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DeepSeq Resources and User Information


Introduction/Basics
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  • For a primer on Illumina sequencing, please read this document explaining the technology, the workflow, and various applications.
  • Illumina's 'beginner's guide' is located here.
  • Publications and information about deep/massively-parallel sequencing (MPSS) can be found on the Publications page at Illumina. We recommend starting with the review by DR Bentley, "Whole-genome re-sequencing".
  • When Do I Use Sanger Sequencing vs NGS?
  • Protocols and sample submission information are available on the Services page. Please follow the Services link in the navigation panel for more information.
  • Tips for library troubleshooting and optimization can be found here.
  • A list of frequently asked questions and answers can be found here.


Data and Bioinformatics
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  • Analytical tools and BioInformatics information are being collected and posted on the DeepSeq Data Page.
  • You can find a Guide for UNIX and many other UMass Bioinformatics resources at http://biotools.umassmed.edu
  • For a link to BioTools for Next Gen Sequencing Documents, go here: http://biotools.umassmed.edu/BioCore/nextgen/
  • The WIKI for the GHPCC is at http://wiki.umassrc.org/wiki/index.php/Main_Page
  • For information about NextGen BioInformatics Tools on GHPCC, click here. Please note that this list references the old HPCC, and some tools may no longer be available.
  • We are establishing a library of reference genomes and analysis tools; we welcome requests and suggestions at Nemo@umassmed.edu.


Other Tools
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  • A handy calculator tool for DNA and RNA: NEBioCalculator
  • A tool for Data Quality Score Viewing: FASTQC
  • The NIH Gene Expression Omnibus accepts Next Generation or Deep Sequencing data. Information about data submission and links to the tools at GEO may be found on the GEO Page.


Library Protocols
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AMPure bead cleanup protocol ( get it )
AMPure PB bead creation protocol ( get it )
Index Pooling Guide ( get it )
ChIP-SEQ Technical Note ( get it )
Small RNA Library FAQs ( get it )
DNA Library FAQs ( get it )

ATAC-Seq Guides

Protocol publication ( click here )
Illumina's guidelines ( click here )
Harvard guidelines ( click here )

Cut&Run Guides

Protocol publication ( click here )

5C Mapping Guides

Protocol publication ( click here )

GuideSeq Guides

Protocol publication ( click here )

Older Protocols

Please note that some details such as recommended adapter sequences may have changed since these were written.
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Illumina TruSeq Prep Guides

TruSeq RNA ( click here )
TruSeq Small RNA ( click here )
TruSeq DNA ( click here )

Chromatin IP Library Protocols

Illumina Chromatin IP ( click here )
Newer Illumina ChIP Seq Prep ( click here )
Data Sheet ( Data Sheet )
Core Lab Notes ( click here )

Genomic DNA Library Protocols

Illumina Genomic DNA ( click here )
Core Lab Notes ( click here )

Small RNA Library Protocols

Illumina Small RNA Protocol NEWER ( click here )
Illumina Small RNA ( click here )
Mello Lab small RNA ( click here )
NEW and IMPROVED 14 JULY Mello Lab small RNA ( click here )

Expression/cDNA libraries

Illumina Protocols (long) available from core lab, please email
Nemo@umassmed.edu to request them.

~ Nemo and Crew (Why "Nemo"?)

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