|
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 |