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Sample GSM7457924 Query DataSets for GSM7457924
Status Public on Jul 27, 2024
Title A673 ARID1A KO RNA-seq
Sample type SRA
 
Source name A673
Organism Homo sapiens
Characteristics cell line: A673
genotype: ARID1A KO
Extracted molecule polyA RNA
Extraction protocol RNA was extracted from 1 million harvested cells with a Nucleospin RNA XS kit (Macherey-Nagel, MN740902). RNA-seq libraries were prepared using TruSeq stranded mRNA library prep kit (Illumina, 20020594). RNA-seq libraries were sequenced in a 100bp paired-end mode.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-G400
 
Data processing RNA-seq reads were aligned to the reference genome (hg38) using STAR software v2.7.8a with default parameters. The gene counts were quantified with RSEM.
The adaptor sequences were trimmed out using Cutadapt. The trimmed paired-end sequences were mapped to the human reference genome hg38 using bowtie 2 with parameters “—very-sensitive –X 1000 –dovetail”. The reads with poor mapping quality (MAPQ < 30) and the reads mapped to the mitochondrial genome were discarded. The potential PCR duplicates were marked using MarkDuplicates of PICARD, and the remaining reads were shifted using the alignmentSieve function of deeptools with the “—ATACshift” parameter. The accessible regions information was obtained using MACS2 narrow callpeak, keeping duplicates with a q-value cutoff of 0.01.
The sequenced reads were mapped to the human reference genome (hg38) using BWA-MEM. Chimeric reads spanning multiple sites of the genome were filtered out. The reads with poor mapping quality (MAPQ < 10) were discarded. Self-ligated reads (genome distance < 15 kb) were also filtered out. Potential PCR duplicates were marked using MarkDuplicates of PICARD. The reads were then assigned into 40 kb genomic bins to generate a 40 kb Hi-C contact map. To consider possible genome-dependent bias, coverage-based contact map normalization was performed with covNorm.
Assembly: GRCh38
Supplementary files format and content: RSEM gene count, MACS2 narrowpeak, covNorm coverage-normalized counts
 
Submission date Jun 06, 2023
Last update date Jul 27, 2024
Contact name Inkyung Jung
E-mail(s) kaistcbfg@gmail.com
Organization name KAIST
Department Biological Sciences
Street address KAIST, 291 Daehak-ro, Yuseong-gu
City Daejeon
ZIP/Postal code 34141
Country South Korea
 
Platform ID GPL28038
Series (1)
GSE234239 Phase Separation of ARID1A Chromatin Remodeling Factor Promotes Oncogenic Potential of Ewing’s Sarcoma
Relations
BioSample SAMN35640533
SRA SRX20601744

Supplementary file Size Download File type/resource
GSM7457924_A673.KO.RNA.genes.results.txt.gz 1.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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