|
| Status |
Public on Jun 15, 2016 |
| Title |
ATAC-Seq early 2-cell alpha amanitin treatment rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Preimplantation embryo
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N x DBA/2N
developmental stage: early 2-cell
|
| Treatment protocol |
Embryos were collected from C57BL/6N mice induced to superovulation by injections of 5 IU of pregnant mare's serum gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours apart and mated to DBA/2N males.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer.
ATAC-Seq libraries were prepared using ATAC-seq developed by Buenrostro et al. with slightly modification
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Processed data file: GSE66581_atac_2cell_early_trx_inhibitor.bedGraph
Processed data file: GSM2108702_2cell_early_trx_inhibitor_re2.bedGraph
|
| Data processing |
Library strategy: ATAC-Seq
Basecalls performed using CASAVA version 1.8
ATAC-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and the coverage of reads in the genome is counted
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files counted by the number of reads falling into 100bp bin in the genome. Bed files with MACS-called peaks are available in a tar archive on the series record.
|
| |
|
| Submission date |
Apr 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Xie |
| E-mail(s) |
xiewei121@tsinghua.edu.cn
|
| Organization name |
Tsinghua University
|
| Street address |
zhongguancun beidajie
|
| City |
Beijing |
| ZIP/Postal code |
100086 |
| Country |
China |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE66390 |
The landscape of accessible chromatin in mammalian pre-implantation embryos |
| GSE66581 |
The landscape of accessible chromatin in mammalian pre-implantation embryos (ATAC-Seq) |
|
| Relations |
| BioSample |
SAMN04612006 |
| SRA |
SRX1680987 |
