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Sample GSM1898781 Query DataSets for GSM1898781
Status Public on Sep 30, 2016
Title shH1.0-1 DOX biological replicate 1 [FAIRE-Seq]
Sample type SRA
 
Source name in vitro transformed human skin fibroblasts
Organism Homo sapiens
Characteristics cell line: SSEA1+ CSCs
treatment: Plus doxycycline
genotype/variation: doxycycline induced histone linker H1.0 knockdown
Treatment protocol SSEA1+ cells were isolated by cell sorting from a population of in vitro-transformed fibrobalsts derived from hTERT-immortalized skin fribroblasts. Cells were infected with lentiviral constructs expressing shRNAs targeting H1F0 under a doxycycline-inducible promoter
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.
Paired end libraries were constructed using standard Illumina protocols, with some modifications. Agencourt AMPure XP (Beckman Coulter) at 0.8x ratio were used to size select out adapter dimers. The Illumina Phusion enzyme was replaced by Kapa HiFi HotStart ready mix (Kapa Biosystems). An Invitrogen SizeSelect R-gel system (Life Technologies) was used to size select following PCR amplification. Sequenced was performed on an Illumina HiSeq 2500 at The Crick Institute, London.
 
Library strategy FAIRE-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description FAIRE-seq
Data processing Alignments were performed using BWA in paired-end mode, allowing three mismatches across a seed length of the full 101bp sequence
Reads were filtered for proper-pairing and non-PCR duplication using Samtools, and non-overlap of ENCODE blacklisted regions using Bamutils
Nucleosome depleted regions were identified using MACS (v2.0.10) without input sample
Genome_build: hg19
Supplementary_files_format_and_content: MACS output peak files
 
Submission date Sep 30, 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 GPL16791
Series (2)
GSE65520 Dynamic regulation of the histone variant H1.0 contributes to intratumor epigenetic and functional heterogeneity
GSE73600 The linker histone H1.0 generates epigenetic and functional intratumor heterogeneity [FAIRE-Seq]
Relations
BioSample SAMN04123331
SRA SRX1297009

Supplementary file Size Download File type/resource
GSM1898781_macs2.0.10_peaks_52_R1_noinput_pval0.99_broad_DOX_peaks.broadPeak.gz 19.3 Mb (ftp)(http) BROADPEAK
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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