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| Status |
Public on Jun 01, 2024 |
| Title |
12570_PCW17_RA_input |
| Sample type |
SRA |
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| Source name |
fetal right atrium, input ChIP
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| Organism |
Homo sapiens |
| Characteristics |
tissue: right atrium
developmental stage: PCW17
chip antibody: -
treatment: untreated
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
input chromatin
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| 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).
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| Submission date |
May 19, 2023 |
| Last update date |
Jun 01, 2024 |
| Contact name |
Marco Osterwalder |
| E-mail(s) |
olheartdev@gmail.com
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| Organization name |
Universiy of Bern
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| Department |
DBMR
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| Lab |
Osterwalder Lab
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| Street address |
Murtenstrasse 24
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| City |
Bern |
| ZIP/Postal code |
3008 |
| Country |
Switzerland |
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| 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 |
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| Relations |
| BioSample |
SAMN35178268 |
| SRA |
SRX20437304 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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