|
| Status |
Public on Sep 15, 2016 |
| Title |
PN3_2cell_early_amanitin_RNA_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Preimplantation embryo
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N x PWK
tissue/cell type: Preimplantation embryo
|
| Treatment protocol |
To inhibit transcription, zygotes at PN2-3 stage were cultured to early 2-cell stage in CZB supplemented with alpha-Amanitin.
|
| 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: early_2cell_alpha_amanitin_FPKM.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 |
Jan 18, 2016 |
| 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) |
| GSE76687 |
Resetting epigenetic memory by reprogramming of histone modifications in mammals |
|
| Relations |
| BioSample |
SAMN04419976 |
| SRA |
SRX1533845 |
