|
| Status |
Public on Sep 15, 2016 |
| Title |
RNA-Seq ICM rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Inner cell mass
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N x PWK
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 PWK males. Blastocysts from E3.5-4.0 were incubated in a 1:3 dilution of anti-mouse rabbit serum in DMEM for 20 min, washed in PBS and further incubated for 20 min in a 1:5 dilution of rat serum in DMEM for the complement reaction. The ICM was subsequently cleaned from lysed trophectoderm with a narrow glass pipette.
|
| 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 |
processed data file: FPKM_stage.txt.gz
|
| Data processing |
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
RNA-Seq reads were aligned to the mm9 genome assembly using Tophat version 2.0.11, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: The bed files include RPKM values in 100bp bins for each ChIP-seq sample. Bed files labeled maternal or paternal contain RPKM values for two parental alleles, allelic reads were normalized to total reads number. Tab-delimited text files include FPKM values RNA-seq sample.
|
| |
|
| Submission date |
Aug 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Bingjie Zhang |
| Organization name |
Tsinghua University
|
| Street address |
30 Shuangqing Rd
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100190 |
| Country |
China |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE71434 |
Allelic reprogramming of the histone modification H3K4me3 in early mammalian development |
|
| Relations |
| Reanalyzed by |
GSE123012 |
| SRA |
SRX1134844 |
| BioSample |
SAMN03979676 |
