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Sample GSM5833803 Query DataSets for GSM5833803
Status Public on Jul 10, 2023
Title cumulus cell-CC_H3K9me3_rep2
Sample type SRA
 
Source name cumulus cell-CC
Organism Mus musculus
Characteristics development stage: CC
chip antibody: H3K9me3 (Active Motif, 39161)
cell type: cumulus cell
Treatment protocol 1 μg antibody was incubated with protein A-beads per sample at 4℃ for 2 hours.
Growth protocol BDF1 mice were used as oocyte donors, and the cumulus cells were used as nuclear donors. The reconstructed oocytes were then cultured in CZB medium for 1h before activation treatment. The cloned constructs were activated by 6 h incubation in 1 mM SrCl2 in Ca2+-free CZB and 5 μg/mL cytochalasin B. Reconstructed embryos were thoroughly washed and cultured in G-1 PLUS medium at 37℃ under 5% CO2. MII oocytes were retrieved from the dissected oviducts of super-ovulated B6D2F1 female mice at 13 h post hCG injection for subsequent SCNT procedure. To get fertilized embryos, the super-ovulated C57BL/6 female mice were mated with C57BL/6 male mice. Then, the zygotes were collected from the oviducts of the female mice at 20 h after hCG injection and were cultured in G-1 PLUS medium until PN5.
Extracted molecule genomic DNA
Extraction protocol All samples were washed three times in 0.5% bovine serum albumin in phosphate-buffered saline (BSA-PBS). Chromatin was fragmented by MNase and was incubated with antibody bound beads at 4℃ for 2 hours. Captured DNA was wahed and isolated by isopropanol.
Libraried were generated using the KAPA HyperPrep Kit for the Illumina platform (kk8504), following the manufacturer's instrunctions. Paired-end 150 bp sequencing was performed in NovaSeq (Illumina) platform in Berry Genomics and Novogen.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Description CC_peaks.broadPeak
CC_K9me3.bw
Data processing Low-quality and the adaptor sequences were trimmed from the reads using cutadapt (v1.16) with parameters: --trim-n -q 25,25 -m 75 -a AGATCGGAAGAGC -A AGATCGGAAGAGC.
Then, All ULI-NChIP-seq and input data reads were aligned to the mm10 reference genome used BWA with mem command.
Signal tracks for each sample were generated using the deepTools bamCoverage function with normalized to RPKM (Reads Per Kilobase Million) and removed PCR duplicates.
The alignment files were first merged using SAMtools, then removed PCR duplicates and down-sample to same number of reads (60 million) using Picard tools
The H3K9me3 peaks were called by MACS2 with “--broad” parameters and over input data.
Genome_build: mm10
Supplementary_files_format_and_content: *.bw are bigWig files generated using deepTools. *.broadPeak are peak files generated by MACS2.
 
Submission date Jan 25, 2022
Last update date Jul 10, 2023
Contact name Qianshu Zhu
E-mail(s) zhuqianshu@tongji.edu.cn
Organization name Tongji University
Department School of Life Science and Technology
Street address Siping Road
City Shanghai
State/province Shanghai
ZIP/Postal code 270000
Country China
 
Platform ID GPL24247
Series (2)
GSE194341 Unreprogrammed H3K9me3 prevents minor zygotic genome activation and lineage commitment in SCNT embryos
GSE195762 Unreprogrammed H3K9me3 prevents minor zygotic genome activation and lineage commitment in SCNT embryos
Relations
BioSample SAMN25243660
SRA SRX13898565

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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