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| Status |
Public on Jan 20, 2017 |
| Title |
SUM229neg_BRD4_30nMtrametinib_24h |
| Sample type |
SRA |
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| Source name |
EpCAM/CD49f negative SUM229 breast carcinoma subpopulation
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| Organism |
Homo sapiens |
| Characteristics |
cell line: SUM229 breast carcinoma cell line, EpCAM/CD49f negative subpopulation
treatment: 30nM trametinib
time: 24h
chip antibody: BRD4 Bethyl Laboratories A301-985A
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| Growth protocol |
culture media: F12 supplemented with 5% FBS, 5 µg/ml insulin, 1 µg/ml hydrocortisone, 10 mM HEPES
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell lysates were sonicated resulting in an average chromatin fragment size of ~300 bp and immunoprecipiated with the indicated antibodies.
All libraries were constructed using KAPA Hyper Prep kits with Illumina TruSeq adapters, 18 cycles of amplification and dual SPRI size selection post-amplification, except where indicated, whereby the libraries were constructed using DNA SMART ChIP Seq kit (Clontech) with dual SPRI size selection following 18 cycles of amplification.
library preparation kit: KAPA Hyper Prep
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
peakclassification_SUM229neg.xlsx
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| Data processing |
Reads were aligned to hg19_M_rCRS using Bowtie v1.1.2 with parameters -v 2 -m 1.
For libraries constructed with Clontech DNA SMART ChIP Seq kit, the first three bases of the sequencing read, corresponding to the template switching oligo, were trimmed prior to mapping.
The following processing steps were performed to generate peakclassification files: Calculating read density: The density of reads in each region was normalized to the total number of million mapped reads producing read density in units of reads per million mapped reads (rpm). The read density of the input chromatin was subtracted from the ChIP read density for normalization. Peak calling: We used a combination of two algorithms, MACS v1.4.2 and HMCan v1.21, to define enriched regions. We used HMCan to call peaks in regions of high CNV, defined as regions of size > 50 kb where no MACS peaks are called, and have read coverage that is >3 times the average read coverage. Peaks within 12.5 kb of each other were stitched as described in Loven et al. 2013 Cell 153. We used default settings for MACS, and HMCan was run with narrow peak calling configuration file with no blacklisted regions. Peak genic classification: A peak region was classified on the basis of its location with respect to GRCh37/hg19 gene annotations. If the region was +/- 5 kb of any transcription start site, it was classified as a promoter peak. If it was within -5kb to -200kb of any transcriptional start site, it was classified as a 5' enhancer peak. If the peak overlapped the gene boundary, and was not classified as a promoter or enhancer peak, it was classified as either a genebody_exon or genebody_intron peak. If the peak resided within 0 to +200kb from the 3'-most exon, and did not fulfill the criteria for the above classifications, it was classified as a 3' enhancer. All remaining peaks were designated as "other".
Genome_build: hg19
Supplementary_files_format_and_content: .bed and .xls
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| Submission date |
Sep 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gary L Johnson |
| E-mail(s) |
[email protected]
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| Organization name |
University of North Carolina School of Medicine
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| Department |
Pharmacology
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| Lab |
Gary L. Johnson Lab
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| Street address |
4009 Genetic Medicine Building, 120 Mason Farm Road
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE87418 |
Enhancer Remodeling During Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacological Targeting of the P-TEFb Complex (ChIP-seq) |
| GSE87424 |
Enhancer Remodeling During Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacological Targeting of the P-TEFb Complex |
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| Relations |
| BioSample |
SAMN05832040 |
| SRA |
SRX2194290 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2330608_SUM229neg_BRD4_30nMtrametinib_24h_HMCan.bed.gz |
376.0 Kb |
(ftp)(http) |
BED |
| GSM2330608_SUM229neg_BRD4_30nMtrametinib_24h_MACS.bed.gz |
355.4 Kb |
(ftp)(http) |
BED |
| GSM2330608_SUM229neg_BRD4_30nMtrametinib_24h_combined.bed.gz |
210.0 Kb |
(ftp)(http) |
BED |
| GSM2330608_SUM229neg_BRD4_30nMtrametinib_24h_stitchedpeaks.bed.gz |
144.0 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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