|
| Status |
Public on Mar 31, 2022 |
| Title |
GV_H3K4me3_IP1 |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Bos taurus |
| Characteristics |
developmental stage: oocyte
age: GV
treatment: Wild type
chipseq antibody: H3K4me3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The embryos were washed 3 times in 0.5% BSA after removal of zona pellucida. After cell lysis, the chromatin was digested with micrococcal nuclease and histone-DNA complexes were isolated with H3K4me3 antibody.
Libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls performed using CASAVA
Reads were trimmed by Trimmomatic to remove the bases with low quality and adapter sequences
The trimmed reads were align to Bos_taurus_UMD_3.1.1 by Bowtie2
Reads with low map quality were removed by Samtools, and PCR duplicates were removed by Picard
Genome_build: Bos_taurus_UMD_3.1.1
Supplementary_files_format_and_content: Bigwig files are generated using bamCoverage mode of DeepTools, and the reads counts were normalized to RPKM.
|
| |
|
| Submission date |
Nov 18, 2021 |
| Last update date |
Mar 31, 2022 |
| Contact name |
Kun Zhang |
| E-mail(s) |
kzhang@zju.edu.cn
|
| Organization name |
Zhejiang University
|
| Street address |
866 Yuhangtang Rd
|
| City |
Hangzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL26012 |
| Series (2) |
| GSE189100 |
Genome-wide mapping of the histone modification H3K4me3 in bovine early embryos [ChIP-seq] |
| GSE189102 |
Genome-wide mapping and gene expression of the histone modification H3K4me3 in bovine early embryos |
|
| Relations |
| BioSample |
SAMN23282598 |
| SRA |
SRX13166066 |
