|
| Status |
Public on Dec 05, 2017 |
| Title |
RNA-Seq E3.5ICM rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Preimplantation embryo_E3.5 Inner cell mass
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N x DBA/2N
developmental stage: E3.5
tissue: Inner cell mass
|
| Treatment protocol |
Embryos were collected from C57BL/6N mice induced for superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin and 5 IU of human chorionic gonadotrophin (44-48 hours apart) and mated to DBA/2N males.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
After removing the zona pellucida, ICM was isolated by immunosurgery and then directly lysed in hypotonic lysis buffer. 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 |
SAMN04383621 |
| SRA |
SRX1515371 |
