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Sample GSM3566928 Query DataSets for GSM3566928
Status Public on Jul 08, 2019
Title Wildtype ESC IP of H3K14ac
Sample type SRA
 
Source name WT_H3K14ac
Organism Mus musculus
Characteristics strain background: 12910la
cell line: J1
genotype/variation: Wildytpe
cell type: embryonic stem cells (ESCs)
chip antibody: H3K14ac (abcam; cat.# ab52946; lot# GR149741-26)
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 10 days 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 (Solarbiol), 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-H3K27ac, anti-H3K4me1 and anti-H3K27ac 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 Cutadapt with parameters " -q 5 -m 30 -n 4 -O 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", then sequence reads were mapped to mm10 genome using Bowtie2 with parameters "-5 1 --very-sensitive -p 20 -I 0 -X 1000 --no-mixed --no-discordant --un-conc-gz".
Enrichment bigwig file was generated by bamCompare from Deeptools with parameter "--scaleFactorsMethod readCount -e --minMappingQuality 1 --samFlagExclude 256 --pseudocount -1 --operation ratio"
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file of histone enrichment
 
Submission date Jan 17, 2019
Last update date Jul 29, 2019
Contact name Weiyu Zhang
E-mail(s) ch8316f5eyu@gmail.com
Phone 18902012072
Organization name Nankai University
Street address No.38 Tongyan Road, Jinnan District
City Tainjin
ZIP/Postal code 300350
Country China
 
Platform ID GPL21273
Series (1)
GSE125238 CHIP-seq analysis about Histones and Zscan4 after Zscan4 overexpression
Relations
BioSample SAMN10762835
SRA SRX5257675

Supplementary file Size Download File type/resource
GSM3566928_WT_H3K27ac_H3K14ac_H3K14ac.bw 264.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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