|
| Status |
Public on Jul 08, 2022 |
| Title |
H3K4me3_1-cell embryo_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Sus scrofa |
| Characteristics |
developmental stage: 1-cell embryo
antibody: H3K4me3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiment were performed with ULI-NChIP protocol
Libraries were prepared with KAPA Hyper Prep Kit for the Illumina platform (kk8504), following the manufacturer's instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
1-cell embryo H3K4me3
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to pig genome susScr11 using bowtie2 v2.4.1 with default parameters. Reads mapped to organelle and mapping quality below 30, as well as PCR duplicates were removed.
Peaks were called with MACS2 with following options: "--nolambda -f BAMPE --broad -f 2e9 --keep-dup all". Signal intersity of Histone modification were calculated as FPKM. To compared FPKM across stages, FPKM was further z-score transformed.
Genome_build: susScr11
Supplementary_files_format_and_content: bigWig files contain z-score transformed FPKM values and broadPeak file are called peaks
|
| |
|
| Submission date |
Dec 22, 2020 |
| Last update date |
Jul 08, 2022 |
| Contact name |
Wei Zhu |
| E-mail(s) |
zhuwei@mail.hzau.edu.cn
|
| Organization name |
Huazhong Agricultural University
|
| Lab |
Yi-Liang Miao Lab
|
| Street address |
No.1,Shizishan Street , Hongshan District
|
| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL22918 |
| Series (1) |
| GSE163709 |
key histone modifications in porcine oocytes and early embryos |
|
| Relations |
| BioSample |
SAMN17138222 |
| SRA |
SRX9718672 |
