|
| Status |
Public on Sep 15, 2016 |
| Title |
ChIP-Seq 2-cell late K4Me3 rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Preimplantation embryo
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N x PWK
developmental stage: Preimplantation embryo
chip antibody: custom-made H3K4Me3 antibody (Abmart)
|
| 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. Each set of embryos at a particular stage was flushed from the reproductive tract at defined time periods after hCG administration: 20h (MII oocyte), 27-28h (PN5 zygote), 30h (early 2-cell), 43h (late 2-cell), 54-56 h (4-cell), 68-70 h (8-cell) and 92-94 h (blastocysts) in Hepes-buffered CZB medium. The zona pellucida of embryos selected by cell number or morphology was gently removed by treatment of 10 IU/ml pronase (Sigma P8811) for several minutes. The embryos were then manually picked and treated with the lysis buffer for STAR ChIP-seq or Smart-seq2.
|
| 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: 2cell_late_K4me3_broadpeak.bed.gz, 2cell_late_maternal_broadpeak.bed.gz, 2cell_late_paternal_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 |
SRX1134806 |
| BioSample |
SAMN03979638 |
