|
| Status |
Public on Sep 15, 2016 |
| Title |
ChIP-Seq Paternal pronucleus of PN3 zygote K4Me3 |
| Sample type |
SRA |
| |
|
| Source name |
Preimplantation embryo
|
| Organism |
Mus musculus |
| Characteristics |
strain: DBA2
tissue: Preimplantation embryo
chip antibody: custom-made H3K4Me3 antibody (Abmart)
|
| Treatment protocol |
Zygotes at PN3-4 stage were collected from superovulated C57BL/6N female that mated to BDA/2N males. Female pronuclei were collected using a piezo-drill micromanipulator and the residuals that contain male pronuclei were then treated by pronase to remove the zona pellucida. After that, these samples were incubated in lysis buffer for ChIP-seq.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Female pronuclei were collected using a piezo-drill micromanipulator and the residuals that contain male pronuclei were then treated by pronase to remove the zona pellucida. After that, these samples were incubated in lysis buffer for ChIP-seq.
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 |
| |
|
| 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 |
Mar 29, 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) |
| GSE71434 |
Allelic reprogramming of the histone modification H3K4me3 in early mammalian development |
|
| Relations |
| BioSample |
SAMN04589804 |
| SRA |
SRX1668472 |
