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Sample GSM1364029 Query DataSets for GSM1364029
Status Public on Aug 04, 2014
Title O-Sf-M
Sample type SRA
 
Source name Human dermal fibroblast
Organism Homo sapiens
Characteristics cell type: OCT3/4, SOX2-overexpressed Human dermal fibroblast
chip antibody: anti flag antibody
Extracted molecule genomic DNA
Extraction protocol Chromatins were fragmentated by sonication and immunoprecipitated with an anti-FLAG M2 antibody or antibodies against protein-of-interest. Immunoprecipitated DNA fragments were purified by QIAGEN's PCR purification Kit.
Ten ng of co-immunoprecipitated DNA fragments, exept for Of-S-M and O-Sf-M, were subjected to preparation of Illumina’s sequencing library using NEBNext ChIP-seq Library Prep Reagent (New England Biolabs), according manifacturer's instruction. After adapter ligation, DNA fragments were amplified by PCR with Illumina primers and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated by Caliper XT(Perkinelmer). For Of-S-M and O-Sf-M, Illumina’s sequencing libraries were generated by Ovation SP Iltralow Library System (NuGEN). The purified DNA was captured on an Illumina flow cell for cluster generation.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing Basecalls performed using BCL2FASTQ version 1.8.3 for Of-S-M and O-Sf-M, and CASAVA version 1.8.1 for others.
For Of-S-K-M,O-Sf-K-M and O-S-Kf-M, the 81th bass were trimmed and filtered using Illumina's Quality Filtering by CASAVA version 1.8.1. For others, data were filtered using Illumina's Quality Filtering and last bases in reads were not used.
ChIP-seq reads were aligned to the hg19 genome assembly using BWA version 0.6.2-r126 with default parameters.
Peaks were detected using MACS version 1.4.2 with parameter --tsize=49 and other parameters were default without control samples.
Genome_build: hg19
Supplementary_files_format_and_content: bed files which contain peak information were generated using MACS version 1.4.2.
 
Submission date Apr 07, 2014
Last update date May 15, 2019
Contact name Akira Watanabe
E-mail(s) a.watanabe@cyberomix.com
Organization name CyberomiX Inc
Street address Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku
City Kyoto
State/province Kyoto
ZIP/Postal code 602-8407
Country Japan
 
Platform ID GPL16791
Series (2)
GSE56567 Critical role of transient activation of human endogenous retroviruses during reprogramming toward pluripotency (Chip-Seq)
GSE56569 Critical role of transient activation of human endogenous retroviruses during reprogramming toward pluripotency
Relations
BioSample SAMN02721099
SRA SRX512373

Supplementary file Size Download File type/resource
GSM1364029_O-Sf-M_Peaks.bed.txt.gz 406.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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