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Sample GSM831870 Query DataSets for GSM831870
Status Public on Jun 04, 2013
Title MelJuSo etoposide FAIRE-seq
Sample type SRA
Source name MelJuSo cells
Organism Homo sapiens
Characteristics cell type: Human skin melanoma cell line
cell line: MelJuSo
treatment: Etoposide 60uM
time point: 4 hours post treatment
Treatment protocol Tissue culture cells were treated with indicated drugs for 4 hours then fixed and collected for processing. Mice were injected iv with a single dose of the indicated drugs and 4 hours later, tissues were fixed and collected for processing.
Growth protocol Tissue culture cells were grown in 15cm dishes around 80% confluency.
Extracted molecule genomic DNA
Extraction protocol After fixation, lysates were cleared from sonicated nuclei and histone-free DNA were isolated by phenol-chloroform extraction. Libraries were prepared according to the provider’s kits and protocols for ChIP samples.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina Genome Analyzer IIx
Description FAIRE-enriched DNA
Data processing Reads were aligned to hg19 using BWA, duplicates and reads with mapping quality less than 60 were removed.
Peaks: Peak regions were called by using F-seq package.
Submission date Nov 11, 2011
Last update date May 15, 2019
Contact name Baoxu Pang
Organization name Stanford University
Department Genetics
Lab Michael Snyder
Street address 3165 Porter Drive
City Palo Alto
State/province CALIFORNIA
ZIP/Postal code 94304
Country USA
Platform ID GPL10999
Series (2)
GSE33632 Genome-wide analysis of histone eviction by FAIRE-Seq
GSE33634 Topoisomerase II inhibitors and histone eviction
SRA SRX105593
BioSample SAMN00754058

Supplementary file Size Download File type/resource
GSM831870_MJ_FAIRE_Etop_fseqpeaks.bed.gz 687.7 Kb (ftp)(http) BED
GSM831870_MJ_FAIRE_Etop_uniq-q37.bam 669.0 Mb (ftp)(http) BAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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