8 Quick Reference Booklet (15011197 B)
This download contains the quick reference booklet for CASAVA v1.8 sequencing analysis software.
CASAVA v1.8.2 Quick Reference Guide (15011197 C)
This download contains the quick reference guide for CASAVA v1.8.2 sequencing analysis software.
cBot Lab Tracking Form
This download contains the interactive lab tracking form for the cBot.
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.
cBot Safety and Compliance Guide
This guide contains safety information and product compliance markings for the cBot Cluster Generation System.
cBot Site Prep and Installation Guide
This guide contains specifications for preparing your lab for installation and operation of the cBot.
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.
ChIP-Seq Sample Prep Guide
Instructions for preparing samples using the ChIP-Seq sample prep Kit.
Cluster Station Decontamination Procedure (15010563)
This download contains instructions on how to prepare a Cluster Station for shipping.
Cluster Station Support - User Guide Download
Instructions for using the Cluster Station for cluster generation.
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.
CytoSNP-850K Assay Experienced User Card (15046993)
Experienced-level instructions for performing the CytoSNP-850K assay protocol.
CytoSNP-850K Assay Protocol Guide (15046990 B)
Instructions for performing the CytoSNP-850K Assay Protocol.
DASL Addendum GoldenGate Automation (11194357 A)
Instructions for performing the GoldenGate DASL assay performing the automated method.
DASL Assay Errata (11216069 A)
Instructions for performing the DASL assay.
DASL Assay GoldenGate Automation EUC (11195173 A)
Experienced-level instructions for performing the DASL assay.
DASL Assay GoldenGate Automation LTW (11194390 A)
Production tracking form for GoldenGate Automation DASL assay.
DASL Assay Single-Use RNA Prep EUC (11175148 A)
Experienced-level instructions for performing the DASL assay.
DASL Assay System Guide for Manual Protocol (11175105 A)
Instructions for performing the DASL assay.
DASL Assay Training Poster for Manual Workflow (11175130 A)
Overview of Gene Expression workflow using Sentrix arrays.
DASL Notificaton - MCS3 Expiration Date Change
Product Quality Notification for Recent DASL Purchases.
DASL Universal-12 BeadChip Product Insert (11326911 A)
Overview of changes introduced with the DASL Universal BeadChip.
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.
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.
DesignStudio Release Notes
DesignStudio release notes describe features and changes introduced in the latest versions of DesignStudio.
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.
Directional mRNA-Seq Sample Preparation Guide (15018460)
Instructions for performing the Directional mRNA-Seq sample prep assay.
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.
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.
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.
Frequently Asked Questions (FAQs) – Certificate of Analysis (CofA)
Frequently Asked Questions (FAQs) for the Certificate of Analysis (CofA)
Frequently Asked Questions (FAQs) – Master Lot Sheet (MLS)
Frequently Asked Questions (FAQs) for the Master Lot Sheet (MLS)
Genome Analyzer IIx Quick Reference Guide
This guide contains instructions for the experienced user for sequencing on the Genome Analyzer.
Genome Analyzer IIx Site Prep Guide
This guide contains lab specifications and requirements for installing and operating the Genome Analyzer.
Genome Analyzer IIx User Guide
This guide contains an overview of instrument components and instructions for operating and maintaining the Genome Analyzer.
Genome Analyzer Lab Tracking Form
This download contains the interactive lab tracking form for the Genome Analyzer.
Genome Analyzer Run Rescue Protocols
Instructions for restoring failed runs on the Genome Analyzer.
GenomeStudio 2008.1 Framework UG (11318815 A)
Overview of the GenomeStudio interface used by all GenomeStudio software modules.
GenomeStudio 2008.1 Framework UG (11318815 A)
Overview of the GenomeStudio interface used by all GenomeStudio software modules.
GenomeStudio Chip-Seq Module v1.0 UG (11319084 A)
Instructions for using the GenomeStudio ChIP Sequencing Module.
GenomeStudio DNA-Seq Module v1.0 UG (11319092 A)
Instructions for using the GenomeStudio DNA Sequencing Module to visualize and analyze sequencing data.
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.
GenomeStudio GT Module Workflow, GoldenGate Indexing Assay
Instructions for performing GenomeStudio Genotyping Module for the GoldenGate Indexing assay.
GenomeStudio GX Module v1.0 UG (11319121 A)
Instructions for using the GenomeStudio Gene Expression Module to view analysis data.
GenomeStudio M Module v1.8 UG (11319130 B)
Instructions for using the GenomeStudio Methylation Module v1.8 software.
GenomeStudio PT Module v1.0 UG (11319148 A)
Instructions for using the GenomeStudio Protein Analysis Module v1.0 to view analysis data.
GenomeStudio RNA-Seq Module v1.0 UG (11319105 A)
Instructions for using the GenomeStudio RNA Sequencing Module v1.0 to view sequencing data.
GenomeStudio Software 2008.1 Release Notes (11319658 A)
Summary of changes introduced in GenomeStudio 2009.1 software.
GenomeStudio Software 2008.1 Release Notes (11319658 A)
Summary of changes introduced in GenomeStudio 2009.1 software.
GenomeStudio Software 2009.1 Release Notes (11319658 B)
This download contains the release notes for GenomeStudio Software 2009.1.
GenomeStudio Software 2009.1 Release Notes (11319658 B)
This download contains the release notes for GenomeStudio Software 2009.1.
GenomeStudio Software 2009.2 Release Notes (11319658 C)
Summary of changes introduced GenomeStudio Software v2011.1.
GenomeStudio Software 2009.2 Release Notes (11319658 C)
Summary of changes introduced GenomeStudio Software v2011.1.
GenomeStudio Software 2011.1 Release Notes (11319658 G)
Summary of new features and known issues in the GenomeStudio Software 2011.1 release.
GenomeStudio Software 2011.1 Release Notes (11319658 G)
Summary of new features and known issues in the GenomeStudio Software 2011.1 release.
Genomic DNA Sample Prep Guide - Oligo Only Kit (1003492)
This download contains the sample preparation guide for sequencing genomic DNA (Oligo Only Kit).
Genomic DNA Sample Prep Guide (1003806)
Instructions for preparing samples using the Genomic DNA kit.
GoldenGate Assay Lab Setup and Procedures Guide (15011642 A)
Lab requirements and preparation instructions for performing the GoldenGate Genotyping assay.
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.
GoldenGate Auto EUC for Universal BeadChips (15004069 B)
Experienced-level instructions for performing the GoldenGate Genotyping assay, Automated.
GoldenGate Automated EUC for BeadLab (11295191 A)
Experienced-level instructions for performing the GoldenGate Genotyping assay.
GoldenGate Genotyping Assay Guide (15004065 B)
Instructions for performing the GoldenGate Genotyping assay
GoldenGate GT on BeadXpress Auto EUC (11312763 A)
Experienced-level instructions for performing the GoldenGate Genotyping assay for VeraCode.
GoldenGate GT on BeadXpress Lab Tracking Form (11312721 A)
Lab tracking form for the GoldenGate GT for VeraCode.
GoldenGate GT on BeadXpress Manual EUC (11312755 A)
Instructions for performing the GoldenGate Genotyping assay for VeraCode.
GoldenGate Indexing Assay Guide (15006937 A)
Instructions for performing the GoldenGate Indexing assay.
GoldenGate Indexing Automated Experienced User Card (15006938 A)
Experienced-level instructions for performing the GoldenGate Indexing assay.
GoldenGate Indexing Lab Tracking Form (16x96 Index) (15006939 A)
Interactive form for recording steps during the GoldenGate Indexing assay.
GoldenGate Indexing LTF (8x192 or 4x384 Index) (15009926 A)
Interactive form for recording steps during the GoldenGate Indexing assay.
GoldenGate Indexing Site Prep Guide (15013485 A)
This download contains lab requirements and specifications for the GoldenGate Indexing assay.
GoldenGate Lab Tracking Form for UAMs (15005077 A)
Lab tracking form for the GoldenGate Genotyping assay for Universal Array.
GoldenGate Lab Tracking Form for Univ. BeadChips (15004071 B)
Lab tracking form for GoldenGate Genotyping assay for Universal BeadChip.
GoldenGate Lab Tracking Worksheet for BeadLab (11295203 A)
Automated GoldenGate Genotyping Assay Lab Track Sheet (11295203)
GoldenGate Manual EUC for Universal Array Matrix (15005074 A)
Experienced-level instructions for performing the GoldenGate Genotyping assay.
GoldenGate Manual EUC for Universal BeadChips (15004070 B)
Instructions for using the GGGT protocol.
GoldenGate Methyl Univ-12 BeadChip Product Insert (11326938 A)
Summary of changes to the 12-Sample Universal BeadChip.
GoldenGate Methyl. on BeadXpress Lab Tracking Form (11312739 A)
Lab tracking form for the Golden Gate Meth for Vera Code.
GoldenGate Methyl. on BeadXpress Manual EUC (11312771 A)
Instructions for performing the GoldenGate Methylation assay for VeraCode.
GoldenGate Methylation Assay Guide (11228975 A)
Instructions for performing the GoldenGate assay for methylation protocol performing the manual method or the automated method.
GoldenGate Methylation Lab Tracking Worksheet (11237396 A)
This download contains the GoldenGate Methylation Lab Tracking Worksheet.
GoldenGate Methylation Multi-Use DNA Auto EUC (11233096 A)
Experienced-level instructions for performing the GoldenGate assay for methylation.
GoldenGate Methylation Multi-Use DNA Manual EUC (11233117 A)
Experienced-level instructions for performing the GoldenGate assay for Methylation.
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.
GoldenGate Methylation Single-Use DNA Manual EUC (11233109 A)
Experienced-level instructions for performing the GoldenGate Methylation assay.
GTS LIMS User Guide (11295182 A)
This download contains the user guide for the Genotyping System Lab Information Management System (GTS LIMS).
HiScanSQ Pausing a Sequencing Run to Scan BeadChips (15023459 A)
Instructions for pausing a sequencing run on the HiScanSQ.
HiScanSQ Pausing a Sequencing Run to Scan BeadChips (15023459 A)
Instructions for pausing a sequencing run on the HiScanSQ.
HiScanSQ System Sequencing Best Practices (15029252 A)
Best practices poster for the HiScanSQ system.
HiScanSQ System Troubleshooting (Excerpt from 15015392 E)
Instructions for troubleshooting problems on the HiScanSQ.
HiScanSQ System User Guide (15015392)
Instructions for using the HiScanSQ.
HiScanSQ System User Guide (15015392)
Instructions for using the HiScanSQ.
HiSeq 1000 User Guide
Instructions for using the HiSeq 1000 system for sequencing.
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 1500/2500 Mode and Instrument Wash (HCS 2.0 and higher)
Provides logistical data, such as expected flow cell volumes, pertaining to changing modes from High Output to Rapid Run and vice-versa.
HiSeq 2000 User Guide
This guide contains an overview of instrument components and instructions for operating and maintaining the HiSeq 2000.
HiSeq 2500 User Guide
This guide contains an overview of instrument components and instructions for operating and maintaining the HiSeq 2500. Workflows include high output and rapid run.
HiSeq Analysis Software User Guide
HiSeq Analysis Software User Guide
HiSeq Cluster Kit v4 Reference Guide
This guide contains instructions for preparing reagents provided in the HiSeq Cluster Kit v4 for use on the cBot and on the HiSeq with HiSeq v4 high output mode.
HiSeq Lab Tracking Form for High Output Runs
This download contains the interactive lab tracking form for high output runs on the HiSeq.
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.
HiSeq Primer Rehybridization Reference Guide
This guide contains instructions for performing primer rehybridization on the HiSeq using the HiSeq Multi-Primer Rehyb Kit v4.
HiSeq Safety and Compliance Guide
This guide contains safety information and product compliance statements for the HiSeq.
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.
HiSeq Site Preparation Guide
This guide contains lab specifications and requirements for HiSeq installation and operation.
HiSeq System Upgrade Information Sheet
This document describes key upgrade features, upgrade components, software upgrade features, and new chemistry features.
HiSeq Upgrade Welcome Letter
This is the welcome letter that was sent to customers about their HiSeq upgrade.
HiSeq v4 System Upgrade FAQ
This document describes key upgrade features, upgrade components, software upgrade features, and new chemistry features.
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.
HiSeq v4 System Upgrade Welcome Letter
This letter was sent to customers about their HiSeq v4 system upgrade.
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.
HiSeq X Lab Tracking Form

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

HiSeq X Safety and Compliance Guide

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

HiSeq X System User Guide

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

HiSeq X Ten System Lab Setup and Site Prep 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.
Human mtDNA D-Loop Hypervariable Region Guide (15034858)
Instructions for Human mtDNA D-Loop Hypervariable Region sample preparation.
Human mtDNA Genome Guide (15037958)
Instructions for Human mtDNA Genome sample preparation.
Hybridization Oven System Guide (11317134 A)
Instructions for performing the Hybridization Oven with Infinium assays.
IEM Nextera Quick Reference Card
Instructions for using IEM with the Nextera sample prep kits.
IEM TruSeq Amplicon Quick Reference Card
Instructions for using IEM with the TruSeq Amplicon kits.
IEM TruSeq DNA, RNA, or ChIP Quick Reference Card
Instructions for using IEM with the TruSeq DNA, RNA, or ChIP sample prep kits.
IEM TruSeq Small RNA Quick Reference Card
Instructions for using IEM with the TruSeq Small RNA Sample Prep Kit.
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.
IEM TruSeq Targeted RNA Expression Quick Reference Card
Instructions for using IEM with the TruSeq Targeted RNA Expression kits.
IEM TruSight Quick Reference Card
Instructions for using IEM with TruSight One, TruSight Enrichment, or TruSight Rapid Capture kits.
Illumina Customer Sequence Letter
This letter contains Illumina adapter 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: Genome Analyzer, HiScanSQ, HiSeq, MiSeq, and NextSeq.
Illumina Experiment Manager User Guide
Instructions for using the Illumina Experiment Manager.
Illumina LIMS Project Manager Guide
Instructions for using Illumina LIMS to manage projects and tasks, generate reports, and track history.
Illumina LIMS User Guide
Instructions for using Illumina LIMS to manage projects and tasks, generate reports, and track history.
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
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.
Inf Multi-Use LCG Assay Auto Experienced User Card (15023286 A)
Experienced-level instructions for performing the Infinium Multi-User LCG assay.
Infinium Assay Best Practices (370-2009-010)
Best practices for performing Infinium assays.
Infinium Assay Glass Cleaning Protocol (11316641 A)
Infinium Assay Glass Cleaning Protocol (11316641)
Infinium Assay Lab Setup and Procedures (11322460 A)
Lab requirements and preparation instructions for performing Infinium assays.
Infinium HD DNA Restoration Protocol (15014614 Rev C)
Instructions for performing the Infinium HD FFPE Restore protocol.
Infinium HD FFPE Assay Auto Experienced User Card (15021524 B)
Experienced-level instructions for performing the Infinium HD FFPE assay automated protocol.
Infinium HD FFPE Assay Manual Experienced User Card (15021526 B)
Experienced-level instructions for performing the Infinium HD FFPE assay manual protocol.
Infinium HD FFPE Assay Protocol Guide (15021525 B)
Instructions for performing the Infinium HD FFPE assay.
Infinium HD FFPE Lab Tracking Form (15021527 A)
Lab tracking form for the Infinium HD FFPE.
Infinium HD FFPE Methylation Assay Auto EUC (15027309 A)
Experienced-level instructions for performing the Infinium HD FFPE assay.
Infinium HD FFPE Methylation Assay Manual EUC (15027310 A)
Experienced-level instructions for performing the Infinium HD FFPE assay.
Infinium HD FFPE QC Assay Insert (15020981 C)
Instructions for determining whether DNA samples are candidates for the Infinium HD FFPE genotyping or methylation assay.
Infinium HD Gemini Assay Automated EUC (11311023 A)
Experienced-level instructions for performing the Infinium HD Gemini assay.
Infinium HD Gemini Assay Lab Tracking Form (11311031 A)
Lab tracking form for the Inf HD Gemini assay.
Infinium HD Gemini Assay Manual EUC (11311015 A)
Experienced-level instructions for performing the Infinium HD assay.
Infinium HD Gemini Assay Protocol Guide (11311007 A)
Instructions for performing the Infinium HD Gemini assay.
Infinium HD Methylation Assay Automated EUC (15019521 B)
Experienced-level instructions for performing the Infinium HD Methylation assay.
Infinium HD Methylation Assay Manual EUC (15019522 B)
Experienced-level instructions for performing the Infinium HD Methylation assay.
Infinium HD Methylation Assay Protocol Guide (15019519 B)
Instructions for performing the Infinium protocol using the manual method or the automated method.
Infinium HD Methylation Lab Tracking Form (15020316 B)
Instructions for performing the Infinium protocol using the manual method or the automated method.
Infinium HD Super Assay Automated EUC (11322291 C)
Experienced-level instructions for performing the Infinium HD Super assay.
Infinium HD Super Assay Lab Tracking Form (11327261 C)
Infinium HD Assay Super Lab Tracking Form (11327261)
Infinium HD Super Assay Manual EUC (11322312 C)
Experienced-level Lab tracking form for the Infinium HD assay.
Infinium HD Super Assay Protocol Guide (11322427 C)
Instructions for performing the Infinium HD Super assay.
Infinium HD Ultra Assay Automated EUC (11328108 B)
Experienced-level instructions for performing the Infinium HD Ultra assay automated protocol.
Infinium HD Ultra Assay Lab Tracking Form (11328116 B)
Lab tracking form for the Infinium HD Ultra.
Infinium HD Ultra Assay Manual EUC (11328095 B)
Experienced-level instructions for performing the Infinium HD assay ultra manual protocol.
Infinium HD Ultra Assay Protocol Guide (11328087 B)
Instructions for performing the Infinium HD Ultra assay.
Infinium HTS Assay Automated EUC (15045736 A)
Experienced-level instructions for performing the Infinium HTS assay.
Infinium HTS Assay Manual Lab Tracking Form (15047409 A)
Manual lab tracking form for the Infinium HTS assay.
Infinium HTS Assay Manual Protocol Experienced User Card (15045737 A)
Experienced-level instructions for performing the Infinium HTS assay manual protocol.
Infinium HTS Assay Protocol (15045738 A)
Instructions for performing the Infinium HTS assay Protocol.
Infinium HTS Automated Lab Tracking Form (15047410 A)
Automated lab tracking form for the Infinium HTS assay.
Infinium II Assay HC Two-Sample Automated EUC (11280811 A)
Experienced-level instructions for performing the Infinium II assay.
Infinium II Assay HC Two-Sample Manual EUC (11280802 A)
Experienced-level instructions for performing the Infinium II assay HC Two-Sample protocol.
Infinium II Assay HC Two-Sample Protocols (11280749 A)
Instructions for performing the Infinium II Two-Sample assay.
Infinium II Assay Multi-Sample Automated EUC (11208018 A)
Experienced-level instructions for performing the Infinium II Multi-Sample assay automated protocol.
Infinium II Assay Multi-Sample Lab Tracking Form (11237695 A)
This download contains the lab tracking form for the multi-sample Infinium II Assay.
Infinium II Assay Multi-Sample Manual EUC (11208000 A)
Experienced-level instructions for performing the Infinium II Multi-Sample assay.
Infinium II Assay Multi-Sample Protocols (11230143 A)
Instructions for performing the Infinium II Multi-Sample assay.
Infinium II Assay Two-Sample Lab Tracking Form (11237708 A)
Interactive form for recording steps during the Infinium II assay.
Infinium Karyomapping Lab Tracking Form (15052711)
Lab tracking form for the Infinium Karyomapping Assay.
Infinium Karyomapping Protocol Guide (15052710 A)
Instructions for performing the Infinium Karyomapping Protocol.
Infinium LCG Assay Automated Experienced User Card (15023141 A)
Experienced-level instructions for performing the Infinium LCG assay automated protocol.
Infinium LCG Assay BeadChip Kit Insert (15024057)
Summary of guidelines and requirements for performing the Infinium LCG assay.
Infinium LCG Assay Guide (15023139 A)
Instructions for performing the Infinium protocol using the manual method or the automated method.
Infinium LCG Assay Lab Tracking Form (15023142 A)
Lab tracking form for the Infinium LCG assay.
Infinium LCG Assay Manual Experienced User Card (15023140 A)
Experienced-level instructions for performing the Infinium LCG assay manual protocol.
Infinium LCG Assay TeFLow Kit Insert (15024058)
Ordering information for the TeFlow components used in the Infinium LCG assay.
Infinium LCG Quad Assay Automated EUC (15025910 A)
Experienced-level instructions for performing the Infinium LCG Quad assay.
Infinium LCG Quad Assay Guide (15025908 B)
Instructions for performing the Inf LCG Quad assay.
Infinium LCG Quad Assay Lab Tracking Form (15025911 A)
Lab tracking form for the Infinium LCG Quad assay.
Infinium LCG Quad Assay Manual EUC (15025909 A)
Experienced-level instructions for using the Infinium LCG Quad.
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.
Infinium Multi-Use LCG Assay Guide (15023284 A)
Instructions for performing the Infinium protocol using the manual method or the automated method.
Infinium Multi-Use LCG Assay Lab Tracking Form (15023287 A)
Lab tracking form for the Infinium Multi-Use LCG assay.
Infinium Multi-Use LCG Assay Manual EUC (15023285 A)
Experienced-level instructions for performing Infinium Multi-Use LCG assay.
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.
Installing MiSeq Reporter Off-Instrument
Instructions for installing MiSeq Reporter software off-instrument.
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.
iScan Control Software Release Notes (15022764 C)
Summary of changes introduced in iScan Control Software (ICS) v3.3.29.
iScan System Quick Reference Card (11313555 A)
Instructions for starting up and shutting down the iScan.
iScan System Quick Reference Guide (15020712 A)
Instructions for using the iScan.
iScan System Safety and Compliance Guide (15022905 B)
Safety information and product compliance statements for the iScan.
iScan System User Guide (11313539 B)
Instructions for using the iScan.
KaryoStudio Software v1.2 Release Notes (11328870 B)
Summary of changes introduced in KaryoStudio Software v1.3.
KaryoStudio Software v1.3 Release Notes (11328870 C)
This download contains the release notes for version 1.3 of the KaryoStudio Software.
KaryoStudio Software v1.4 Release Notes (11328870 D)
This download contains the release notes for version 1.4 of the KaryoStudio Software.
KaryoStudio Software v1.4 User Guide (11328837 C)
Instructions for using KaryoStudio Software v1.4 to analyze detected regions, match results to known variants, and generate a cytogenetics report.
Mate Pair v2 Sample Prep Guide For 2-5 kb Libraries (15008135)
Instructions for preparing samples using the Mate Pair Library Kit v2.
MicroRNA Assay for BeadChips EUC (11317329 A)
Experienced-level instructions for performing the MicroRNA Expression Profiling assay for BeadChips.
MicroRNA Assay for BeadChips Lab Tracking Form (11317345 A)
Lab tracking form for the MicroRNA Expression Profiling assay for BeadChips.
MicroRNA Assay for SAMs EUC (11317311 A)
Experienced-level instructions for performing the MicroRNA Expression Profiling assay.
MicroRNA Assay for SAMs Lab Tracking Form (11317337 A)
Lab tracking form for the microRNA Expression Profiling assay for SAMs.
MicroRNA Assay Guide (11317302 A)
Instructions for performing the MicroRNA Expression Profiling assay.
MicroRNA Universal-12 BeadChip Product Insert (11326920 B)
Information about changes to the miRNA Universal BeadChip protocol.
MiSeq Analysis 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.
MiSeq Enhancements Customer Letter
This customer letter describes enhancements and components associated with the MiSeq upgrade, and how upgrades are schedule.
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.
MiSeq Reagent Kit What's New Insert
Overview of changes introduced with the MiSeq reagent kit versions, related documentation, and software requirements.
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.
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.

MiSeq Reporter Theory of Operation
Summary of concepts and workflows in the MiSeq Reporter software.
MiSeq Reporter User Guide
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.
MiSeq Reporter v2.2.31.1 Software Reference Guide
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.
MiSeq Reporter Workflows in BaseSpace
Release notes for MiSeq Reporter workflows in BaseSpace.
MiSeq Run Folder Quick Reference Card
Quick reference overview of the MiSeq Output and Analysis Folders.
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.
MiSeq Sample Sheet Quick Ref Guide
This guide provides guidance for setting up sample sheets for sequencing on the MiSeq.
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.
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.

MiSeq System Safety and Compliance Guide
This guide contains safety information and product compliance markings for the MiSeq System.
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.
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.
MiSeqDx Cystic Fibrosis 139-Variant Assay Lab Tracking Form (US)

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.

MiSeqDx Cystic Fibrosis 139-Variant Assay Package Insert (US)

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

MiSeqDx Cystic Fibrosis 139-Variant Assay Physician Insert (US)

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

MiSeqDx Cystic Fibrosis 139-Variant Assay Reference Guide (US)

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

MiSeqDx Cystic Fibrosis Carrier Screening Assay Lab Tracking Form (CE)

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

MiSeqDx Cystic Fibrosis Carrier Screening Assay Package Insert (CE)

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

MiSeqDx Cystic Fibrosis Carrier Screening Assay Reference Guide (CE)

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

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.

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.

MiSeqDx Cystic Fibrosis Clinical Sequencing Assay Physician Insert

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

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.

MiSeqDx Instrument Package Insert

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

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.
MiSeqDx Instrument Safety and Compliance Guide
This guide contains safety information and product compliance markings for the MiSeqDx instrument.
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.
MiSeqDx Library Prep Check Kit Quick Reference Card

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

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

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

mRNA-Seq Sample Prep Guide (1004898 D)
This download contains the sample preparation guide for mRNA sequencing.
Multiplexing Sample Prep Guide (1005361)
Instructions for performing the Multiplexing sample prep assay.
Nextera DNA Assembly Plan-Run-Analyze Workflow Cards
These application workflow cards provide guidance for planning, running, and analyzing a Nextera DNA Assembly project.
Nextera DNA Resequencing Plan-Run-Analyze Workflow Cards
These application workflow cards provide guidance for planning, running, and analyzing a Nextera DNA Resequencing project.
Nextera DNA Sample Preparation Experienced User Card
Experienced-level instructions for preparing samples using the Nextera DNA sample preparation Kit.
Nextera DNA Sample Preparation Guide
Instructions for preparing samples using the Nextera DNA sample preparation Kit.
Nextera DNA Sample Preparation Lab Tracking Form
Interactive form for recording sample preparation steps using the Nextera DNA sample prep Kit.
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.
Nextera Enrichment Sample Prep Experienced User Card
Experienced-level instructions for preparing samples using the Nextera Enrichment Kit.
Nextera Enrichment Sample Prep Lab Tracking Form
Interactive form for recording sample preparation steps using the Nextera Enrichment sample prep Kit.
Nextera Enrichment Sample Preparation Guide
Instructions for preparing samples using the Nextera Enrichment sample prep Kit.
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.
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 Mate Pair Sample Preparation Guide
This guide explains how to prepare samples using the Nextera Mate Pair Sample Preparation Kit.
Nextera Rapid Capture Enrichment Experienced User Card and Lab Tracking Form
Experienced-level instructions for preparing samples using the Nextera Rapid Capture Enrichment Kit.
Nextera Rapid Capture Enrichment Guide
Instructions for preparing samples using the Nextera Rapid Capture Enrichment Kit.
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.
Nextera Rapid Capture Enrichment User-Supplied Consumables and Equipment
Consumables and equipment excerpt from the Nextera Rapid Capture Enrichment Guide.
Nextera XT DNA Sample Preparation Insert
Summary of the Nextera XT DNA sample preparation.
Nextera XT PCR Amplicon Plan-Run-Analyze Workflow Cards
These application workflow cards provide guidance for planning, running, and analyzing a Nextera XT PCR Amplicon project.
Nextera XT Sample Preparation Experienced User Card
Experienced-level instructions for preparing samples using the Nextera XT sample prep Kit.
Nextera XT Sample Preparation Guide
Instructions for preparing samples using the Nextera XT DNA sample preparation Kit.
Nextera XT Sample Preparation Lab Tracking Form
Interactive form for recording sample preparation steps using the Nextera XT sample prep Kit.
Nextera XT Small Genomes Assembly Plan-Run-Analyze 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 Small Genomes Resequencing Plan-Run-Analyze Workflow 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.

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.
NextSeq 500 Plan-Run-Analyze Quick Reference Cards

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

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

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.

NextSeq 500 System Site Preparation Guide
This guide contains lab specifications and requirements for NextSeq 500 installation and operation.
NextSeq 500 System User Guide
This guide contains an overview of instrument components and instructions for operating and maintaining the NextSeq 500.
NuPCR Assay Guide
This download contains the assay guide for the NuPCR assay.
Off-Line Basecaller User Guide 15009920 Rev. D
Instructions for using OLB v1.9.4 for basecalling and converting *.bcl files to *qseq.txt files.
Paired-End Cluster Generation Kit v2 Guide (1005629 C)
Instructions for using the Paired-End Cluster Generation Kit v2 on the Cluster Station and Paired-End Module.
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.
Paired-End Sample Preparation Guide (1005063)
Instructions for preparing samples using the Paired-End sample prep Kit.
Paired-End Sample Preparation User-Supplied Consumables and Equipment
Consumables and equipment excerpt from the Paired-End Sample Preparation Guide.
Performing Clustering in the GenomeStudio Polyploid Clustering Module UG (15044760 A)
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.
Performing Rapid Run Primer Rehybridization
Instructions for performing rapid run primer rehybridization on the HiSeq 2500 and HiSeq 1500.
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.
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.
Protocol Scanning Matrix GGGT Automation 370-2010-015
Summary of workflow requirements and estimated scan times for GoldenGate assays.
Protocol Scanning Matrix Infinium Automation 370-2010-014
Summary of workflow requirements and estimated scan times for Infinium BeadChips.
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.

Read 2 Rehybridization on a HiSeq Flow Cell
Instructions for performing a Read 2 rehybridization on a HiSeq flow cell.
RRBS for Methylation Guide (15021647)
Instructions for RRBS for Methylation Analysis.
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.
Sequencing Dual-Indexed Libraries on the HiSeq
This guide contains instructions for sequencing dual-indexed libraries on the HiSeq.
Sequencing Kit v4 Reagent Preparation Guide (15002739 A)
Instructions for using the Reagent Preparation for the Genome Analyzer - Sequencing Kit v4
Sequencing Library qPCR Quantification Guide
This download contains the protocol guide for SBS library qPCR quantification.
Sequencing Library qPCR Quantification Guide
This download contains the protocol guide for SBS library qPCR quantification.
Sequencing Mixed Libraries on a HiSeq or GA Flow Cell
Summary of guidelines and requirements for sequencing mixed libraries on the same flow cell.
Ship Schedule Form
Shipping schedule change request form.
Single-Read Cluster Generation Lab Tracking Form (15019439)
Lab Tracking Form Single-Read Cluster Station v5 (15019439)
Small RNA Plan-Run-Analyze Workflow Cards
These application workflow cards provide guidance for planning, running, and analyzing a Small RNA project.
Small RNA Sample Prep Guide - Oligo Only Kit (1003651)
Instructions for preparing samples using the Small RNA Oligo Only Kit.
Small RNA Sample Prep Guide (1004239)
Instructions for performing the Small RNA sample prep assay.
Small RNA v1.5 Sample Prep Guide (15002615)
Instructions for using the Small RNA v1.5 sample prep.
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.
Thermocycler Control Software User Guide (15004310 A)
Instructions for using the Thermocycler Control Software.
TruSeq Amplicon - Cancer Panel FFPE QC Insert
Instructions for using the FFPE QC kit with the TruSeq Amplicon - Cancer Panel.
TruSeq Amplicon - Cancer Panel Library Prep Experienced User Card
Experienced-level instructions for preparing samples using the TruSeq Amplicon - Cancer Panel Library Preparation Kit.
TruSeq Amplicon - Cancer Panel Library Prep Guide
Instructions for preparing samples using the TruSeq Amplicon - Cancer Panel Library Preparation Kit.
TruSeq Amplicon - Cancer Panel Library Prep Lab Tracking Form
Interactive form for recording sample preparation steps using the TruSeq Amplicon - Cancer Panel kit.
TruSeq Amplicon - Cancer Panel Plan-Run-Analyze 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.

TruSeq Amplicon - Cancer Panel Resources Insert
Links to documentation, accessories, and product files for the TruSeq Amplicon - Cancel Panel.
TruSeq ChIP Sample Preparation Experienced User Card and Lab Tracking Form
Experienced-level instructions for using the TruSeq ChIP Sample Prep Kit to prepare samples for sequencing.
TruSeq ChIP Sample Preparation Guide
Instructions for using the TruSeq ChIP Sample Prep Kit to prepare samples for sequencing.
TruSeq ChIP Sample Preparation User-Supplied Consumables and Equipment
Consumables and equipment excerpt from the TruSeq ChIP Sample Preparation Guide.
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.
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 Cluster Kit v5 (CS-GA) Reagent Prep Guide

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

TruSeq Custom Amplicon Library Experienced User Card and Lab Tracking Form
Experienced user level instructions for preparing samples using the TruSeq Custom Amplicon Library Preparation Kit.
TruSeq Custom Amplicon Library Preparation Guide
Instructions for preparing samples using the TruSeq Custom Amplicon Library Preparation Kit.
TruSeq Custom Amplicon Plan-Run-Analyze 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 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.
TruSeq DNA PCR-Free Sample Preparation Guide
Instructions for preparing samples using the TruSeq DNA PCR-Free Sample Preparation Kit.
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.
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.
TruSeq DNA PCR-Free Sample Preparation User-Supplied Consumables and Equipment
Consumables and equipment excerpt from the TruSeq DNA PCR-Free Sample Preparation Guide.
TruSeq DNA Sample Prep Dual Index Product Insert
Summary of instructions for using the TruSeq DNA Dual Index.
TruSeq DNA Sample Preparation (v1) Guide
Instructions for using the TruSeq DNA sample prep (v1) protocol.
TruSeq DNA Sample Preparation (v1) High Throughput Experienced User Card
Instructions for using TruSeq DNA sample prep HT protocol.
TruSeq DNA Sample Preparation (v1) High Throughput Lab Tracking Form
Lab tracking form for the TruSeq DNA sample prep HT assay.
TruSeq DNA Sample Preparation (v1) Low Throughput Experienced User Card
Instructions for using the TruSeq DNA sample prep LT protocol.
TruSeq DNA Sample Preparation (v1) Low Throughput Lab Tracking Form
Lab tracking form for the TruSeq DNA sample prep protocol.
TruSeq DNA Sample Preparation Guide
Instructions for preparing samples using the TruSeq DNA Sample Prep Kit.
TruSeq DNA Sample Preparation High Sample Experienced User Card
Experienced-level instructions for using the TruSeq DNA sample prep HS protocol.
TruSeq DNA Sample Preparation High Sample Lab Tracking Form
Lab tracking form for the TruSeq DNA sample prep HS protocol.
TruSeq DNA Sample Preparation Low Sample Experienced User Card
Experienced-level instructions for using the TruSeq DNA sample prep LS protocol.
TruSeq DNA Sample Preparation Low Sample Lab Tracking Form
Lab tracking form for the TruSeq DNA sample prep LS protocol.
TruSeq DNA Sample Preparation User-Supplied Consumables and Equipment
Consumables and equipment excerpt from the TruSeq DNA Sample Preparation Guide.
TruSeq Enrichment Analysis Guide (15029648 A)
Instructions for TruSeq Enrichment Analysis.
TruSeq Enrichment Experienced User Card
Experienced-level instructions for using the TruSeq Enrichment protocol.
TruSeq Enrichment Guide
Instructions for performing the TruSeq Enrichment protocol.
TruSeq Enrichment Lab Tracking Form
Lab tracking form for the TruSeq Enrichment protocol.
TruSeq Enrichment User-Supplied Consumables and Equipment
Consumables and equipment excerpt from the TruSeq Enrichment Guide.
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.
TruSeq Nano DNA Sample Preparation Guide
Instructions for preparing samples using the TruSeq Nano DNA Sample Prep Kit.
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.
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.
TruSeq Nano DNA Sample Preparation User-Supplied Consumables and Equipment
Consumables and equipment excerpt from the TruSeq Nano DNA Sample Preparation Guide.
TruSeq Rapid Cluster Kit Reagent Prep Guide
This guide contains instructions for preparing reagents provided in the TruSeq Rapid Cluster Kit for rapid runs on the HiSeq 2500 and HiSeq 1500.
TruSeq Rapid Duo Sample Loading Kit Reagent Prep Guide
Instructions for preparing reagents in the TruSeq Rapid Duo Sample Loading Kit for the cBot.
TruSeq Rapid SBS Kit Reagent Prep Guide
This guide contains instructions for preparing SBS reagents provided in the TruSeq Rapid SBS Kit for rapid runs on the HiSeq 1500 and 2500.
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 Guide
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 Sample Preparation Guide
This download contains the guide for the TruSeq RNA Sample Preparation protocol for sequencing.
TruSeq RNA Sample Preparation High Throughput Experienced User Card
Instructions for using the TruSeq RNA sample prep HT protocol.
TruSeq RNA Sample Preparation High Throughput Lab Tracking Form
Instructions for using the TruSeq RNA sample prep HT protocol.
TruSeq RNA Sample Preparation Low Throughput Experienced User Card
Experienced-level instructions for using the TruSeq RNA sample prep LT protocol.
TruSeq RNA Sample Preparation Low Throughput Lab Tracking Form
Lab tracking form for the TruSeq RNA sample prep LT protocol.
TruSeq RNA Sample Preparation v2 Guide
Instructions for preparing samples using the TruSeq RNA Sample Preparation Kit v2.
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.
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.
TruSeq RNA Sample Preparation v2 User-Supplied Consumables and Equipment
Consumables and equipment excerpt from the TruSeq RNA Sample Preparation v2 Guide.
TruSeq Sample Preparation Best Practices Guide
Overview of the best practices for the TruSeq sample prep protocol.
TruSeq Sample Preparation Pooling Guide
Instructions for pooling samples using the TruSeq LT, HT, Small RNA, or ChIP sample prep kits.
TruSeq SBS Kit v3 Reagent Prep Guide
This guide contains instructions for preparing SBS reagents provided in TruSeq SBS Kit v3 for the HiSeq.
TruSeq SBS Kit v5 (GA) Reagent Prep Guide
Instructions for preparing TruSeq SBS v5 reagents for the Genome Analyzer.
TruSeq Small RNA Sample Preparation Experienced User Card and Lab Tracking Form
Experienced-level instructions for the TruSeq Small RNA Sample Prep Kit.
TruSeq Small RNA Sample Preparation Guide
Instructions for using the TruSeq Small RNA sample prep protocol.
TruSeq Small RNA Sample Preparation User-Supplied Consumables and Equipment
Consumables and equipment excerpt from the TruSeq Small RNA Sample Preparation Guide.
TruSeq Stranded mRNA HT Sample Prep Dual Index Insert
Instructions for dual-indexing with TruSeq Stranded mRNA HT Sample Prep.
TruSeq Stranded mRNA Sample Preparation Guide
Instructions for using the TruSeq Stranded mRNA sample prep protocol.
TruSeq Stranded mRNA Sample Preparation HS Experienced User Card and Lab Tracking Form
Experienced-level instructions for preparing samples using the HS protocol for the TruSeq Stranded mRNA Sample Prep Kit.
TruSeq Stranded mRNA Sample Preparation LS Experienced User Card and Lab Tracking Form
Experienced-level instructions for preparing samples using the LS protocol for the TruSeq Stranded mRNA Sample Prep Kit.
TruSeq Stranded mRNA Sample Preparation User-Supplied Consumables and Equipment
Consumables and equipment excerpt from the TruSeq Stranded mRNA Sample Preparation Guide.
TruSeq Stranded Total RNA HT Sample Prep Dual Index Insert
Instructions for dual-indexing with TruSeq Stranded Total RNA HT Sample Prep.
TruSeq Stranded Total RNA Sample Preparation Guide
Instructions for preparing samples using the TruSeq Stranded Total RNA Sample Prep Kit.
TruSeq Stranded Total RNA Sample Preparation HS Experienced User Card and Lab Tracking Form
Experienced-level instructions for preparing samples using the HS protocol for the TruSeq Stranded Total RNA Sample Prep Kit.
TruSeq Stranded Total RNA Sample Preparation LS Experienced User Card and Lab Tracking Form
Experienced-level instructions for preparing samples using the LS protocol for the TruSeq Stranded Total RNA Sample Prep Kit.
TruSeq Stranded Total RNA Sample Preparation User-Supplied Consumables and Equipment
Consumables and equipment excerpt from the TruSeq Stranded Total RNA Sample Preparation Guide.
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.
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.
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.
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.
TruSeq Targeted RNA Expression Experienced User Card and Lab Tracking Form
Experienced-level instructions for preparing samples using the TruSeq Targeted RNA Expression Kit.
TruSeq Targeted RNA Expression Guide
Instructions for preparing samples using the TruSeq Targeted RNA Expression Kit.
TruSeq Targeted RNA Expression User-Supplied Consumables and Equipment
Consumables and equipment excerpt from the TruSeq Targeted RNA Expression Guide.
TruSight DNA Amplicon Library Experienced User Card and Lab Tracking Form
Experienced user level instructions for preparing samples using the TruSight DNA Amplicon Library Preparation Kit.
TruSight DNA Amplicon Library Preparation Guide
Instructions for preparing samples using the TruSight DNA Amplicon Library Preparation Kit.
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).
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).
TruSight Enrichment DNA Sample Prep Kit Lab Tracking Form
This download contains the lab tracking form for the TruSight Enrichment DNA Sample Prep Kit.
TruSight One Consumables and Equipment
This document provides a list of all of the necessary user-supplied consumables and equipment.
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.
TruSight One Sequencing Panel Library Preparation Experienced User Card and Lab Tracking Form
Intended for the experienced user, this document summarizes the steps for preparing samples using the TruSight One Sequencing Panel Sample Prep protocol.
TruSight One Sequencing Panel Plan-Run-Analyze Workflow Cards
These application workflow cards provide guidance for planning, running, and analyzing a TruSight One Sequencing Panel project.
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).
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).
TruSight Tumor Analysis on HiSeq 2500

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

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.
TruSight Tumor Sample Prep Guide
Instructions for using the TruSight Tumor Sample Prep protocol.
Ultra Low Input mRNA-Seq Guide (11322751)
Instructions for Ultra Low mRNA-Seq sample preparation.
Universal-12 BeadChip Booklet (11325425 B)
Instructions for performing the MicroRNA GoldenGate Methylation and DASL Gene Expression assays.
Using Custom Primers on the MiSeq
This guide provides instructions for using custom primers for sequencing on the MiSeq.
Using eQTL Demo Data (970-2009-011)
This download contains documentation explaining how to use eQTL Demo Data in GenomeStudio.
VariantStudio Release Notes

Summary of changes introduced in VariantStudio software.

VariantStudio User Guide
This guide provides an overview of the Illumina VariantStudio desktop application and instructions for importing, annotating, and filtering variants.
VeraCode ADME Core Panel Assay Guide
Instructions for performing the VeraCode ADME assay.
VeraCode ADME Core Panel Lab Tracking Form
Lab tracking form for the VeraCode ADME Core Panel assay.
VeraCode ADME Kit Module Software Release Notes
Summary of instructions for using the VeraCode ADME Kit Module Software.
VeraCode ADME Software v1.0.1.4 Release Notes
Summary of instructions for using the VeraCode ADME Software.
VeraCode and BeadXpress EMR Checklist
List of equipment, materials, and reagents required for VeraCode and BeadXpress.
VeraCode Assay Guide
This download contains the user guide for performing multiple assays using VeraCode technology on the BeadXpress platform.
Veracode Bead Kitting System Guide (11248010 B)
Instructions for kitting and storing VeraCode beads, as well as cleaning the bead kitting system.
VeraCode DASL Assay Lab Tracking Form (11312747 A)
Lab tracking form for DASL for VeraCode.
VeraCode DASL Assay Manual EUC (11312780 A)
Experienced-level instructions for performing the DASL Gene Expression assay for VeraCode.
Veracode Vortex Incubator User Guide (11251876 A)
This download contains the Vortex Incubator User Guide for use with VeraCode Assays.
WGBS for Methylation Analysis Guide (15021861)
Instructions for WGBS for Methylation Analysis.
WG-DASL Assay Guide (11322443 B)
This download contains the user guide for performing the Whole-Genome Gene Expression DASL Assay.
WG-DASL Experienced User Card (11322347 B)
Instructions for performing the Whole-Genome Gene Expression DASL assay.
WG-DASL Lab Tracking Form (11327210 B)
Lab tracking form for the Whole-Genome Gene Expression DASL assay.
WGGEX Direct Hybridization Assay Guide (11322355 A)
Instructions for performing the Whole-Genome Gene Expression Direct Hybridization assay.
WGGEX Direct Hybridization Assay Lab Tracking Form (11327279 A)
Interactive form for recording steps during the Whole-Genome Gene Expression Direct Hybridization assay.
WGGEX Direct Hybridization Experienced User Card (11322187 A)
Experienced-level instructions for performing the Whole-Genome Gene Expression Direct Hybridization assay.
Whole-Genome Gene Expression DASL HT Assay EUC (15018211 D)
Experienced-level instructions for using the WGDASL HT.
Whole-Genome Gene Expression DASL HT Assay Guide (15018210 D)
Instructions for performing the WGDASL HT assay.
Whole-Genome Gene Expression DASL HT Assay LTF (15018212 B)
Lab tracking form for the Whole-Genome Gene Expression DASL HT assay.