|
| Status |
Public on Apr 17, 2017 |
| Title |
4C-Seq for PAX3 promoter in patient-derived RMS cells |
| Sample type |
SRA |
| |
|
| Source name |
RMS cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RMS
|
| Growth protocol |
Cells were grown in DMEM supplemented with 10% v/v FCS, 60 mg/ml Benzylpenicillin and 100 mg/ml Streptomycin sulphate at 37ºC and 5% of CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was extracted from single cells preparations from different samples. DNA was digested with DpnII and ligated. Then sample was de-crosslinked, digested with Csp6I and ligated again.
Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
library strategy: 4C-seq
|
| Data processing |
Mapping: reads were mapped to the Mus musculus (mm9 assembly) or Homo sapiens (hg19 assembly) genomes using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
|
| |
|
| Submission date |
Jun 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Juan J. Tena |
| E-mail(s) |
jjtenagu@upo.es
|
| Organization name |
CABD/CSIC
|
| Street address |
Univ. Pablo Olavide, Ctra. Utrera km1
|
| City |
Sevilla |
| ZIP/Postal code |
41013 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE69439 |
Regulatory landscape fusion in rhabdomyosarcoma by interactions between the PAX3 promoter and FOXO1 regulatory elements |
|
| Relations |
| BioSample |
SAMN03754574 |
| SRA |
SRX1045298 |
