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| Status |
Public on Feb 01, 2016 |
| Title |
X5M1_H3K27ac |
| Sample type |
SRA |
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| Source name |
ACC Primagraft
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| Organism |
Homo sapiens |
| Characteristics |
tissue type: adenoid cystic carcinoma (ACC)
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| Growth protocol |
The HPV-transformed ACC cell line ACC112 was cultured in RPMI supplemented with 10% fetal bovine serum, Epidermal Growth Factor, Hydrocortisone and Insulin (all from R&D).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Frozen tissue was chopped up using a scalpel before fixation and then further dissociated after fixation by shearing with an 18G needle. Chromatin from formaldehyde-fixed cells (1–5 × 106 cells per histone mark, 107 cells for MYB binding) was fragmented to a size range of 200–700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with antibody against H3K4me3 (2.5 μl; Millipore, 07-473CA), H3K27ac (2.5 μl; Abcam, ab4729), MYB (10 μl; Bethyl, A304-136A) and TP63 (5 μl; ActiveMotif, #39739). Each of these antibodies was validated by protein blot or dot blot as described45. Antibody-chromatin complexes were pulled down with protein G magnetic beads (Dynabead, 10003D), washed and then eluted. After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was treated with RNase and purified with Agencourt AMPure XP (Beckman Coulter A63880).
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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
antibody: H3K27ac (Abcam, ab4729)
Raw files have been deposited at the European Genome-phenome Archive (EGA), which is hosted by the EBI, under accession number EGAS00001001457
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| Data processing |
Reads were aligned to hg19 using BWA.
The resulting alignment files were then filtered to remove PCR duplicates and reads mapping to >2 sites genome-wide
ChIP-Seq density tracks were generated with ‘igvtools count’ and visualized with IGV.
Peaks were called with HOMER 4.6 (Hypergeometric Optimization of Motif EnRichment). Peaks in Duke excluded regions list (wgEncodeDukeMapabilityRegionsExcludable table from UCSC genome browser) were removed.
Genome_build: hg19
Supplementary_files_format_and_content: TDF density files were generate by igvtools
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| Submission date |
Jan 03, 2016 |
| Last update date |
Feb 01, 2016 |
| Contact name |
Yotam Drier |
| E-mail(s) |
yotam.drier@mail.huji.ac.il
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| Organization name |
The Hebrew University of Jerusalem
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| Department |
Immunology and Cancer Research
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| Lab |
Drier
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| Street address |
Faculty of Medicine, The Hebrew University, Ein Kerem
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| City |
Jerusalem |
| State/province |
Israel |
| ZIP/Postal code |
9112102 |
| Country |
Israel |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE76465 |
An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma |
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| Relations |
| BioSample |
SAMN04382005 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2026103_acc_xenograft_h3k27ac_5539.tdf |
99.9 Mb |
(ftp)(http) |
TDF |
| GSM2026103_acc_xenograft_h3k27ac_5539_fp-stylehistone-size1000-minDist2500-L0.bed.gz |
527.9 Kb |
(ftp)(http) |
BED |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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