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DeepSeq Resources and User Information


Introduction/Basics
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Grant Support and Funding
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Data and Bioinformatics
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Other Tools
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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 )

CRISPR-Cas9 Guides

A comparison of Alt-R S.p. Cas9 nuclease with its variants ( click here )

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 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
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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"?)

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