|
| Status |
Public on Mar 15, 2021 |
| Title |
Input |
| Sample type |
SRA |
| |
|
| Source name |
RT112
|
| Organism |
Homo sapiens |
| Characteristics |
tissue origin: bladder carcinoma
cell type: Cancer cell line
cell line: RT112
Sex: female
chip antibody: none
|
| Treatment protocol |
Cells were harvested after 48h in serum-free medium.
|
| Growth protocol |
RT112 bladder cancer cells (from F. Radvanyi, Institut Curie, Paris, France) were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% heat-inactivated FBS (Fetal Bovine Serum) and 1 mM sodium pyruvate.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cross-linked with 1% formaldehyde added to the media for 15 minutes at RT. After quenching with 0.125M Glycine, fixed cells were washed twice with PBS, pelleted and lysed in lysis buffer (1%SDS, 10mM EDTA, 50mM Tris-HCl pH8.1) at 2x107 cells/ml. Sonication was performed with a Covaris system (shearing time 20 min, 20% duty cycle, intensity 6, 200 cycles per burst and 30s per cycle) in a minimum volume of 2ml.
1 to 5ng of DNA per sample were used as provided by the user. Samples were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II DNA Library Prep Kit for Illumina" from New England BioLabs (catalog # E7645). Adapter-ligated libraries were completed by limited-cycle PCR and extracted with a [single] double-sided SPRI size selection. Resulting average fragment size is 370 bp from which 120 bp correspond to adaptor sequences. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Input DNA
|
| Data processing |
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Conversion of BCL files to FASTQ format was performed with the bcl2fastq Software (Illumina).
ChIP-seq reads were aligned to the hg19 genome assembly using RubioSeq version 3.8.1 with parameters by default (https://www.sciencedirect.com/science/article/pii/S0169260716307386?via%3Dihub)
libraries were normalized to the lowest number of reads
peaks were called using RubioSeq version 3.8.1 with parameters by default (https://www.sciencedirect.com/science/article/pii/S0169260716307386?via%3Dihub)
Genome_build: hg19
Supplementary_files_format_and_content: txt files: original output from MACS software for peaks; bw: BigWig for visualization in UCSC genome browser; txt *mod* files: MACS output removing paths
|
| |
|
| Submission date |
Mar 15, 2018 |
| Last update date |
Sep 08, 2021 |
| Contact name |
Enrique Carrillo de Santa Pau |
| E-mail(s) |
enrique.carrillo@imdea.org
|
| Organization name |
Spanish National Cancer Research Centre (CNIO)
|
| Department |
Cancer Cell Biology Programme
|
| Lab |
Epithelial Carcinogenesis group
|
| Street address |
C/ Melchor Fernández Almagro, 3
|
| City |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE111913 |
Genome-wide map of cohesin positions in RT112 bladder cancer cells |
|
| Relations |
| BioSample |
SAMN08720161 |
| SRA |
SRX3800336 |
