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| Status |
Public on Jul 11, 2019 |
| Title |
ESC_EpiLC_exp1_cell11 |
| Sample type |
SRA |
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| Source name |
cultured mESC_EpiLC
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
fixed by: formaldehyde
cell type: cultured mESC_EpiLC
chip antibody: H3K27ac, Abcam, ab4729, Lot: GR3205526-1
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| Growth protocol |
Mouse embryonic stem cells were cultured in DMEM/F12 and neurobasal with 2i or 15% fetal bovine serum
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinked cells were treated with 0.3% SDS at 37°C and followed by gentle sonication. Transposition was set up by incubation at 37°C for 1 h, followed by addition of stopping buffer. Soluble chromatin was used for following ChIP experiments. DNA was eluted from beads, reverse crosslinked and treated with proteinase K. Finally, DNA was extracted by pheno-chloroform.
After PCR enrichment using NEBNext Q5 Ultra II master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.
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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 |
Basecalls performed using CASAVA version 1.8.2.
Sequenced reads were trimmed and filtered by cutadapt (v 1.11) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "-N 1".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Peaks were called by MACS2 (v 2.1.1), with parameter of "--broad"
Bigwig files were generated from bam files using deeptools (v 2.2.3) bamCoverage. All samples were normalized to 10 million reads with binsize as 50 bp by “--scaleFactor, --binSize 50” parameters.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bed files of non-duplicated reads.
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| Submission date |
Feb 14, 2019 |
| Last update date |
Jul 11, 2019 |
| Contact name |
Chen Li |
| E-mail(s) |
chenli_imm@pku.edu.cn
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| Organization name |
Peking University
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| Department |
Institute of Molecular Medicine
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| Lab |
Aibin He Lab
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| Street address |
Yihe Yuan Road No.5
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE109762 |
Profiling chromatin state by single-cell itChIP-seq |
| GSE126572 |
Profiling chromatin state by single-cell itChIP-seq [ESC_EpiLC] |
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| Relations |
| BioSample |
SAMN10936473 |
| SRA |
SRX5376734 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3605174_ESC_EpiLC_exp1_cell11.bed.gz |
65.7 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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