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Sample GSM5694562 Query DataSets for GSM5694562
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.
 
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

Supplementary data files not provided
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available on Series record

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