|
| Status |
Public on Dec 05, 2017 |
| Title |
RNA-Seq PS rep1 |
| Sample type |
SRA |
| |
|
| Source name |
postimplantation embryo_E7.5 Primitive streak
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N x DBA/2N
developmental stage: E7.5
tissue: Primitive streak
|
| Treatment protocol |
Embryos were collected from C57BL/6N female mice mated naturally to DBA/2N males. The day when vaginal plug was observed was considered to be E0.5.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNAs of E5.5 to E7.5 embryos were extracted by RNeasy Plus Micro Kit according to the manufacturer’s protocol. RNA-Seq libraries were prepared using Smart-Seq2 protocol with slight modification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Processed data file: FPKM_stage.txt.gz
Processed data file: FPKM_replicates.txt.gz
|
| Data processing |
RNA-Seq reads were aligned to the mm9 genome assembly using Tophat2 version 2.0.11. The replicates were merged together, and transcript abundance (FPKM) was calculated based on Refseq annotation using Cufflinks version 2.0.2.
Genome_build: mm9.
Bedgraph files are available in a tar archive on the series record. A tab-delimited text file includes RPKM values for each sample.
|
| |
|
| Submission date |
Jan 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Xie |
| E-mail(s) |
xiewei121@tsinghua.edu.cn
|
| Organization name |
Tsinghua University
|
| Street address |
Zhongguancun north street
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE76505 |
Dynamic epigenomic landscapes during early lineage specification in mouse embryos |
|
| Relations |
| BioSample |
SAMN04383637 |
| SRA |
SRX1515386 |
