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Sample GSM7385437 Query DataSets for GSM7385437
Status Public on Jun 01, 2024
Title 12570_PCW17_RV_input
Sample type SRA
 
Source name fetal right ventricle, input ChIP
Organism Homo sapiens
Characteristics tissue: right ventricle
developmental stage: PCW17
chip antibody: -
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 input chromatin
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 SAMN35178272
SRA SRX20437300

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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