|
| Status |
Public on Jun 15, 2016 |
| Title |
RNA-Seq ICM rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Inner cell mass
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N x DBA/2N
developmental stage: Inner cell mass
|
| Treatment protocol |
Embryos were collected from C57BL/6N mice induced to superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours apart and mated to DBA/2N males. ICM cells were generally identified by immunosurgery from the blastocysts.
|
| 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_stage.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 |
| Reanalyzed by |
GSE123012 |
| BioSample |
SAMN03389624 |
| SRA |
SRX902558 |
