|
| Status |
Public on Jan 25, 2017 |
| Title |
H3K4me3_GSC8_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
H3K4me3_GSC8
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Patient-derived neurosphere line GSC8
drug treatment: none
chip-antibody: H3K4me3 (Millipore, 07-473, Lot 2207275)
|
| Treatment protocol |
Cells were treated with drugs with a final DMSO concentration of either 0.1 or 0.15% DMSO.
|
| Growth protocol |
Neurosphere cultures were maintained in Neurobasal media supplemented with 20 ng/mL recombinant EGF (R and D Systems), 20ng/mL FGF2 (R and D Systems), 1X B27 supplement (Invitrogen), 0.5X N2 supplement (Invitrogen), 3mM L-glutamine, and penicillin/ streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells was fixed in 1% formaldehyde and snap frozen in liquid nitrogen and stored at -80ºC for at least overnight. Sonication of crosslinked cells was calibrated such that DNA was sheared to between 400bp and 2000bp.
ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3’ A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned to hg19 using BWA.
Resulting alignment files were filtered to remove PCR duplicates and reads mapping to >2 sites genome-wide
ChIP-Seq BigWig tracks were generated using the 'BEDTools' tool 'genomeCoverageBed' and the UCSC tool 'bedGraphToBigWig'
Genome_build: hg19
Supplementary_files_format_and_content: BigWig density files were generated by BEDTools and UCSC tools
|
| |
|
| Submission date |
Nov 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Cem Sievers |
| E-mail(s) |
csievers@mgh.harvard.edu
|
| Organization name |
MGH
|
| Department |
Molecular Pathology
|
| Lab |
Bernstein
|
| Street address |
165 Cambridge Street
|
| City |
Boston |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE74557 |
Adaptive chromatin remodeling in glioblastoma stem cell plasticity and drug tolerance |
|
| Relations |
| BioSample |
SAMN04229275 |
| SRA |
SRX2242964 |
