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DeepSeq Resources and User Information

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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
AMPure PB bead creation protocol
Index Pooling Guide
ChIP-SEQ Technical Note
Small RNA Library FAQs
DNA Library FAQs

Single Cell Guides

Perturb-seq publication

CRISPR-Cas9 Guides

A comparison of Alt-R S.p. Cas9 nuclease with its variants

ATAC-Seq Guides

ATAC Protocol publication
Illumina's ATAC guidelines

10X Genomics Guides

10X Genomics Support for correct protocol selection

Guides for difficult-to-prepare samples

White paper on preparing cell-free DNA and FFPE samples

Cut&Run Guides

Cut & Run Protocol publication

5C Mapping Guides

5C Protocol publication

GuideSeq Guides

GuideSeq Protocol publication

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
TruSeq Small RNA
TruSeq DNA

Chromatin IP Library Protocols

Illumina Chromatin IP
Newer Illumina ChIP Seq Prep
Data Sheet
Core Lab ChIP Notes

Genomic DNA Library Protocols

Illumina Genomic DNA
Core Lab Genomic Notes

Small RNA Library Protocols

Illumina Small RNA Protocol NEWER
Illumina Small RNA
Mello Lab small RNA
NEW and IMPROVED 14JUL08 Mello Lab small RNA

Expression/cDNA libraries

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

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The UMass Chan 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

Publications of general interest:
Single-cell nascent RNA sequencing unveils coordinated global transcription; Nature. 2024 Jul;631(8019):216-223

Microfluidics-free single-cell genomics with templated emulsification; Nat Biotechnol. 2023 Nov;41(11):1557-1566

Simultaneous sequencing of genetic and epigenetic bases in DNA; Nat Biotechnol. 2023 Oct;41(10):1457-1464

Molecular spikes: a gold standard for single-cell RNA counting; Nat Methods. 2022 May;19(5):560-566

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C; Nat Methods. 2023 Jul;20(7):1037-1047

Whole genome sequencing reveals host factors underlying critical Covid-19; Nature. 2022 Mar 7. doi: 10.1038/s41586-022-04576-6

Optimization of enzymatic fragmentation is crucial to maximize genome coverage: a comparison of library preparation methods for Illumina sequencing; BMC Genomics. 2022 Feb 1;23(1):92

A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples; Nat Biotechnol. 2021 Sep;39(9):1103-1114

RNA timestamps identify the age of single molecules in RNA sequencing; Nat Biotechnol. 2021 Mar;39(3):320-325

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin; Cell. 2020 Nov 12;183(4):1103-1116.e20

A Simple, Cost-Effective, and Robust Method for rRNA Depletion in RNA-Sequencing Studies; mBio. 2020 Apr 21;11(2)

Short paired-end reads trump long single-end reads for expression analysis; BMC Bioinformatics. 2020 Apr 19;21(1):149

~ Nemo and Crew (Why "Nemo"?)

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