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| Status |
Public on Oct 25, 2022 |
| Title |
Treated2_00251275_HDAC1 |
| Sample type |
SRA |
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| Source name |
CLL,1275 Abexinostat 400mM 6h
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Blood, PBMC
cell type: Human peripheral blood mononuclear cells
genotype: del 11q
disease state: CLL
chip antibody: HDAC1 (Active Motif # 40967)
treatment: Abexinostat
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| Growth protocol |
RPMI, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. 15 ug of chromatin was immunoprecipitated per sample using antibodies against HDAC1 (Active Motif # 40967) and BRD4 (Active Motif # 91301, 4l), H3K9Ac (Active Motif # 39917), H3K27Ac (Active Motif # 39133), and RNA Pol II (Active Motif # 91151),
Illumina sequencing libraries were prepared from the ChIP and input DNAs by the standard consecutive enzymatic steps of end-polishing, dA addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina's NextSeq 500.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
The 75-nt single end sequence reads were mapped to the human reference genome (GRCh37/hg19) using the BWA algorithm with default settings.
Duplicate reads were removed and only uniquely mapped reads were used for further analysis.
Peak locations (enriched regions) for HDAC1, BRD4, H3K9Ac, H3K27ac were determined using the MACS algorithm (v1.4.2) with a cutoff p-value of 1E-7 for narrow peaks and 1E-1 for broad peaks.
Assembly: GRCh37/hg19
Supplementary files format and content: narrowPeak
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| Submission date |
Oct 21, 2022 |
| Last update date |
Oct 28, 2022 |
| Contact name |
Ayse Selen Yilmaz |
| E-mail(s) |
[email protected]
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| Organization name |
OSU
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| Department |
Biomedical Informatics
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| Lab |
Bioinformatics shared Resource
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| Street address |
1800 Cannon Drive
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| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43210 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE216287 |
HDAC1 regulates the chromatin landscape to control transcriptional dependencies in chronic lymphocytic leukemia [ChIP-seq] |
| GSE216290 |
HDAC1 regulates the chromatin landscape to control transcriptional dependencies in chronic lymphocytic leukemia |
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| Relations |
| BioSample |
SAMN31402225 |
| SRA |
SRX17989498 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6665995_Treated2_HDAC1_peaks_p5.narrowPeak.gz |
1.8 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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