|
| Status |
Public on Sep 30, 2016 |
| Title |
shH1.0-1 NT 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: No treatment
genotype/variation: wildtype
|
| 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 |
SAMN04123330 |
| SRA |
SRX1297008 |
