|
| Status |
Public on Apr 29, 2021 |
| Title |
A673_siEWS-FLI1 rep2 |
| 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 |
SAMN12092321 |
| SRA |
SRX6093115 |
