|
| Status |
Public on Dec 08, 2015 |
| Title |
M3 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 |
SRX982591 |
