DNA, RNA, & Epigenetic Sequencing and Microarray Workflow Resources.

DNA-Seq, RNA-Seq, ChIP-Seq Sample Prep | Library & Microarray Preparation | NGS & Microarray Systems | Bioinformatics Software | Genomics Applications & Dataset Examples

DNA-Seq Sample Prep RNA-Seq Sample Prep ChIP-Seq Sample Prep Microarrays Sample Prep
Automated Sample Prep Qiagen QIAcube User Guide Qiagen QIAcube User Guide EMD Millipore EZ-Magna ChIP HT96 Qiagen QIAcube User Guide
Perkin Elmer Automated Liquid Handling
PK JANUS Automated Workstation Options
Hamilton Automated Liquid Handling
Hamilton Automated Liquid Handling Brochure
Fluidigm C1 Single-Cell User Guide Diagenode SX-8G IP-Star User Guide
Diagenode Auto IPure Kit Guide (for SX-8G IP-Star)
Sample Prep Kits Qiagen QIAamp DNA Mini Kit Guide Qiagen RNeasy Plus Kit Guide Abcam AB500 ChIP Kit Protocol Guide Qiagen RNeasy Tissue Kit User Guide
Qiagen AllPrep DNA/RNA Kit Guide
Magna HT96 ChIP-Seq Workflow
Bioassay Development Assay Review MicroArray Quality Control (MAQC) project II
Resource2 Resource2 Resource2 Resource2
DNA-Seq Library Prep RNA-Seq Library Prep ChIP-Seq Library Prep Microarray Chip Prep
Automated Library & Microarray Prep Mondrian SP User guide Mondrian SP+ User Guide Mondrian SP User Guide Ovation WGA User Guide
Encore User Guide Mondrian SP+ Cartridge User Guide Mondrian SP Cartridge User Guide
Encore 384 User Guide Ovation System V2 User Guide
Fluidigm Access Array, Target Resequence
Library & Microarray Prep Kits Illumina TruSeq DNA User Guide
TruSeq Enrichment Guide
TruSeq Exome Enrichment Kit
Illumina TruSeq Total RNA User Guide Illumina TruSeq ChIP User Guide Affy GeneChip Exon ST 1.0 Array Datasheet
Illumina TruSeq mRNA User Guide Affy GeneChip Gene ST 1.0 Array Datasheet
Affy Ambion WT Expression Kit User Guide
Affy GeneChip WT Term Label & Hybridization User Guide
Protocols Mondrian SP Protocol Ovation System V2 Quick Protocol Mondrian SP Protocol Ovation WGA Quick Protocol
AB SOLID 4 System User Guide Poly(A)+ RNA App Resource
Fluidigm Access Array Microfluidic Chip
Illumina Total RNA-Seq Library Workflow
Illumina ChIP-Seq Library Workflow
Affy GeneChip WT Chip Prep Workflow
DNA-Seq Systems RNA-Seq Systems ChIP-Seq Systems Microarrays Systems
Illumina HiSeq2500 User Guide
Illumina HiSeq2500 Application Note
Quality Scores for NGS
Illumina TruSeq Cluster and SBS kits
SOLID 5500W Series
SOLID System Accuracy Note
Ion Proton System
Ion Proton Specification Sheet
Illumina HiSeq2500 User Guide
SOLID 5500W Series
SOLID ChIP-Seq Protocol
Affy GeneChip System 3000Dx v.2 Brochure (FDA-cleared)
Affy GeneChip System 3000Dx v.2 Assay Menu
Affy Molecular Diagnostic Software Guide
Affy GeneChip Human Gene 1.0 ST Assay Software Module
Affy GeneChip Human Exon 1.0 ST Assay Software Module
DNA-Seq Data Analysis RNA-Seq Data Analysis ChIP-Seq Data Analysis Microarrays Data Analysis
Open Source Tools R & Bioconductor R & Bioconductor R & Bioconductor R & Bioconductor
Amazon Elastic Compute Cloud Amazon Elastic Compute Cloud Amazon Elastic Compute Cloud Amazon Elastic Compute Cloud
SRA ToolKit
Aspera Connect Browser Plug-in
for NCBI Data Download
FastX Toolkit
Bowtie 2
Bowtie 2
Samtools Samtools PeakSeq
Edena (de novo)
Velvet (de novo)
TopHat BSSeeker (MethylC-Seq) Affy Power Tools
UCSC Browser CuffLinks
Tuxedo Suite Workflow
UCSC Browser Affy Exon Support & Library Files (for APT)
Pubs SRA Handbook Download Guide
Aspera Connect Guide
AWS Elastic Cloud Compute Guide
IGV User Guide
BEDTools User Guide
BaseSpace User Guide
Aligning short sequencing reads with Bowtie
The Sequence Alignment Map format and SAMtools
Sam BAM Format
Variant Call Format (VCF) Poster
TopHat discovering splice junctions with RNA-Seq
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks"
RNA Sequencing Analysis With TopHat User Guide (Illumina)
Model-based Analysis of ChIP-Seq (MACS) Exon array data analysis using Affymetrix power tools and R statistical software
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
Databases Sequence Read Archive
Illumina BaseSpace
Sequence Read Archive NIH Roadmap Epigenomics Project Data Listings EMBL-EBI ArrayExpress Data
DNA-Seq Applications & Examples RNA-Seq Applications & Examples ChIP-Seq Applications & Examples Microarrays Applications & Examples
Applications Human Genome Resources Human Transcriptome Project Human Epigenome Project
The ENCODE Project
Analyzed Dataset Examples Alternative Splicing of Exons in Human Hematopoietic Stem cells
Alternative Splicing of Exons in Human Hematopoietic Stem Cells Code

©2013 Phillip Woolwine
Life Biotechnology Resource