DeepSeq Resources and User Information
Introduction/Basics
- A primer on Illumina sequencing explaining the technology, the workflow, and various applications.
- Illumina's 'beginner's guide' discussing the technology and when to use it.
- 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?
- Illumina's e-book on Multiomics (2021).
- A description of the Illumina Library Structure.
- A discussion on indexing/barcoding.
- Library Prep and other Protocols are available in the sections below, and information on the sample submission process is available on its own page. Please follow the link in the navigation panel for more information.
- Tips for library troubleshooting and optimization.
- A list of frequently asked questions and answers.
Grant Support and Funding
- The UMass Deep Sequencing Core (DSCL) will provide a formal letter of support to include in grant applications.
- For small and medium businesses, the Massachusetts State Innovation Voucher Program allows access to Core facilities in the UMass system.
Data and Bioinformatics
- The WIKI for the GHPCC is at https://www.umassrc.org/wiki/index.php/Main_Page
- A tool for Data Quality Score Viewing: FASTQC
- Open source software GenomeBrowse for adding and viewing genome annotations
- Illumina (Solexa) Data Analysis, a presentation by Dr. David Lapointe, 20 Mar 2008 - please note some links are out of date!
- A Short-Read Sequence Alignment Software List on Wikipedia
- We are establishing a library of reference genomes and analysis tools; we welcome requests and suggestions at DeepSequencingCoreLabs@umassmed.edu.
Other Tools
- A handy calculator tool for DNA and RNA: NEBioCalculator
- GMOD: Generic Model Organism Database
- 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
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 )
A comparison of Alt-R S.p. Cas9 nuclease with its variants ( click here )
Protocol publication ( click here )
Illumina's guidelines ( click here )
Harvard guidelines ( click here )
Protocol publication ( click here )
Protocol publication ( click here )
Protocol publication ( click here )
Older Protocols
Please note that some details such as recommended adapter sequences may have changed since these were written.
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 14JUL08 Mello Lab small RNA ( click here )
Expression/cDNA libraries
Illumina Protocols (long) available from core lab, please email
DeepSequencingCoreLabs@umassmed.edu to request them.
Publications
The UMMS Deep Sequencing Core Labs would be pleased to have you mention us in the acknowledgements section of any publications or presentations of data generated with our support. Our Research Resource Identifier is RRID: SCR_017702.
If you would like to have your publication listed on the Core's website to help highlight the work UMass researchers are doing, email us the reference at DeepSequencingCoreLabs@umassmed.edu.
Publications of general interest:
A Simple, Cost-Effective, and Robust Method for rRNA Depletion in RNA-Sequencing Studies; mBio. 2020 Apr 21;11(2)
https://www.ncbi.nlm.nih.gov/pubmed/32317317
Short paired-end reads trump long single-end reads for expression analysis; BMC Bioinformatics. 2020 Apr 19;21(1):149
https://www.ncbi.nlm.nih.gov/pubmed/32306895
RNA timestamps identify the age of single molecules in RNA sequencing; Nat Biotechnol. 2021 Mar;39(3):320-325
https://pubmed.ncbi.nlm.nih.gov/33077959/
Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin; Cell. 2020 Nov 12;183(4):1103-1116.e20
https://pubmed.ncbi.nlm.nih.gov/33098772/
~ Nemo and Crew (Why "Nemo"?)