 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 15, 2019 |
| Title |
H3K27ac_2K_ESC_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
H3K27ac_2K_ESC
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: native, cultured mESC (V6.5)
chip antibody: H3K27ac, Abcam, ab4729, Lot: GR3211959-1
|
| Growth protocol |
Mouse embryonic stem cells were cultured in DMEM/F12 and neurobasal with 2i or 15% fetal bovine serum
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The ESC was dissociated by 0.1% Trypsin digestion, and aliquot of cell numbers were directly used for in-situ ChIP
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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 "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
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 bigwig files. Bigwig files of replicates data show reproducbility.
|
| |
|
| Submission date |
Apr 04, 2019 |
| Last update date |
Jul 15, 2019 |
| Contact name |
Haiqing Xiong |
| E-mail(s) |
haiqingxiong@pku.edu.cn
|
| Organization name |
Peking University
|
| Street address |
5 Yiheyuan Road, Haidian District
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE129333 |
CoBATCH for high-throughput single-cell epigenomic profiling [low input in situ ChIP] |
| GSE129335 |
CoBATCH for high-throughput single-cell epigenomic profiling |
|
| Relations |
| BioSample |
SAMN11340816 |
| SRA |
SRX5637721 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3711217_H3K27ac_2K_ESC_rep2.bw |
121.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
