|
| Status |
Public on May 01, 2016 |
| Title |
hTERT 66A biological replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
hTERT-immortalized human skin fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: hTERT skin fibroblasts
|
| Treatment protocol |
SSEA1+ cells were isolated by cell sorting from a population of in vitro-transformed fibrobalsts derived from hTERT-immortalized skin fribroblasts.
|
| Growth protocol |
Cells were grown in minimum essential medium (MEM) containing 15% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, at 37 °C in 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
FAIRE DNA was purified by phenol-chloroform extraction follwing the protocol decribed in Simon et al. Nat Protocols, 2012.
Library construction (Illumina TruSeq 2.0 protocol) and sequencing was performed at NCI sequencing facility (SAIC-Frederick, MD) on the Illumina HiSeq 2000.
|
| |
|
| Library strategy |
FAIRE-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
FAIRE-Seq
|
| Data processing |
Alignments were performed using the CASAVA pipeline (version 1.8.2) with default parameters.
Nucleosome-depleted regions were identified by the peak calling program F-seq (Boyle, Bioinformatics., 2008).
Genome_build: hg19
Supplementary_files_format_and_content: Bed files containing coordinates of FAIRE peaks for each FAIRE-Seq samples generated in the study. Called sites were filtered to only include the top 50000 regions for each sample.
|
| |
|
| Submission date |
Feb 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Paola Scaffidi |
| E-mail(s) |
paola.scaffidi@crick.ac.uk
|
| Organization name |
Francis Crick Institute
|
| Lab |
Cancer Epigenetics Laboratory
|
| Street address |
1 Midland Road
|
| City |
London |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE65519 |
Dynamic regulation of the histone variant H1.0 contributes to intratumor epigenetic and functional heterogeneity [FAIRE-Seq] |
| GSE65520 |
Dynamic regulation of the histone variant H1.0 contributes to intratumor epigenetic and functional heterogeneity |
|
| Relations |
| BioSample |
SAMN03324424 |
| SRA |
SRX863231 |
