GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1652450 Query DataSets for GSM1652450
Status Public on Dec 08, 2015
Title E2 ATAC Seq
Sample type SRA
Source name GBM primary culture G514NS
Organism Homo sapiens
Characteristics tumor: glioblastoma
transfection construct: EGFP
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
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]
BioSample SAMN03465345
SRA SRX982583

Supplementary file Size Download File type/resource
GSM1652450_E2_NoM_peaks.narrowPeak.gz 25.4 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap