دورية أكاديمية
A Computational Workflow for Analysis of 3' Tag-Seq Data.
| العنوان: | A Computational Workflow for Analysis of 3' Tag-Seq Data. |
|---|---|
| المؤلفون: | Paropkari AD; Quantitative and Systems Biology Graduate Program, University of California, Merced, California.; Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, California., Bapat PS; Quantitative and Systems Biology Graduate Program, University of California, Merced, California.; Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, California., Sindi SS; Department of Applied Mathematics, School of Natural Sciences, University of California, Merced, California., Nobile CJ; Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, California.; Health Science Research Institute, University of California, Merced, California. |
| المصدر: | Current protocols [Curr Protoc] 2023 Feb; Vol. 3 (2), pp. e664. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: John Wiley & Sons Country of Publication: United States NLM ID: 101773894 Publication Model: Print Cited Medium: Internet ISSN: 2691-1299 (Electronic) Linking ISSN: 26911299 NLM ISO Abbreviation: Curr Protoc Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Hoboken, NJ : John Wiley & Sons, [2021]- |
| مواضيع طبية MeSH: | Gene Expression Profiling*/methods , Software*, Workflow ; RNA-Seq ; RNA, Messenger |
| مستخلص: | RNA-sequencing (RNA-seq) is a gold-standard method to profile genome-wide changes in gene expression. RNA-seq uses high-throughput sequencing technology to quantify the amount of RNA in a biological sample. With the increasing popularity of RNA-seq, many variations on the protocol have been proposed to extract unique and relevant information from biological samples. 3' Tag-Seq (also called TagSeq, 3' Tag-RNA-Seq, and Quant-Seq 3' mRNA-Seq) is one RNA-seq variation where the 3' end of the transcript is selected and amplified to yield one copy of cDNA from each transcript in the biological sample. We present a simple, easy-to-use, and publicly available computational workflow to analyze 3' Tag-Seq data. The workflow begins by trimming sequence adapters from raw FASTQ files. The trimmed sequence reads are checked for quality using FastQC and aligned to the reference genome, and then read counts are obtained using STAR. Differential gene expression analysis is performed using DESeq2, based on differential analysis of gene count data. The outputs of this workflow are MA plots, tables of differentially expressed genes, and UpSet plots. This protocol is intended for users specifically interested in analyzing 3' Tag-Seq data, and thus normalizations based on transcript length are not performed within the workflow. Future updates to this workflow could include custom analyses based on the gene counts table as well as data visualization enhancements. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Running the 3' Tag-Seq workflow Support Protocol: Generating genome indices. (© 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.) |
| References: | Genome Res. 2008 Jan;18(1):172-7. (PMID: 18032722) Genome Biol. 2014;15(12):550. (PMID: 25516281) Nucleic Acids Res. 2010 Apr;38(6):1767-71. (PMID: 20015970) Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1513-8. (PMID: 21187386) Sci Rep. 2018 Mar 19;8(1):4781. (PMID: 29556074) Nucleic Acids Res. 2017 Jan 4;45(D1):D592-D596. (PMID: 27738138) BMC Genomics. 2019 Jan 7;20(1):9. (PMID: 30616562) Nucleic Acids Res. 2012 Jan;40(Database issue):D700-5. (PMID: 22110037) IEEE Trans Vis Comput Graph. 2014 Dec;20(12):1983-92. (PMID: 26356912) Science. 2008 Jun 6;320(5881):1344-9. (PMID: 18451266) Nat Rev Genet. 2009 Jan;10(1):57-63. (PMID: 19015660) G3 (Bethesda). 2015 Jun 24;5(8):1721-36. (PMID: 26109357) Bioinformatics. 2013 Jan 1;29(1):15-21. (PMID: 23104886) Nature. 2004 Oct 21;431(7011):931-45. (PMID: 15496913) Genome Biol. 2016 Jan 26;17:13. (PMID: 26813401) |
| معلومات مُعتمدة: | R35 GM124594 United States GM NIGMS NIH HHS |
| فهرسة مساهمة: | Keywords: 3′ Tag-Seq; RNA sequencing; computational pipeline; differential gene expression |
| المشرفين على المادة: | 0 (RNA, Messenger) |
| تواريخ الأحداث: | Date Created: 20230213 Date Completed: 20230215 Latest Revision: 20240202 |
| رمز التحديث: | 20240202 |
| مُعرف محوري في PubMed: | PMC9930165 |
| DOI: | 10.1002/cpz1.664 |
| PMID: | 36779816 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 2691-1299 |
|---|---|
| DOI: | 10.1002/cpz1.664 |