|
Status |
Public on Apr 29, 2021 |
Title |
A673_SA1m#1 rep2 |
Sample type |
SRA |
|
|
Source name |
Ewing sarcoma cell line (A673)
|
Organism |
Homo sapiens |
Characteristics |
genotype: SA1 KO 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 NovaSeq 6000 |
|
|
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.
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|
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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 |
GPL24676 |
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 |
SAMN12092333 |
SRA |
SRX6093104 |