GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2481689 Query DataSets for GSM2481689
Status Public on Jul 10, 2018
Title ST1 JQ1 Treated BRD4
Sample type SRA
Source name ST1 JQ1 Treated BRD4
Organism Homo sapiens
Characteristics cell line: ST1
disease state: Adult T-cell Leukemia/Lymphoma (ATLL)
Treatment protocol Treatment type: compound
Agent: JQ1
Treatment dose: 250 nM
Treatment time: 24 hours
In-vitro treatment: ST1 cells were treated with JQ1 (Constellation Pharmaceuticals) for 24 hours.
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.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Description No additional information.
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
Submission date Feb 09, 2017
Last update date May 15, 2019
Contact name Louis M. Staudt
Phone 301-402-1892
Organization name National Cancer Institute
Department Lymphoid Malignancies Branch
Lab Louis M Staudt
Street address 9000 Rockville Pike, Bldg 10, Rm 4N114
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platform ID GPL18573
Series (1)
GSE94732 Targeting the HBZ Viral Oncoprotein Transcriptional Network in Adult T-cell leukemia/lymphoma (ChIP-Seq)
BioSample SAMN06318279
SRA SRX2548298

Supplementary file Size Download File type/resource
GSM2481689_ch296_S9_R1_001.fastq.gz.wig.gz 847.5 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap