|
| Status |
Public on May 21, 2022 |
| Title |
H2O_H3K4me3_input1 |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Mus musculus |
| Characteristics |
tissue: embryo
developmental stage: late 2-cell
age: 36h after fertilization
treatment: embryos were injected with H2O at zygote stage
chip antibody: None
|
| 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 corresponding antibodies.
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 |
| |
|
| Description |
H2O_H3K4me3_input.bw
|
| 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 mm10 by Bowtie2.
Reads with low map quality were removed by Samtools, and PCR duplicates were removed by Picard.
The peaks were called by MACS2 with the parameters -p 1e-5 --nomodel --broad.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.bw: Bigwig files are generated using bamCoverage mode of DeepTools, and the reads counts were normalized to RPKM.
Supplementary_files_format_and_content: *.bed: The peak files are generated by MACS2, and peaks with fold enrichment less than 2 were removed.
|
| |
|
| Submission date |
Aug 22, 2021 |
| Last update date |
May 21, 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 |
GPL24247 |
| Series (2) |
| GSE182554 |
HDAC1/2 is indispensable for mouse and bovine ZGA via regulating distribution of H3K27ac and H3K4me3 [ChIP-seq] |
| GSE182555 |
HDAC1/2 is indispensable for mouse and bovine ZGA via regulating distribution of H3K27ac and H3K4me3 |
|
| Relations |
| BioSample |
SAMN20926182 |
| SRA |
SRX11859120 |
