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| Status |
Public on May 16, 2014 |
| Title |
J1_NT_input |
| Sample type |
SRA |
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| Source name |
cell line
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| Organism |
Mus musculus |
| Characteristics |
cell line: J1
transfection: lentiviral mediated-shRNA against non-targeting NT
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| Growth protocol |
J1 cell were maintianed in ESGRO medium. Cell were cultured in M15 medium when ChIP was performed.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde, sonicated and precipitated by Ino80, Oct4, Klf4, Med1, or Pol2 antibodies. Then precipitated DNA was reverse crosslinked, extracted and quantified for library.
Library was prepared by TruSeq DNA Sample Prep kit (Illumina) or Nextera XT DNA sample prep kit (Illumina) according to the manufacturer's protocol.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
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| Description |
Library was prepared by Nextera XT kit
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| Data processing |
Basecalls performed using CASAVA version 1.7
Raw data from the replicates were merged.
Raw data was filtered by the following steps: reads were filtered if the average base quality score <20 and duplicate reads removed (based on identical sequences)
Reads were mapped against hg19 reference genome (excluding haplotype chromosomes) with Bowtie (v0.12.8 using the following parameters: -v 2 -m 1)
Mapped data was filtered to remove hits with >2 mismatches to the reference genome.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file per sample per strand showing normalized mapped read coverage; generated by BEDtools genomeCoverageBed and bedGraphToBigWig.
Supplementary_files_format_and_content: Ino80 peak bed files were generated by SICER v1.1 (redundancy threshold=1, window size=200, gap size=800, fragment size=300, FDR=1e-6)
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| Submission date |
Sep 18, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Li Wang |
| Organization name |
NIH
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| Street address |
111 T.W. Alexander Dr
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| City |
Durham |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platform ID |
GPL16417 |
| Series (1) |
| GSE49137 |
INO80 complex in the core regulatory network governing ESC self-renewal [ChIP-Seq] |
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| Relations |
| BioSample |
SAMN02359196 |
| SRA |
SRX355573 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1234308_J1_NT_input.bw |
107.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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