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Sample GSM7385436 Query DataSets for GSM7385436
Status Public on Jun 01, 2024
Title 12570_PCW17_RV_H3K27ac
Sample type SRA
 
Source name fetal right ventricle, H3K27ac ChIP
Organism Homo sapiens
Characteristics tissue: right ventricle
developmental stage: PCW17
chip antibody: anti-H3K27ac (Active motif, 39133)
treatment: untreated
Extracted molecule genomic DNA
Extraction protocol Chromatin immunoprecipitation were performed as previously described (PMID: 19212405) with some modifications. Briefly, frozen tissue was pulverized with a mortar and pestle, resuspeneded in PBS, and cross-linked with 1% formaldehyde at room temperature for 10 min. Chromatin was sonicated to obtain fragments with an average size ranging between 100-600 bp. Chromatin was inclubated for 2h at 4 C with 5 µg of antibody. Protein A and G Dynabeads (Invitrogen) were then added to this chromatin/antibody mixture for 30 minutes at 4 C. Immuno-complexes were sequentially washed. The protein/DNA complexes were eluted in an SDS buffer (1% SDS, 50 mM Tris pH 8.0, 10 mM EDTA) at 37 C for one hour. Samples were treated with Proteinase K at 37 C and reverse-crosslinked overnight. Finally, the DNA was purified on Zymo ChIP clean and concentrate columns (Zymo Research) and the quality was assessed on the Agilent bioanalyzer.
The ChIP-seq libraries were prepared using the Illumina TruSeq library preparation kit followed by sequencing on an Illumina HiSeq 2000.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Chromatin IP against H3K27ac
Data processing Single-end reads were obtained by quality filtering and adaptor trimming using cutadapt_v1.1 with parameter ‘-m 25 -q 20’ and were mapped to the reference genome NCBI37/hg19 using Bowtie version 2.0.2.0 (Langmead 2009) with parameter ‘-m 1 -v 2 -p 16’. Duplicates were removed with samtools and MACS (Zhang 2008) (version 1.4.2) with parameter ‘-mfold = 10,30 -nomodel -p 0.0001’ was used for peak calling.
Assembly: hg19
Supplementary files format and content: Normalized bigWig files were generated using bedtools (bedGraphToBigWig).
Supplementary files format and content: Peak files were generated using MACS (Zhang 2008).
 
Submission date May 19, 2023
Last update date Jun 01, 2024
Contact name Marco Osterwalder
E-mail(s) olheartdev@gmail.com
Organization name Universiy of Bern
Department DBMR
Lab Osterwalder Lab
Street address Murtenstrasse 24
City Bern
ZIP/Postal code 3008
Country Switzerland
 
Platform ID GPL11154
Series (2)
GSE232883 A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival [ChIP-seq]
GSE232887 A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival
Relations
BioSample SAMN35178273
SRA SRX20437299

Supplementary file Size Download File type/resource
GSM7385436_pcw17_12570_rv_h3k27ac.hg19.uu.sort.ext.rpm.bw.gz 144.9 Mb (ftp)(http) BW
GSM7385436_pcw17_12570_rv_h3k27ac_peaks.bed.gz 701.8 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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