|
| Status |
Public on Dec 05, 2017 |
| Title |
STEM-seq E3.5ICM |
| Sample type |
SRA |
| |
|
| Source name |
Preimplantation embryo_E3.5 Inner cell mass
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N x DBA/2N
developmental stage: E3.5
tissue: Inner cell mass
|
| Treatment protocol |
C57BL/6N female mice were induced for superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin and 5 IU of human chorionic gonadotrophin (44-48 hours apart) and mated to DBA/2N males.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryos were washed with PBS and incubated in lysis buffer. STEM-seq libraries were constructed following the protocol described in this study (Zhang et al., Nature Genetics, 2017).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Processed data file: stage.mCG.gz in STEM-seq-methylC_mCG.tar.gz.
The format for mCG files is as below:
chr position methylated_crick, un-methylated_crick, methylated_watson, un-methylated watson.
|
| Data processing |
Base calls were performed using CASAVA version 1.8. Early embryo STEM-seq reads were aligned to the mm9 genome using BSseeker2.0.8. Replicates of same stage were pooled together and methylation values in wiggle files were computed for each single base. ES cell STEM-seq and MethylC-seq reads were aligned to the mm9 genome using BSseeker2.0.8. Replicates of same stage were pooled together and methylation values in wiggle files were computed by the number of reads falling into 1,000bp bin in the genome.
Genome_build: mm9.
Supplementary_files_format_and_content: The bedgraph files counted the number of reads falling on each base or 1,000bp bin in the genome.
|
| |
|
| Submission date |
Jan 04, 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 north street
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE76505 |
Dynamic epigenomic landscapes during early lineage specification in mouse embryos |
|
| Relations |
| BioSample |
SAMN04383643 |
| SRA |
SRX1515392 |
