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Sample GSM3494260 Query DataSets for GSM3494260
Status Public on May 01, 2019
Title ChIP_ST_8C_Setd2_KO_H3K4me3
Sample type SRA
 
Source name embryo
Organism Mus musculus
Characteristics tissue: embryo
developmental stage: 8C
chip-antibody: H3K4me3(home made)
genotype: Setd2-/-
Treatment protocol 8-week-old control and Setd2mNull female mice were superovulated by PMSG (5 IU) and hCG (5 IU) injection at 48 hours apart. Denuded oocytes were washed in M2 and incubated in normal M16 medium. Transferring of spindle-chromosome complex of Setd2mNull (or control) donor oocyte and enucleation of control (or Setd2mNull) recipient oocyte were done with a piezo-driven actuator. Then donor spindle-chromosome complex was gently aspirated to a pipette, exposed to the HVJ-E (CosmoBio), and transferred to an enucleated recipient oocyte. About 15 minutes later, reconstructed oocytes were fertilized by intracytoplasmic sperm injection (ICSI). Then reconstructed zygotes were incubated in M16 medium to 8-cell stage.
Extracted molecule genomic DNA
Extraction protocol The DNA extraction follows STAR ChIP-seq protocol
The STAR ChIP-seq libraries were generated following the protocol as described previously(Zhang et al., 2016).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
 
Description processed data file:
ST_8C_Setd2_KO_H3K4me3.bed.gz
Data processing STAR ChIP-seq datasets were mapped to the mouse mm9 reference genome using Bowtie2 (version 2.2.2) with the parameter:–t –q –N 1 –L 25. Multiple mapped reads and PCR duplicates were removed. After validating the reproducibility, replicates were pooled for downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files for STAR ChIP-seq contains the RPKM value in 100bp bin across the mm9 genome.
 
Submission date Nov 28, 2018
Last update date May 01, 2019
Contact name Wei Xie
E-mail(s) xiewei121@tsinghua.edu.cn
Organization name Tsinghua University
Department School of Life Science
Street address Haidian District
City Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL21273
Series (2)
GSE112834 SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development [ChIP-seq]
GSE112835 SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development
Relations
BioSample SAMN10492286
SRA SRX5073843

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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