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Sample GSM5444714 Query DataSets for GSM5444714
Status Public on Jun 30, 2023
Title Zscan4 OE ESC input of H3K9me3
Sample type SRA
Source name J1
Organism Mus musculus
Characteristics strain: 12910la
cell line: J1
cell type: Embryonic stem cell
genotype: Zscan4 overexpression
chip antibody: none
Treatment protocol The CDS region of Zscan4c was cloned into pCMV-FLAG vector.WT mESCs were transfected with 1000ng pCMV-tag2 vector.After transfection for 24h,the cells were treated with 500ug/ml G418 for 10days and the medium were changed every 24h,then we picked monoclonal cells.
Growth protocol Mouse J1 embryonic stem cells (ESCs) were cultured under 5% CO2 at 37℃ on well plate coated with 0.2% gelatin(Sigma),in medium(Hyclone) that supplement with15% FBS(Hyclone),10ng/ml mLIF (GeneScript),1% Penicillin-Streptomycin (Solarbio),1% GlutaMAX(Solarbio), 1% nonessential amino acids(Gibco), 0.1 mM β-mercaptoethanol (Sigma). .
Extracted molecule genomic DNA
Extraction protocol Cells were lysed and chromatin was extracted. Anti-H3K9me3 antibodies were used to immunoprecipiate FLAG-Zscan4 in mESCs. Proteins on chromatin associated with Zscan4 was digested and chromatin was decrosslinked at 65 degree overnight. DNA was extracted in phenol-chloroform.
For ChIP-seq, 5ng of Zscan4-assocated chromatin DNA was used in ChIP-seq library preparation. Libraries were prepared according to Illumina protocols and library fragments of ~250 bp were used for sequencing.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
Data processing Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Cutdadpt, then sequence reads were mapped to mm10 genome using Bowtie2.
Bigwig file was generated by bamCompare from Deeptools
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files, ChIP-seq normalized signal
Submission date Jul 13, 2021
Last update date Jun 30, 2023
Contact name Xuan Zhao
Phone 13780330130
Organization name Nankai University
Department State Key Laboratory of Medicinal Chemical Biology
Lab XinyiLu-Lab
Street address No. 38 Tongyan Road, Haihe Education Park, Tianjin
City Tianjin
State/province Tianjin
ZIP/Postal code 300000
Country China
Platform ID GPL21273
Series (1)
GSE180003 CHIP-seq analysis about H3K9me3 change after Zscan4 overexpression
BioSample SAMN20197336
SRA SRX11430309

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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