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| Status |
Public on Jan 26, 2016 |
| Title |
Colo205_Brd4 |
| Sample type |
SRA |
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| Source name |
COLO 205
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| Organism |
Homo sapiens |
| Characteristics |
cimp status: CIMP (+)
chip antibody: Brd4
cell line: COLO 205
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| Treatment protocol |
None
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| Growth protocol |
Cell lines were grown at 37 degrees celsius and crosslinked for ChIP during logarithmic growth phase.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 15 minutes (Brd4 ChIP) or 5 minutes (H3K27ac ChIP). DNA was sonicated to an average length of 200 - 500 bp. IP and Input DNA was reverse crosslinked and purified for library preparation.
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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Brd4 ChIP
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| Data processing |
Reads were aligned to the human genome (hg19) using the BWA algorithm (default settings).
Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis.
For Brd4 ChIP-seq, samples were normalized using Drosophila chromatin spike-in. Briefly, normalization was performed by equalizing the Drosophila tag counts across all samples so that the final tag counts were based off of the sample containing the lowest number of Drosophila tags. Then the human tags counts for all samples were proportionally scaled based on the ratios used to adjust the drosophila tag counts. Scaling to the target tag number was performed by randomly removing excess tags. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome to generate bigWig files.
For H3K27ac ChIP-seq, samples were normalized by random downsampling to a specific number of total reads and bedgraph files were generated using Bedtools (default settings).
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files, bigWig files
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| Submission date |
Sep 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Florian Gnad |
| Organization name |
Genentech
|
| Street address |
1 DNA Way
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| City |
South San Francisco |
| ZIP/Postal code |
94080 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE73319 |
CCAT1 is a cMYC super-enhancer templated RNA that predicts BET sensitivity in cancer |
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| Relations |
| BioSample |
SAMN04100861 |
| SRA |
SRX1272790 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1890740_COLO205_BRD4_i82_dmnorm_signal.bw |
113.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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