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| Status |
Public on Jun 21, 2022 |
| Title |
293T cells expressing Empty vector |
| Sample type |
SRA |
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| Source name |
human embryonic kidney cells
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| Organism |
Homo sapiens |
| Characteristics |
treatment (transfection): pMIGII_Mock
transfection type: transient
cell line: HEK293T
chip antibody: anti-HA (Roche, 3F10)
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| Growth protocol |
293T cells were cultured with DMEM, supplemented with 10% fetal bovine serum, 100 u/ml penicillin, and 100 µg/ml streptomycin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin fractions from HEK293T cells were prepared using the fanChIP method, as described previously (doi.org/10.1016/j.xpro.2021.100404). Cells were suspended in CSK buffer (100 mM NaCl, 10 mM PIPES [pH 6.8], 3 mM MgCl2, 1 mM EGTA, 0.3 M sucrose, 0.5% Triton X-100, 5 mM sodium butyrate, 0.5 mM DTT, and protease inhibitor cocktail) and centrifuged (400× g for 5 min, at 4°C) to remove the soluble fraction. The pellet was resuspended in MNase buffer (50 mM Tris-HCl [pH 7.5], 4 mM MgCl2, 1 mM CaCl2, 0.3 M sucrose, 5 mM sodium butyrate, 0.5 mM DTT, and protease inhibitor cocktail) and treated with MNase at 37°C for 3–6 min to obtain oligonucleosomes. MNase reaction was then stopped by adding EDTA (pH 8.0) to a final concentration of 20 mM. An equal amount of lysis buffer (250 mM NaCl, 20 mM sodium phosphate [pH 7.0], 30 mM sodium pyrophosphate, 5 mM EDTA, 10 mM NaF, 0.1% NP-40, 10% glycerol, 1 mM DTT, and EDTA-free protease inhibitor cocktail) was added to increase solubility. The chromatin fraction was cleared by centrifugation (15,000 rpm for 5 min, 4°C) and subjected to immunoprecipitation with anti-HA antibody (3F10, Roche) and Protein-G magnetic microbeads (Invitrogen). Immunoprecipitates were then washed five times with washing buffer (1:1 mixture of lysis buffer and MNase buffer with 20 mM EDTA) and eluted in elution buffer (1% SDS and 50 mM NaHCO3). The eluted DNA material was fragmented by DNA shearing system (M220 Covaris).
TruSeq ChIP Sample Prep Kit (illumina)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
bcl2fastq
MACS 2.0.10
Genome_build: hg19
Supplementary_files_format_and_content: peak filles
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| Submission date |
Dec 10, 2021 |
| Last update date |
Jun 21, 2022 |
| Contact name |
Masaki Nomura |
| E-mail(s) |
[email protected]
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| Organization name |
Foundation for Biomedical Research and Innovation at Kobe
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| Street address |
6-3-7 Minatojima Minamimachi, Chuo Ward
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| City |
Kobe |
| State/province |
Hyogo |
| ZIP/Postal code |
650-0047 |
| Country |
Japan |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE190652 |
Aberrant EVI1 splicing contributes to EVI1-rearranged leukemia [ChIP-seq] |
| GSE190656 |
Aberrant EVI1 splicing contributes to EVI1-rearranged leukemia |
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| Relations |
| BioSample |
SAMN23887264 |
| SRA |
SRX13377166 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not provided for this record |
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