|
| Status |
Public on Apr 29, 2021 |
| Title |
TC71_SA2m#1_CTCF |
| Sample type |
SRA |
| |
|
| Source name |
Ewing sarcoma cell line (TC71)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: TC71
cell type: Ewing sarcoma cell line
genotype: SA2 KO
antibody: CTCF (provided in iDeal ChIP-seq kit Diagenode)
|
| Growth protocol |
A673 and TC71 were cultured respectively in DMEM or RPMI supplemented with 10% fetal bovine serum. Two days before performing the ChIP experiments, cells were seeded in T150 flask at a concentration allowing to reach a cellular confluence of approximately 90% at the time of fixation of the cells with formaldehyde.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChiP were performed following manufacturer instructions using iDeal ChIP-seq kit for transcription factors and for histones (Diagenode). For this, Ewing cell lines were fixed for 10 minutes with 1% of methanol-free formaldehyde (28908, Thermo-Scientific). Chromatin was sonicated (Bioruptor, Diagenode) for 20 cycles (30-sec on, 30-sec off) set at position “high” to generate DNA fragments with an average size around 150-300pb.
The library were constructed using TruSeq ChIP library preparation kit (Illumina) according to manufacturer recommendations
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were mapped with bowtie2 against human genome (hg19)
Peaks were called with MACS2 2.1.1 with the option narrow for FLI1, CTCF and cohesin members ChIP-seq and broad for histone marks. For each cell line, ChIP-seq were normalized according to their respective input DNA sample.
Genome_build: hg19
Supplementary_files_format_and_content: peaks
|
| |
|
| Submission date |
Jun 21, 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) |
| GSE133154 |
ChIP-seq data in A673 & TC71 Ewing cell lines (STAG1 and STAG2 knock-out) |
| GSE133228 |
STAG2 promotes CTCF-anchored loop extrusion and cis-promoter and -enhancer interactions |
|
| Relations |
| BioSample |
SAMN12107994 |
| SRA |
SRX6175625 |
