|
Status |
Public on Mar 31, 2022 |
Title |
MII_H3K4me3_IP2 |
Sample type |
SRA |
|
|
Source name |
embryo
|
Organism |
Bos taurus |
Characteristics |
developmental stage: oocyte age: MII 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.
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|
|
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 |
SAMN23282593 |
SRA |
SRX13166071 |