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| Status |
Public on Jun 12, 2019 |
| Title |
pnet_31_h3k27ac |
| Sample type |
SRA |
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| Source name |
pnet_31_h3k27ac
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| Organism |
Homo sapiens |
| Characteristics |
chip antibody: H3K27ac
pnet subtype: NA
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
30-μm sections from frozen samples with >90% tumor enrichment were collected in microtubes, washed in phosphate-buffered saline (PBS), cross-linked with 1% formaldehyde for 5 min, and quenched with 0.125 M glycine for 5 min at room temperature. Cross-linked material was resuspended in 0.1% SDS (50 mM Tris-HCl pH8, 10 mM EDTA) and sonicated for 40 min in a Covaris E210 instrument (duty cycle 20%; intensity 8; cycles per burst 200).
Soluble chromatin (5 µg) was immunoprecipitated with 10 μg H3K4me2 (Millipore 07-030) or H3K27ac (Active Motif 39133) antibodies (Ab). ChIP-seq libraries were constructed by end repair (Epicentre ER0720) of precipitated DNA, base extension with Klenow fragment (New England Biolabs M0212L), and ligation (New England Biolabs M220S) of Y-form sequencing adapters (Illumina), followed by 14 cycles of PCR. Between enzymatic steps, fragments of the desired size were enriched using AMPure XP beads (Beckman Coulter).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
ChIP-seq reads were aligned to the reference genome (hg19) using BWA 0.7.10. Reads with mapping scores <10 were discarded, and those aligned to the same position and strand were only counted once. Density signals were calculated by igvtools, and converted to bigWigs with bedGraphToBigWig. Peaks were called with HOMER 4.6, using parameters -style histone -L 0. Genome_build: hg19
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| Submission date |
Jan 25, 2019 |
| Last update date |
Jun 14, 2019 |
| Contact name |
Yotam Drier |
| E-mail(s) |
[email protected]
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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) |
| GSE116356 |
Developmental enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors |
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| Relations |
| BioSample |
SAMN10818538 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3579211_pnet_31_h3k27ac_20232.bw |
585.4 Mb |
(ftp)(http) |
BW |
| GSM3579211_pnet_31_h3k27ac_20232_fp-stylehistone-L0.bed.gz |
479.1 Kb |
(ftp)(http) |
BED |
| Processed data provided as supplementary file |
| Raw data provided as supplementary file |
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