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Sample GSM4119874 Query DataSets for GSM4119874
Status Public on Oct 20, 2021
Title oe rep1
Sample type SRA
 
Source name MEFs_KDM6A_H3K27me3
Organism Mus musculus
Characteristics strain: B6D2F1
cell type: Mouse embryonic fibroblasts (MEFs)
genotype/variation: KDM6A overexpression
chip antibody: H3K27me3 9733 CST
Growth protocol Mouse embryonic fibroblasts (MEFs) were obtained from 13.5-dpc embryos collected from C57BL/6 females which had been mated with DBA/2 males. 293T and MEFs were cultured in Dulbecco's modified eagle medium (DMEM) containing 15%(vol/vol) fetal bovine serum (FBS), 1X MEM NEAA, 1X L-Glutamine and 1X Penicillin-Streptomycin. (FBS from BI and others from Invitrogen). For iPSC reprogramming, infected or drug treated 4F2A MEFs were cultured in KnockOut DMEM with 15% KnockOut Serum Replacement, 1X MEM NEAA, 1X L-Glutamine, 1X Penicillin-Streptomycin, 1X Sodium Pyruvate, 1000U/ml LIF, 1X 2-Mercaptoethanol and 2 μg/ml doxycycline (LIF from Millipore, doxycycline from Sigma-Aldrich and others from Invitrogen), the medium were changed every day.
Extracted molecule genomic DNA
Extraction protocol 48 hrs after infection,The DNA was extracted using H3K27me3 antibody.
10 ng DNA of each sample was converted to phosphorylated blunt-ended; An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments; Illumina's genomic adapters were ligated to the A tailed DNA fragments; PCR amplification was performed to enrich ligated fragments. The enriched product of ~200-1500 bp was size selected using AMPure XP beads.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8). Sequence quality was examined using the FastQC software. After passing Solexa CHASTITY quality filter, the clean reads were aligned to mouse reference genome UCSC MM10 using BOWTIE (V2.1.0). Aligned reads were used for peak calling of the ChIP regions using MACS V1.4.2. Statistically significant ChIP-enriched regions (peaks) were identified by comparison of IP vs Input or comparison to a Poisson background model, using a p-value threshold of 10-4. Then the peaks were annotated by the nearest gene using the newest UCSC RefSeq database.
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: wig files were generated using MACS
 
Submission date Oct 14, 2019
Last update date Oct 20, 2021
Contact name Qi Jiang
E-mail(s) jiangqi1002@126.com
Organization name Harbin Medical University
Department Department of histology and embryology
Street address baojian road 157
City harbin
State/province heilongjiang
ZIP/Postal code 150081
Country China
 
Platform ID GPL24247
Series (2)
GSE138816 Histone demethylase KDM6A promotes somatic cell reprogramming by epigenetically regulate PTEN and IL-6 signal pathway [ChIP-seq]
GSE138817 Histone demethylase KDM6A promotes somatic cell reprogramming by epigenetically regulate PTEN and IL-6 signal pathway
Relations
BioSample SAMN13025380
SRA SRX6986737

Supplementary file Size Download File type/resource
GSM4119874_OE-1.wig.gz 329.9 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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