NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7792026 Query DataSets for GSM7792026
Status Public on Jan 25, 2024
Title Human_ZSCAN4_Rabbit_Ab_DUX4_plus
Sample type SRA
 
Source name Embryonic cells
Organism Homo sapiens
Characteristics tissue: Embryonic cells
cell line: ES cells (SEES3)
cell type: Pluripotent stem cells
genotype: Male
antibody: Human_Zscan4_Rabbit_Ab
treatment: DUX4_plus
replication: Technical replicate 2
Extracted molecule genomic DNA
Extraction protocol Cells were cross-linked with 2 mM disuccinimidyl glutarate in PBS/1 mM MgCl2 for 40 min at room temperature followed by 1% formaldehyde in PBS for 15 min at room temperature. The reaction was stopped by 125 mM glycine. The cells were washed with PBS and stored at –80°C prior to use. The cells were lysed in Lysis buffer (10 mM Tris-HCl, pH8.0, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroyl sarcosine) containing proteinase inhibitor cocktail (Roche). Sonication was conducted with the Handy sonicator UR-21P (Tomy) to generate DNA fragments of approximately 150-450 bp. The sonicated lysates from approximately 2 x 106 cells were diluted in ChIP dilution buffer (10 mM HEPES, pH 7.4, 50 mM NaCl, 1% IGEPAL-CA-630, 10% glycerol) containing proteinase inhibitor cocktail and incubated overnight at 4°C with 50 µl of protein G magnetic beads (Invitrogen) that were preincubated with ~2 µg of mouse Zscan4 antibodies. The precipitants were washed once with high salt wash buffer (20 mM Tris-HCl, pH8.0, 400 mM NaCl, 2 mM EDTA, 0.1% SDS, 0.2% Triton-X), three times with LiCl wash buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% NP40, 1% Na-deoxycholate) and once with 10 mM Tris-HCl, pH 8.0, 5 mM EDTA, 10 mM NaCl. Bound chromatin was eluted in elution buffer (90 mM NaHCO3, 1% SDS), followed by RNase treatment at 37°C for 30 min and crosslink reversal with decross-linking mixture (2 M NaCl, 0.1 M EDTA, 0.4 M Tris-HCl, pH 6.8) containing proteinase K at 65°C for 3 h. DNA was purified by a phenol-chloroform-isoamylalcohol extraction and ethanol precipitation.
ChIP DNA libraries were prepared with the NEBNext ChIP-Seq Library Prep Kit for Illumina (NEB)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing Fastq files were processed and analyzed on the Biowardrobe platform
Sequence reads were aligned using bowtie (version 1.2.0)
MACS2 (version 2.1.1.20160309) was used to estimate fragment size and to find islands of enrichment with q-value threshold less than 0.2
To visualize the data, the data were uploaded to UCSC genome browser
MAnorm was used for comparison of ChIP peaks
Heat maps and average signal profiles were generated by Easeq
Assembly: mm10, hg19
Supplementary files format and content: bigwig
 
Submission date Sep 20, 2023
Last update date Jan 25, 2024
Contact name Tomohiko Akiyama
E-mail(s) akiakiakit@hotmail.com
Phone 0457872596
Organization name Yokohama city university
Department School of medicine
Street address 3-9 Fuku-ura
City Yokohama
State/province Kanagawa
ZIP/Postal code 236-0004
Country Japan
 
Platform ID GPL16791
Series (2)
GSE243626 ZSCAN4-binding motif - TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes [ChIP-Seq]
GSE243628 ZSCAN4-binding motif - TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes
Relations
BioSample SAMN37480942
SRA SRX21841556

Supplementary file Size Download File type/resource
GSM7792026_Human_ZSCAN4_Rabbit_Ab_DUX4_plus.bw 116.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap