|
| Status |
Public on Apr 02, 2022 |
| Title |
2-cell-siRfx1-3 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryo
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mouse embryo
development stage: Late 2-cell stage (36 hr post fertilization)
overexpression: siRfx1
strain: B6D2F1 (C57BL/6xDBA/2)
|
| Treatment protocol |
Embryos were treated with 0.5% protease E to remove zona pellucida and the released blastomeres were washed thoroughly in PBS with 0.5% BSA.
|
| Growth protocol |
After siRNA injection, GV-stage oocytes were incubated in αMEM medium with 5% FBS and 1.5 IU/ml hCG for in vitro maturation. Then the matured MII oocytes were incubated with sperm for in vitro fertilization. The fertilized embryos were cultured in Q2 medium until harvested.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Harvested blastomeres were placed into lysis buffer, and Superscript II-triggered reverse transcription followed by cDNA amplification were performed. The amplified cDNA was then fragmented using a Covaris sonicator.
The fragmented DNA were subjected to library construction using KAPA Hyper Prep Kit for the Illumina platform, following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
genomic |
| Library selection |
cDNA |
| 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 STAR (v2.5.2b) with default parameters.
Gene expression for each sample was quantified to TPM using stringtie v1.3.4.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each transcript.
|
| |
|
| Submission date |
Nov 22, 2019 |
| Last update date |
Apr 04, 2022 |
| 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) |
| GSE140876 |
Nucleosome organization dynamics during fertilization reveals regulation factors of zygotic gene activation in mouse (RNA-seq) |
| GSE140877 |
Nucleosome organization dynamics during fertilization reveals regulation factors of zygotic gene activation in mouse |
|
| Relations |
| BioSample |
SAMN13353801 |
| SRA |
SRX7202760 |
