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Sample GSM7036770 Query DataSets for GSM7036770
Status Public on Sep 27, 2023
Title COS-7, siNT, biol rep 1
Sample type SRA
 
Source name kidney
Organism Chlorocebus aethiops
Characteristics tissue: kidney
cell line: COS-7
cell type: fibroblast-like cell
genotype: WT
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from each cell using RNeasy Plus (QIAGEN) after 168 h siRNA transfection.
RNA libraries for RNA-seq were prepared using KAPA stranded RNA‐seq LibraryPrep Kit following manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing STAR version 2.7.1a
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35.
Trimmed sequence reads were aligned to the reference Chlorocebus sabaeus genome version ChlSab1.1 (gene annotation from Ensembl 104) or Homo sapiens genome version GRCh38 (gene annotation from Gencode version 37) using STAR version 2.7.1a.
Raw gene expression counts were obtained directly from STAR, and normalization and differential expression analysis were performed using DESeq2 version 1.30.1.
For comparison analyses between COS-7 and U2OS, gene identifiers were converted from C. sabaeus to H. sapiens using the R/Bioconductor package biomaRt (version 2.48.3).
Assembly: ChlSab1.1 and GRCh38
Supplementary files format and content: tab-delimited excel file includes normilised read counts for genes and differential expression analysis for each samples
 
Submission date Feb 09, 2023
Last update date Sep 27, 2023
Contact name Akihiro Yamashita
E-mail(s) akihiro.yamashita@mail.mcgill.ca
Organization name McGill University
Street address 3801 University Ave
City Montreal
ZIP/Postal code H3A 2B4
Country Canada
 
Platform ID GPL22096
Series (1)
GSE224992 Effect of peroxisomal proteotoxic stress on gene expression in mammalian cells
Relations
BioSample SAMN33230429
SRA SRX19325500

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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