|
| Status |
Public on May 01, 2019 |
| Title |
RNA_ST_8C_Setd2_KO_RNA_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Mus musculus |
| Characteristics |
tissue: embryo
developmental stage: 8C
genotype: Setd2-/-
|
| Treatment protocol |
8-week-old control and Setd2mNull female mice were superovulated by PMSG (5 IU) and hCG (5 IU) injection at 48 hours apart. Denuded oocytes were washed in M2 and incubated in normal M16 medium. Transferring of spindle-chromosome complex of Setd2mNull (or control) donor oocyte and enucleation of control (or Setd2mNull) recipient oocyte were done with a piezo-driven actuator. Then donor spindle-chromosome complex was gently aspirated to a pipette, exposed to the HVJ-E (CosmoBio), and transferred to an enucleated recipient oocyte. About 15 minutes later, reconstructed oocytes were fertilized by intracytoplasmic sperm injection (ICSI). Then reconstructed zygotes were incubated in M16 medium to 8-cell stage.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA extraction follows smart-seq2 protocol
The RNA-seq libraries were generated following the Smart-seq2 protocol with minor modification (Picelli et al., 2014).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
processed data file:
ST_8C_Setd2_KO_RNA_FPKM.txt.gz
|
| Data processing |
RNA-seq datasets were mapped to the mouse mm9 reference genome by Tophat 2.0.11. Gene expression was then calculated according to refFlat database by cufflinks 2.0.2.
Genome_build: mm9
Supplementary_files_format_and_content: The RNA FPKM txt file contains FPKM value for each sample.
|
| |
|
| Submission date |
Nov 27, 2018 |
| Last update date |
May 01, 2019 |
| Contact name |
Wei Xie |
| E-mail(s) |
xiewei121@tsinghua.edu.cn
|
| Organization name |
Tsinghua University
|
| Department |
School of Life Science
|
| Street address |
Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE112832 |
SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development [RNA-seq] |
| GSE112835 |
SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development |
|
| Relations |
| BioSample |
SAMN10490847 |
| SRA |
SRX5070519 |
