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Sample GSM7103807 Query DataSets for GSM7103807
Status Public on Oct 02, 2023
Title PAPgamma siRNA rep3
Sample type SRA
 
Source name HeLa
Organism Homo sapiens
Characteristics cell line: HeLa
genotype: PAPgamma siRNA
time: Day 3
Treatment protocol siRNA (30nM) was transfected in HeLa cells using Interferin
Extracted molecule total RNA
Extraction protocol RNA was harvested using Trizol
RNA libraries for RNA-seq were prepared by Novogene
RNA-seq stranded paired-end, rRNA removal
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing CutAdapt to cut adapters
FASTQC for quality control
STAR_PE for alignment of reads on reference genome
samtools index to index bam files
HTSEQ_count_stranded to count reads on genes for differential expression analysis
extract_stranded_bam_PE to sort out forward and reverse reads
samtools_strd_index to index strand specific bam files
bamCoverage_RPGC to convert bam to bigwig
bamCoverage_strd_RPGC to convert stranded bam in bigwig
profmat_stranded_tss_gb to get wuantification matrix around TSS and scaled gene body for stranded bigwig
Assembly: hg38
Supplementary files format and content: bigwig files
 
Submission date Mar 17, 2023
Last update date Oct 02, 2023
Contact name Rosemary Kiernan
Organization name UMR9002 CNRS-UM
Lab Gene Regulation lab
Street address 141 rue de la cardonille
City Montpellier
ZIP/Postal code 34396
Country France
 
Platform ID GPL16791
Series (1)
GSE189157 PAP-gamma associates with PAXT nuclear exosome to control the abundance of PROMPT ncRNAs
Relations
BioSample SAMN33796380
SRA SRX19698693

Supplementary file Size Download File type/resource
GSM7103807_RNAseq_rep3_siPapG_FWD_RPGC.bw 17.3 Mb (ftp)(http) BW
GSM7103807_RNAseq_rep3_siPapG_REV_RPGC.bw 16.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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