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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 25, 2020 |
| Title |
ESC Ctr9-EGFP ChIP-Seq |
| Sample type |
SRA |
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| Source name |
Embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: ES-E14
chip antibody: Anti-GFP antibody, MPI-CBG
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| Growth protocol |
mESCs E14TG2a (E14) and NIH3T3 cells were cultured in Glasgow Minimum Essential Medium (GMEM, Sigma-Aldrich, G5154), supplemented with 10% FBS (Pan-biotech, 2602-P290705), 1,000 U/ml LIF (ESGRO, ESG1106), 100 mM nonessential amino acids (Invitrogen, 11140-050), 2 mM L-glutamine (Invitrogen, 25030-081), and 50 µM 2-mercaptoethanol (Invitrogen, 31350-010).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation was done as described previously (Ding et al., 2015) using 20 μl of the antibody. DNA was fragmented to 200-500bp with a Covaris water-bath sonicator before the IP. DNA was purified and eluted using a PCR purification kit (Qiagen) in 30 μl HPLC-grade water.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Alignment of filtered reads to the mouse genome (mm10 assembly) was performed with bowtie2 (ver. 2.3.5.1), using the default parameters.
Aligned reads were filtered to remove sequences mapped to problematic regions, using the ENCODE blacklist downloaded from https://github.com/Boyle-Lab/Blacklist/raw/master/lists/mm10-blacklist.v2.bed.gz
Peak calling was performed using macs2 (ver. 2.2.6), using a q-value cutoff 0.01 and a fixed fragment extension mode (200 bp). Sample "ESC Input ChIP-Seq (A)" was used as a control.
Genome_build: mm10
Supplementary_files_format_and_content: Abundance files report transcript expression levels, as reported by kallisto. Putative binding sites or chromatine modification regions are provided in a narrowPeak format, as repored by macs2.
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| Submission date |
May 06, 2020 |
| Last update date |
Dec 26, 2020 |
| Contact name |
Maciej Paszkowski-Rogacz |
| Organization name |
Technische Universität Dresden
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| Department |
UCC / Medical Faculty and University Hospital Carl Gustav Carus
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| Lab |
Medical Systems Biology (Prof. Buchholz)
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| Street address |
Tatzberg 47/49
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| City |
Dresden |
| ZIP/Postal code |
01307 |
| Country |
Germany |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE149999 |
The Paf1 complex positively regulates enhancer activity in mouse embryonic stem cells |
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| Relations |
| BioSample |
SAMN14844563 |
| SRA |
SRX8273532 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4519334_ESE14_ChIPSeq_Ctr9_Peaks.narrowPeak.gz |
902.2 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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