|
| Status |
Public on Jun 15, 2016 |
| Title |
RNA-Seq blastocyst KD control rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Preimplantation embryo
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N x DBA/2N
developmental stage: Blastocyst
|
| Growth protocol |
Knockdown siRNA injected embryos were cultured in CZB medium containing glutamine at 37℃ under 5% CO2 in air.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer.
RNA-Seq libraries were prepared using Smart-Seq2 protocol with slightly modification
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
FPKM_blastocyst.txt.gz
|
| Data processing |
Basecalls performed using CASAVA version 1.8
RNA-Seq reads were aligned to the mm9 genome assembly using STAR version 2.4.0, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: The wig files counted by the number of reads falling into 100bp bin in the genome. Tab-delimited text files include RPKM values for each sample
|
| |
|
| Submission date |
Mar 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Xie |
| E-mail(s) |
xiewei121@tsinghua.edu.cn
|
| Organization name |
Tsinghua University
|
| Street address |
zhongguancun beidajie
|
| City |
Beijing |
| ZIP/Postal code |
100086 |
| Country |
China |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE66390 |
The landscape of accessible chromatin in mammalian pre-implantation embryos |
| GSE66582 |
The landscape of accessible chromatin in mammalian pre-implantation embryos (RNA-Seq) |
|
| Relations |
| BioSample |
SAMN03389628 |
| SRA |
SRX902564 |
