|
| Status |
Public on Feb 14, 2020 |
| Title |
ASP14_d7_FLI1 |
| Sample type |
SRA |
| |
|
| Source name |
A673/TR/shEF Ewing sarcoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
chip-antibody: FLI1 rabbit polyclonal antibody (abcam, ab15289-ChIP grade)
|
| Treatment protocol |
EWSR1-FLI1 specific small hairpin RNA was induced in A673/TR/shEF cells by adding DOX at 1 ug/mL. After 7 days, DOX was removed and cells were washed three times to allow silencing of the shRNA and induction of EWSR1-FLI1
|
| Growth protocol |
A673/TR/shEF are cultured in DMEM (Gibco) 10% FBS (Eurobio), with 50 μg/mL Zeocin (Invitrogen), 2 μg/mL Blasticidin (Invitrogen) added ex-tempo.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA-protein cross-linking was performed in the presence of 1% of paraformaldehyde. Cell lysis, chromatin shearing, immunoprecipitation and DNA purification was performed with reagents from iDealChIP-seq kit for Transcription Factors
ChIP-seq - HiSeq2500 (Illumina) using 100 bp single-end sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads mapped with bowtie2 version 2.1.10 against human genome (hg19)
Peaks called with MACS2 version 2.0.10 with option narrow for FLI1 (default option) and broad for H3K27ac (input DNA was used as control)
Genome_build: hg19
Supplementary_files_format_and_content: peaks called by MACS2
|
| |
|
| Submission date |
Apr 01, 2019 |
| Last update date |
Feb 14, 2020 |
| Contact name |
Olivier Delattre |
| Organization name |
Institut Curie
|
| Street address |
26 rue d'Ulm
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE129155 |
Characterization of the specific EWSR1-FLI1 activity signature |
| GSE130025 |
Transcriptional programs define intratumoral heterogeneity of Ewing sarcoma at single cell resolution |
|
| Relations |
| BioSample |
SAMN11309503 |
| SRA |
SRX5620949 |
