|
| Status |
Public on Sep 15, 2016 |
| Title |
ChIP-Seq MII oocyte K4Me3 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MII oocyte
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N
developmental stage: MII oocyte
chip antibody: custom-made H3K4Me3 antibody (Abmart)
|
| Treatment protocol |
Collection of MII oocytes from superovulated C57BL/6N mice was performed 20h after hCG injection.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer.
ChIP-Seq libraries were prepared using TELP developed by PengXu et al. with slightly modification
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
processed data files: MII_oocyte_K4me3_broadpeak.bed.gz
|
| Data processing |
Basecalls performed using CASAVA version 1.8
ChIP-seq peaks were called using MACS2 with the parameters --broad --nomodel --nolambda and noisy peaks with very weak signals (summed RPKM < 30) were removed.
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 counted by the number of reads falling into 100bp bin in the genome. Tab-delimited bed files include RPKM values for each sample. The peak files included regions of all peaks called in each 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 |
| SRA |
SRX1134799 |
| BioSample |
SAMN03979631 |
