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Page 1
RNA-Seq Experiment and Data Analysis.
Withanage MHH, Liang H, Zeng E. Withanage MHH, et al. Methods Mol Biol. 2022;2418:405-424. doi: 10.1007/978-1-0716-1920-9_22. Methods Mol Biol. 2022. PMID: 35119677
Not just the messenger RNA (mRNA), but a wide variety of different RNA populations (e.g., total RNA, microRNA, long ncRNA, pre-mRNA) can also be investigated using RNA-Seq. ...In this chapter, we describe a protocol to construct an RNA- …
Not just the messenger RNA (mRNA), but a wide variety of different RNA populations (e.g., total RNA, microRNA, long ncR …
Processing and Analysis of RNA-seq Data from Public Resources.
Zoabi Y, Shomron N. Zoabi Y, et al. Methods Mol Biol. 2021;2243:81-94. doi: 10.1007/978-1-0716-1103-6_4. Methods Mol Biol. 2021. PMID: 33606253 Review.
Advances in next generation sequencing (NGS) technologies resulted in a broad array of large-scale gene expression studies and an unprecedented volume of whole messenger RNA (mRNA) sequencing data, or the transcriptome (also known as RNA sequencing, or RNA …
Advances in next generation sequencing (NGS) technologies resulted in a broad array of large-scale gene expression studies and an unpreceden …
Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications.
Su M, Pan T, Chen QZ, Zhou WW, Gong Y, Xu G, Yan HY, Li S, Shi QZ, Zhang Y, He X, Jiang CJ, Fan SC, Li X, Cairns MJ, Wang X, Li YS. Su M, et al. Mil Med Res. 2022 Dec 2;9(1):68. doi: 10.1186/s40779-022-00434-8. Mil Med Res. 2022. PMID: 36461064 Free PMC article. Review.
With the expansion of capacity for high-throughput scRNA-seq, including clinical samples, the analysis of these huge volumes of data has become a daunting prospect for researchers entering this field. Here, we review the workflow for typical scRNA-seq data …
With the expansion of capacity for high-throughput scRNA-seq, including clinical samples, the analysis of these huge volumes of da …
RNA-seq Data Analysis for Differential Expression.
Gill N, Dhillon B. Gill N, et al. Methods Mol Biol. 2022;2391:45-54. doi: 10.1007/978-1-0716-1795-3_4. Methods Mol Biol. 2022. PMID: 34686975
Determining the transcriptional profile could provide valuable clues on how an organism responds to defined stimuli, in this case, how a pathogen colonizes its host. Several robust data analysis methods and pipelines are available that can identify these differentially exp …
Determining the transcriptional profile could provide valuable clues on how an organism responds to defined stimuli, in this case, how a pat …
Representation and relative abundance of cell-type selective markers in whole-kidney RNA-Seq data.
Clark JZ, Chen L, Chou CL, Jung HJ, Lee JW, Knepper MA. Clark JZ, et al. Kidney Int. 2019 Apr;95(4):787-796. doi: 10.1016/j.kint.2018.11.028. Epub 2019 Feb 27. Kidney Int. 2019. PMID: 30826016 Free PMC article.
We addressed the question of which cell types are represented in whole-kidney RNA-Seq data in order to identify circumstances in which bulk-kidney RNA-Seq can be successfully interpreted. ...RNA-Seq data for cell-type select …
We addressed the question of which cell types are represented in whole-kidney RNA-Seq data in order to identify circums …
Variant Calling from RNA-seq Data Using the GATK Joint Genotyping Workflow.
Brouard JS, Bissonnette N. Brouard JS, et al. Methods Mol Biol. 2022;2493:205-233. doi: 10.1007/978-1-0716-2293-3_13. Methods Mol Biol. 2022. PMID: 35751817
Unfortunately, the fully validated GATK pipeline for calling variant on RNAseq data is a Per-sample workflow that does not include the recent improvements seen in modern workflows, especially the possibility to perform joint genotyping analysis. ...
Unfortunately, the fully validated GATK pipeline for calling variant on RNAseq data is a Per-sample workflow that does not include th …
TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository.
Zhao Y, Li MC, Konaté MM, Chen L, Das B, Karlovich C, Williams PM, Evrard YA, Doroshow JH, McShane LM. Zhao Y, et al. J Transl Med. 2021 Jun 22;19(1):269. doi: 10.1186/s12967-021-02936-w. J Transl Med. 2021. PMID: 34158060 Free PMC article.
BACKGROUND: In order to correctly decode phenotypic information from RNA-sequencing (RNA-seq) data, careful selection of the RNA-seq quantification measure is critical for inter-sample comparisons and for downstream analyses, such as diff …
BACKGROUND: In order to correctly decode phenotypic information from RNA-sequencing (RNA-seq) data, careful sele …
A scoping review on deep learning for next-generation RNA-Seq. data analysis.
Pandey D, Onkara Perumal P. Pandey D, et al. Funct Integr Genomics. 2023 Apr 21;23(2):134. doi: 10.1007/s10142-023-01064-6. Funct Integr Genomics. 2023. PMID: 37084004 Review.
Nevertheless, knowledge discovery from these next-generation RNA-Seq. data analysis necessitates extensive bioinformatics know-how besides elaborate data analysis software packages consistent with the type and context of data analysis. ...In thi …
Nevertheless, knowledge discovery from these next-generation RNA-Seq. data analysis necessitates extensive bioinformati …
Sequences to Differences in Gene Expression: Analysis of RNA-Seq Data.
Pavlovich PV, Cauchy P. Pavlovich PV, et al. Methods Mol Biol. 2022;2508:279-318. doi: 10.1007/978-1-0716-2376-3_20. Methods Mol Biol. 2022. PMID: 35737247 Review.
RNA-Seq is now a routinely employed assay to measure gene expression. ...We illustrate these steps with analysis of publicly available RNA-Seq data....
RNA-Seq is now a routinely employed assay to measure gene expression. ...We illustrate these steps with analysis of publicly a …
Strategy for RNA-Seq Experimental Design and Data Analysis.
Gimenez G, Stockwell PA, Rodger EJ, Chatterjee A. Gimenez G, et al. Methods Mol Biol. 2023;2588:249-278. doi: 10.1007/978-1-0716-2780-8_16. Methods Mol Biol. 2023. PMID: 36418693
However, the strategy for RNA-Seq experimental design and data analysis can substantially differ depending on the biological application. The design choice could also have significant impact for downstream results and interpretation of data. Here we de …
However, the strategy for RNA-Seq experimental design and data analysis can substantially differ depending on the biolo …
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