|
| Status |
Public on May 16, 2016 |
| Title |
NT 4-cell to blastocyst 5 [RRBS] |
| Sample type |
SRA |
| |
|
| Source name |
NT 4-cell to blastocyst
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6D2F1 (C57BL/6 X DBA/2)
development stage: 4-cell
tissue: nuclear transfer embryo
|
| Treatment protocol |
We separated the blastomeres of lived 2- or 4-cell stage embryos. One blastomere was harvested for single-cell sequencing, and the rest were further cultured in an aggregation plate to record the final development fate
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Harvested cells were washed three times in 0.5% BSA-PBS solution and transferred into the lysis buffer. After lysed for 3h at 50°C, naked genomic DNA were relesed.
The released naked DNA was digested by MspI(Fermentas,ER0541),The digested DNA was then end-repaired and tailed with an extra A to the 3'blunted ends.Illumina standard premethylated indexed adaptors were ligated with the dA-tailed DNA fragments. Bisulfite conversion was then performed using the MethyCode bisulfite conversion kit (Invitrogen,MECOV-50) followed by two rounds of PCR enrichment.After PCR enrichment, DNA fragments between 200 and 500bp were size-selected by a 12% native polyacrylamide TBE gel.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using using bsmap(v 2.89) with parameter “-D C-CGG -w 100 -s 12 -v 0.1 -m 32 -x 1000 -R".
Methylation level of each CpG site was estimated using mcall(v 1.3.0) with default parameters, and output bed format files are transformed to tab-delimited text files using custom python scripts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include methylation level and coverage for each CpG site.
|
| |
|
| Submission date |
Jul 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Shaorong Gao |
| Organization name |
Tongji University
|
| Department |
School of life science and technology
|
| Lab |
Gaolab
|
| Street address |
1239 Siping Road, Yangpu District
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE70607 |
Single Cell Sequencing Identifies Key Epigenetic Regulators in Nuclear Transfer Mediated Reprogramming [RRBS] |
| GSE70608 |
Single Cell Sequencing Identifies Key Epigenetic Regulators in Nuclear Transfer Mediated Reprogramming. |
|
| Relations |
| BioSample |
SAMN03842690 |
| SRA |
SRX1084938 |
