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?
• A detailed poster from Illumina with visual descriptions of sequencing methods (2024).
• A description of the Illumina Library Structure.
• IDT's Guide to Next-Gen Sequencing.

Applications of NGS

• Illumina's e-book on Multiomics (2022).
• Illumina's e-book on Cancer Research Methods (2024).

Adapters and Indexing

• Illumina's Adapter Sequences document describing the standard adapters that can be used without requiring custom sequencing primers.
• A discussion on indexing/barcoding.
• Illumina's Overview of Indexed Sequencing.

Data and Bioinformatics

• A tool for Data Quality Score Viewing: FASTQC
• Some information on using Quality Scores: Q/Phred Scores
• Open source software GBrowse for adding and viewing genome annotations
• A Short-Read Sequence Alignment Software List on Wikipedia
• A review of bioinformatics tools from the Journal of Clinical Medicine
• Data analysis guides from 10X Genomics
• 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
• A sequencing coverage calculator from Illumina: Illumina Sequencing Coverage Calculator
• A read coverage calculator from NEB: NEB Read Coverage Calculator
• GMOD: Generic Model Organism Database
• The NIH Gene Expression Omnibus, a repository for data from gene expression experiments, accepts Next Generation or Deep Sequencing data. Information about data submission and links to the tools at GEO may be found on the GEO Submission Information Page: https://www.ncbi.nlm.nih.gov/geo/info/submission.html. The GEO Projects page is located here: https://www.ncbi.nlm.nih.gov/geo/summary/?type=taxfull

Publications

The Core would appreciate a mention in the acknowledgements section of any publications or data presentations generated with our support. Our Research Resource Identifier is RRID:SCR_017702.

The Core would like to help highlight the work UMass researchers are doing. If you wish to have your publication listed on the Core's website, email us the reference at DeepSequencingCoreLabs@umassmed.edu.

Publications of general interest:
Swatting Flies: Biting Insects as Non-Invasive Samplers for Mammalian Population Genomics; Mol Ecol. 2025 Jan 22:e17661.doi: 10.1111/mec.17661
https://pubmed.ncbi.nlm.nih.gov/39838904/

Genomic profiling of circulating tumor DNA for childhood cancers; Leukemia. 2024 Nov 10.doi: 10.1038/s41375-024-02461-x
https://pubmed.ncbi.nlm.nih.gov/39523434/

Single-cell nascent RNA sequencing unveils coordinated global transcription; Nature. 2024 Jul;631(8019):216-223
https://pubmed.ncbi.nlm.nih.gov/38839954/

Microfluidics-free single-cell genomics with templated emulsification; Nat Biotechnol. 2023 Nov;41(11):1557-1566
https://pubmed.ncbi.nlm.nih.gov/36879006/

Simultaneous sequencing of genetic and epigenetic bases in DNA; Nat Biotechnol. 2023 Oct;41(10):1457-1464
https://pubmed.ncbi.nlm.nih.gov/36747096/

Molecular spikes: a gold standard for single-cell RNA counting; Nat Methods. 2022 May;19(5):560-566
https://pubmed.ncbi.nlm.nih.gov/35468967/

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C; Nat Methods. 2023 Jul;20(7):1037-1047
https://pubmed.ncbi.nlm.nih.gov/37336949/

Whole genome sequencing reveals host factors underlying critical Covid-19; Nature. 2022 Mar 7. doi: 10.1038/s41586-022-04576-6
https://pubmed.ncbi.nlm.nih.gov/35255492/

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
https://pubmed.ncbi.nlm.nih.gov/35105301/

A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples; Nat Biotechnol. 2021 Sep;39(9):1103-1114
https://pubmed.ncbi.nlm.nih.gov/33349700/

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/

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

~ Nemo and Crew (Why "Nemo"?)