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| Status |
Public on Jul 10, 2018 |
| Title |
ST1 DMSO Treated BRD4 |
| Sample type |
SRA |
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| Source name |
ST1 DMSO Treated BRD4
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| Organism |
Homo sapiens |
| Characteristics |
cell line: ST1
disease state: Adult T-cell Leukemia/Lymphoma (ATLL)
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| Treatment protocol |
Treatment type: compound
Agent: DMSO (Dimethyl sulfoxide)
Treatment time: 24 hours
In-vitro treatment: Cells were treated with DMSO.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
BRD4 Antibody Extraction
Other: 20 million exponentially growing cells were collected per sample and cross-linked with 1% formaldehyde for 10 min at room temperature. The cross-linked cells were resuspended in ice-cold RIPA buffer (10mM Tris-HCl pH8, 140 mM NaCl, 1mM EDTA pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS and 0.1% sodium deoxycholate) to a final concentration of 4 million cells/ml. DNA was sheared with a Misonix XL sonicator. For each immune precipitation reaction, the chromatins were incubated overnight with 100 ug (1 mg/ml) of BRD4 antibody (Bethyl, Cat No. A301-985A100). The following day, chromatin/antibody complexes were incubated with Protein G Dynabeads (50 ul; Thermo Fisher Scientific) for 4 h at 4 C, washed 3 times with RIPA Buffer, once with LiCl Buffer (10 mM Tris-HCl pH8, 250 mM LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate, 1 mM EDTA), once with TE pH 8.0 and finally resuspended in 100 ul TE pH8 containing RNase A (0.2 ug/ul). Reverse crosslinking was performed overnight at 65 C, followed by treatment with 20 ug Proteinase K (Invitrogen) for 2 h at 50 C. Final DNA purification was performed with QIAquick PCR Purification columns (QIAGEN).
ChIP DNA was used to generate ChIP-seq libraries with the NEXTflex Illumina ChIP-seq Library Prep Kit (Bio Scientific) according to manufacturer's instructions.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
No additional information.
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| Data processing |
ChIP-Seq Analysis - NextSeq
Calculation Method: Sequencing of ChIP-seq samples was performed on a NextSeq 500 sequencer (Illumina), with single reads of 76 bp length. Reads were aligned to human genome build 36 (hg18) with Bowtie software. Redundant reads were removed and reads uniquely mapping to reference genome were used for further analysis. To perform peak calling, the genome was divided into "bins" of 25 bp. Each sequencing tag was associated with the bin of its start site and an additional extension of seven bins (for a total of 200 bp) along the direction of its read to match the average library size. For a given experiment, the number of "hits" in a bin was defined as the number of extended tags associated with that bin. Bins with fewer than three hits were removed. Peaks were formed by merging consecutive significant bins. The height of the peak was defined as the largest number of hits in any of the bins forming the peak. The "apex" of the peak was defined as the bin that had this largest number of hits. In the case of ties, the earliest such peak was chosen as the apex.
Supplementary_files_format_and_content: wig file
Genome_build: hg18
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| Submission date |
Feb 09, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Louis M. Staudt |
| E-mail(s) |
lstaudt@mail.nih.gov
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| Phone |
301-402-1892
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| Organization name |
National Cancer Institute
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| Department |
Lymphoid Malignancies Branch
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| Lab |
Louis M Staudt
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| Street address |
9000 Rockville Pike, Bldg 10, Rm 4N114
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE94732 |
Targeting the HBZ Viral Oncoprotein Transcriptional Network in Adult T-cell leukemia/lymphoma (ChIP-Seq) |
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| Relations |
| BioSample |
SAMN06318281 |
| SRA |
SRX2548296 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2481687_ch291_S4_R1_001.fastq.gz.wig.gz |
1.7 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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