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| Status |
Public on Apr 25, 2019 |
| Title |
LAN-6-IRF2-3496plusDOX_S39 |
| Sample type |
SRA |
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| Source name |
Primarily cultured iKAP CRC cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: Primarily cultured iKAP CRC cells
passage: 18-20
strain: B6/129
antibdoy: IRF2 (Bethyl, A303-381A)
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| Growth protocol |
Primarily cultured iKAP CRC cells were routinely cultured in DMEM plus 10% FBS (Tetracycline-Free) and 1ug/ml Doxycycline.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Immune complexes were then washed three times with RIPA buffer, once with RIPA-500 (RIPA with 500 mM NaCl), and once with LiCl wash buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA [pH 8.0], 250 mM LiCl, 0.5% NP-40, 0.5% deoxycholic acid). Elution and reverse-crosslinking were performed in direct elution buffer (10 mM Tris-Cl [pH 8.0], 5 mM EDTA, 300 mM NaCl, 0.5% SDS) with proteinase K (20 mg/ml) at 65°C overnight. Eluted DNA was purified using AMPure beads (Beckman-Coulter). Libraries were prepared using NEBNext Ultra DNA Library kit (E7370).
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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 CASAVA version 1.4
Reads were aligned to a reference genome (UCSC mm9; Assembly http://hgdownload.cse.ucsc.edu/downloads. html#mouse) using the Burrows–Wheeler Aligner.
Reads mapping to more than two genomic loci were ignored.
The peaks are called with p-value 1e-6, corresponding to the Peak score column: 10*log10(pvalue)
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using deeptools bamCoverage 2.3.3
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| Submission date |
Feb 05, 2018 |
| Last update date |
Apr 25, 2019 |
| Contact name |
Wenting Liao |
| E-mail(s) |
Wliao2@mdanderson.org
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| Organization name |
md anderson
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| Street address |
1881 east road
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| City |
houston |
| ZIP/Postal code |
77051 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
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| Relations |
| BioSample |
SAMN08469553 |
| SRA |
SRX3651821 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2981758_LAN-6-IRF2-3496plusDOX_S39.bw |
274.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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