NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2863239 Query DataSets for GSM2863239
Status Public on Nov 23, 2017
Title ChIP-Seq MCM7 exp1
Sample type SRA
 
Source name Cervical carcinoma
Organism Homo sapiens
Characteristics cell line: HeLa
cell type: Human cervical carcinoma
chip antibody: MCM7 (Fujita et al., PMID 8626784; Fujita et al., PMID 9099751)
Treatment protocol Cells grown to ~90% confluent were fixed directly with 1% formaldehyde.
Growth protocol Human cervical carcinoma HeLa cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% (v/v) fetal bovine serum (FBS) and antibiotics.
Extracted molecule genomic DNA
Extraction protocol For ChIP-seq, fixation was stopped by adding Glycine (125mM) and incubating for 5 min at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 300–500 bp average in size through sonication. Resultant was immunoprecipitated with MCM7 antibodies 18 hr at 4°C, followed by incubation with protein G magnetic beads (Invitrogen) for an additional 3 h. After washing and elution, the protein–DNA complex was reversed by heating at 65°C 6hr. Immunoprecipitated DNA was purified by phenol/chloroform extraction and ethanol precipitation.
According to Illumina protocol
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Description PRJDB2761
Data processing The sequence reads were aligned to the hg19 genome using the Bowtie software (version 0.12.8; parameter -v3 -m1).
Signal data (bigWig) were generated using bamCoverage command of deepTools (version 2.4.2) with the option: --smoothLength 60 --binSize 1 --extendReads.
Peak calling was performed using MACS2 (version 2.0.10.20131216).
Genome_build: hg19
Supplementary_files_format_and_content: .bw file available on sample record. ChIP-Seq peak list as tab delimited .txt (available on the series record).
 
Submission date Nov 21, 2017
Last update date May 15, 2019
Contact name Nozomi Sugimoto
E-mail(s) sugimoto@phar.kyushu-u.ac.jp
Organization name Kyushu University
Street address 3-1-1, Maidashi, Higashiku
City Fukuoka
ZIP/Postal code 812-0054
Country Japan
 
Platform ID GPL18460
Series (1)
GSE107248 Genome wide identification of MCM7 binding sites as replication origins
Relations
BioSample SAMD00015878
SRA DRX013514

Supplementary file Size Download File type/resource
GSM2863239_MCM7ChIP_exp1.bw 176.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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