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Sample GSM3897559 Query DataSets for GSM3897559
Status Public on Apr 29, 2021
Title A673_siEWS-FLI1 rep1
Sample type SRA
 
Source name Ewing sarcoma cell line (A673)
Organism Homo sapiens
Characteristics genotype: siEF1
cell line: Ewing sarcoma cell line (A673)
Growth protocol A673 and TC71 were cultured respectively in DMEM or RPMI supplemented with 10% fetal bovine serum. Two days before RNA extraction, cells were seeded in 6 well plate dishes at a concentration allowing to reach a cellular confluence of approximately 90% at the time of RNA extraction.
Extracted molecule polyA RNA
Extraction protocol RNA was extracted using RNeasy plus mini kit (Qiagen, ref 74134)
The library construction was performed using TruSeq Stranded mRNA (Illumina, ref #20020594) according to manufacturer recommendations.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Reads were trimmed with Atropos
Mapping and gene quantification were performed with STAR version 2.5.3 againt human genome (hg19, gencode V19). Option "--quantMode GeneCounts" was used to get abundance measurements.
DESEQ2 1.20.0 was used to perform differential gene expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited files with raw counts for each genes.
 
Submission date Jun 19, 2019
Last update date Apr 29, 2021
Contact name Olivier Delattre
Organization name Institut Curie
Department U830
Lab Olivier Delattre
Street address 26 rue d'ulm
City Paris
ZIP/Postal code 75005
Country France
 
Platform ID GPL16791
Series (2)
GSE132966 RNA-seq data in A673 & TC71 Ewing cell lines (STAG1 and STAG2 knock-out and proficient models and silenced for EWS-FLI1)
GSE133228 STAG2 promotes CTCF-anchored loop extrusion and cis-promoter and -enhancer interactions
Relations
BioSample SAMN12092322
SRA SRX6093114

Supplementary file Size Download File type/resource
GSM3897559_B115T34_ReadsPerGene.out.tab.gz 339.6 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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