|
| Status |
Public on Dec 07, 2017 |
| Title |
RNA-seq IVC+1d rep2 |
| Sample type |
SRA |
| |
|
| Source name |
In vitro culture embryo
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N x DBA/2N
developmental stage: Embryo
tissue: whole embryo
|
| Treatment protocol |
C57BL/6N female mice were 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. Embryos were flushed out from uterus at E4.5 and cultured 1, 2 or 4 days in CMRL 1066 supplemented with 1mM glutamine, 1mM sodium pyruvate and 20% fetal bovine serum.
|
| Extracted molecule |
genomic DNA |
| 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.
RNA-Seq libraries were prepared using Smart-Seq2 protocol with slight modification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
genomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
FPKM_IVC_D1-2.txt
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
Supplementary_files_format_and_content: A tab-delimited text file includes RPKM values for each sample, available on the series record.
|
| |
|
| Submission date |
Dec 07, 2017 |
| 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 |
GPL17021 |
| Series (1) |
| GSE76505 |
Dynamic epigenomic landscapes during early lineage specification in mouse embryos |
|
| Relations |
| BioSample |
SAMN08145906 |
| SRA |
SRX3455647 |
