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Sample GSM3579210 Query DataSets for GSM3579210
Status Public on Jun 12, 2019
Title pnet_14_h3k27ac
Sample type SRA
 
Source name pnet_14_h3k27ac
Organism Homo sapiens
Characteristics chip antibody: H3K27ac
pnet subtype: NA
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).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
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
 
Submission date Jan 25, 2019
Last update date Jun 14, 2019
Contact name Yotam Drier
E-mail(s) [email protected]
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 GPL16791
Series (1)
GSE116356 Developmental enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors
Relations
BioSample SAMN10818539

Supplementary file Size Download File type/resource
GSM3579210_pnet_14_h3k27ac_20234.bw 646.8 Mb (ftp)(http) BW
GSM3579210_pnet_14_h3k27ac_20234_fp-stylehistone-L0.bed.gz 527.5 Kb (ftp)(http) BED
Processed data provided as supplementary file
Raw data provided as supplementary file

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