|
|
GEO help: Mouse over screen elements for information. |
|
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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|