|
| Status |
Public on Jun 23, 2020 |
| Title |
RNA_SCNT_8C_MEF_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: SCNT 8-cell_MEF
tissue: embryo
|
| Treatment protocol |
SCNT 8-cell embryos are collected 56 hours after the donor nucleus get injected into the enucleated MII oocytes. The reconstructed oocytes were incubated in CZB medium. The first polar body was removed by enucleation pipette on the micromanipulator, while the zona pellucida was gently removed by treatment with acid Tyrode’s solution (Sigma, Cat # T-1788) for several minutes.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The RNA extraction follows smart-seq2 protocol
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously with minor modification (Picelli et al., 2014). Cells were lysed in hypotonic lysis buffer (Amresco, M334), and the polyadenylated mRNAs were captured by the PolyT primers. After ~3–10 min lysis at 72 °C, the Smart-seq2 reverse transcription reactions were performed. After pre-amplification and AMPure XP beads purification, cDNAs were sheared by Covaris and were subject to Illumina TruSeq library preparation. All libraries were sequenced on Illumina HiSeq 2500 according to the manufacturer’s instruction.
Nextera
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
For RNA-seq samples: SMART-seq2 reads were aligned to the mm9 genome assembly using tophat2 version 2.1.1, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2.
Genome_build: mm9
Supplementary_files_format_and_content: The gene rpkm txt file contains FPKM value for all samples.
|
| |
|
| Submission date |
Oct 26, 2019 |
| Last update date |
Jun 23, 2020 |
| Contact name |
Ke Zhang |
| E-mail(s) |
zhangke16@mails.tsinghua.edu.cn
|
| Organization name |
Tsinghua university
|
| Department |
School of Life Sciences
|
| Lab |
Wei Xie
|
| Street address |
Haidian District
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE139430 |
Analysis of genome architecture during SCNT reveals a role of cohesin in impeding minor ZGA |
|
| Relations |
| BioSample |
SAMN13118472 |
| SRA |
SRX7060400 |
