|
| Status |
Public on Dec 23, 2015 |
| Title |
GBM6w CTCF |
| Sample type |
SRA |
| |
|
| Source name |
BT6w CTCF
|
| Organism |
Homo sapiens |
| Characteristics |
material type: GBM Surgical Resection
chip antibody: CTCF (D31H2), Cell Signaling #3418
idh1 status: Wild Type
|
| 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 |
Cultured cells or minced tissue was fixed in 1% formaldehyde and snap frozen in liquid nitrogen and stored at -80ºC for at least overnight. Sonication of tumor specimens and gliomaspheres was calibrated such that DNA was sheared to between 400bp and 2000bp. CTCF was immunoprecipitated with a monoclonal rabbit CTCF antibody, clone D31H2 (Cell Signaling 3418). H3K27ac was immunoprecipitated with an antibody from Active Motif (cat 39133).
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 density tracks were generated with ‘igvtools count’.
Genome_build: hg19
Supplementary_files_format_and_content: TDF density files were generate by igvtools
|
| |
|
| Submission date |
Oct 14, 2015 |
| Last update date |
Dec 24, 2015 |
| Contact name |
Yotam Drier |
| E-mail(s) |
yotam.drier@mail.huji.ac.il
|
| Organization name |
The Hebrew University of Jerusalem
|
| Department |
Immunology and Cancer Research
|
| Lab |
Drier
|
| Street address |
Faculty of Medicine, The Hebrew University, Ein Kerem
|
| City |
Jerusalem |
| State/province |
Israel |
| ZIP/Postal code |
9112102 |
| Country |
Israel |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE70991 |
Insulator dysfunction and oncogene activation in IDH mutant gliomas |
|
| Relations |
| BioSample |
SAMN04166641 |
