RNA-seq Analysis of VHL-deficient Renal Cancer

RNA was extracted in duplicates from 786-O-Ctrl and 786-O-VHL cells using the Quick-RNA Miniprep Kit (Zymo Research, #R1054) following the manufacturer’s manual. RNA quality was assessed with Agilent Bioanalyzer 2100. Purified RNA (1 μg) was used for the Illumina NovaSeq 6000 Sequencing (Novagene). RNA-seq sequencing reads were aligned to hg19, and the DESeq2 package [37 (link)] was used to calculate differential expression genes. Pathway analysis was performed using Gene Set Enrichment Analysis (GSEA) [38 (link)]. Gene list enrichment was analyzed by MetaCore (version 21.3 build 70600) or Enrichr [39 (link),40 (link)].

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Wang X., Hu J., Fang Y., Fu Y., Liu B., Zhang C., Feng S, & Lu X. (2022). Multi-Omics Profiling to Assess Signaling Changes upon VHL Restoration and Identify Putative VHL Substrates in Clear Cell Renal Cell Carcinoma Cell Lines. Cells, 11(3), 472.

Publication 2022

Quick-RNA Miniprep Kit Agilent Bioanalyzer 2100 Illumina NovaSeq 6000 Sequencing

Cells Expression genes Gene Rna seq

Corresponding Organization : Westlake University

Other organizations : Eastern Hepatobiliary Surgery Hospital, Second Military Medical University

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Variable analysis

independent variables

Cell line (786-O-Ctrl and 786-O-VHL)

dependent variables

Gene expression (differential expression genes)

control variables

RNA extraction protocol (Quick-RNA Miniprep Kit)
RNA quality assessment (Agilent Bioanalyzer 2100)
RNA sequencing (Illumina NovaSeq 6000)
Alignment to reference genome (hg19)
Differential expression analysis (DESeq2)
Pathway analysis (GSEA)
Gene list enrichment analysis (MetaCore, Enrichr)

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

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