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Sample GSM1599215 Query DataSets for GSM1599215
Status Public on May 01, 2016
Title hERT 66B biological replicate 2
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 SAMN03324409
SRA SRX863232

Supplementary file Size Download File type/resource
GSM1599215_hTERT_66B.bed.gz 757.2 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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