|
| Status |
Public on May 14, 2021 |
| Title |
mESC_DNA_cell132 |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell type: cultured mouse embryonic stem cells
strain: C57BL/6
chip antibody: H3K4me3, Millipore 04-745, lot:3243412, H3K27me3,millipore 07-449, #3146226
|
| Treatment protocol |
The mESCs were dissociated by 0.1% Trypsin digestion, and aliquot of cell numbers were directly used for CoTECH
|
| Growth protocol |
mESCs were cultured at 37 °C with 5% CO2 and was maintained in high glucose DMEM
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
folloing CoTECH protocol
After PCR enrichment using Q5 polymerase, the 300-1,000 bp fragments were isolated using the 1.5% (w/v) agarose gel and purified once with 0.8 x AMpure XP beads
|
| |
|
| 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.
For ChIP part, Reads were de-multiplexed to generate single cell profiles by custom scripts.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1) (ChIP part) and Hisat2 (version 2.0.4) (RNA part).
ChIP part: Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard. RNA part: reads were counted by HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were aggregate bigwig files.
|
| |
|
| Submission date |
May 13, 2021 |
| Last update date |
May 15, 2021 |
| 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 (1) |
| GSE158435 |
Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions |
|
| Relations |
| BioSample |
SAMN19164778 |
| SRA |
SRX10882008 |
