|
| Status |
Public on Jul 15, 2019 |
| Title |
H3K27ac_right_forebrain_EC_cell_80 |
| Sample type |
SRA |
| |
|
| Source name |
H3K27ac_right_forebrain_EC_cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: right forebrain
cell statement: Fixed by formaldehyde
chip antibody: H3K27ac
|
| Treatment protocol |
Organs were digested with 0.06 Collagenase II + 0.08% Trypsin and 0.09% Collagenase II + 0.12% Trypsin at 37 °C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Following CoBATCH protocol.
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.
Reads were de-multiplexed to generate single cell profiles by custom scripts. For spliting single cell, we cut the first 21 bp of the read1 and the first 27 bp of the read2.
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.
Cells with less than 3,000 non-duplicated were excluded.
Bed files were generated from bam files using bedtools (v2.25.0) bamToBed.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bed files. Each single cell bed file contain non-duplicated alignments as is in the bam file.
|
| |
|
| 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) |
| GSE129327 |
CoBATCH for high-throughput single-cell epigenomic profiling [EC_CoBATCH] |
| GSE129335 |
CoBATCH for high-throughput single-cell epigenomic profiling |
|
| Relations |
| BioSample |
SAMN11341333 |
| SRA |
SRX5639460 |
