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| Status |
Public on Aug 04, 2014 |
| Title |
O-S-Kf-M |
| Sample type |
SRA |
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| Source name |
Human dermal fibroblast
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| Organism |
Homo sapiens |
| Characteristics |
cell type: OCT3/4, SOX2 and KLF4-overexpressed Human dermal fibroblast
chip antibody: anti flag antibody
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| 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.
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| Submission date |
Apr 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Akira Watanabe |
| E-mail(s) |
a.watanabe@cyberomix.com
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| Organization name |
CyberomiX Inc
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| Street address |
Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku
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| City |
Kyoto |
| State/province |
Kyoto |
| ZIP/Postal code |
602-8407 |
| Country |
Japan |
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| Platform ID |
GPL11154 |
| 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 |
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| Relations |
| BioSample |
SAMN02721090 |
| SRA |
SRX512368 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1364024_O-S-Kf-M_Peaks.bed.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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