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Sample GSM1652457 Query DataSets for GSM1652457
Status Public on Dec 08, 2015
Title M2_input ATAC Seq
Sample type SRA
 
Source name GBM primary culture G514NS
Organism Homo sapiens
Characteristics tumor: glioblastoma
transfection construct: epigenetic regulator
technique: ATAC
developmental stage: adult
Treatment protocol One million cells were transfected with plasmids for the expression of either EGFP or the N-terminal isoform of the ER. Plasmid backbone was pcDNA-DEST40. Three independent transfections were performed per construct.
Growth protocol Cells derived from an adult GBM patient and mantained in neural stem-like conditions according to a paper by Pollard et al (2009) Cell Stem Cell.
Extracted molecule genomic DNA
Extraction protocol ATAC was performed on 50,000 cells with Nextera® DNA Sample Preparation Kit (FC-121-1030, Illumina). In parallel, 50,000 cells from each biological replicate were used to extract total DNA that was later sequenced as input.
Library construction was performed as per manual of the Nextera® DNA Sample Preparation Kit (FC-121-1030, Illumina).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description accessible chromatin
Data processing Library strategy: ATAC-Seq
Alignment - BWA 0.7.2
Strip mitochondrial reads/Sort (samtools 0.1.18)
Deduplicate Reads (Picard 1.9.1 MarkDuplicates)
Call Peaks (MACS2.0.10 default settings plus -q 0.05)
Genome_build: HG19
Supplementary_files_format_and_content: Encode Format NarrowPeak files for each Sample. The narrowPeak files were generated with input samples using MACS2 with settings described above; column 7 is the fold change over local background.
 
Submission date Apr 07, 2015
Last update date May 15, 2019
Contact name Alexander James Murison
E-mail(s) alexander.murison@uhnresearch.ca
Organization name University Health Network
Lab Dick Lab
Street address 101 College Street, TMDT room 11-706
City Toronto
State/province Ontario
ZIP/Postal code M5G 1L7
Country Canada
 
Platform ID GPL16791
Series (1)
GSE67633 Epigenetic determinants of self-renewal in glioblastoma [ATAC-seq]
Relations
BioSample SAMN03465345
SRA SRX982590

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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