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| Status |
Public on Dec 31, 2013 |
| Title |
H3K4me3_ChIP_Seq_rep2 |
| Sample type |
SRA |
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| Source name |
MDAMB231
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MDAMB231
chip antibody: H3K4me3
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| Treatment protocol |
None
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| Growth protocol |
MDAMB231 cells were obtained from American Type Culture Collection (ATCC, Manassas, VA). MDAMB231 cells were cultured in DMEM with 5% FBS.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For FAIRE, nuclei were extracted after the crosslinking step (1% formaldehyde in PBS) of intact cells, followed by re-suspension in SDS lysis buffer before sonication. FAIRE DNA samples were purified by phenol/chloroform extraction. Input DNA was also purified by phenol/chloroform extraction after the crosslinking was reversed. ChIP assays were performed in MDAMB231 as previously described (Jia et al, 2009).
Libraries were prepared according to Illumina's instructions (refer to http://epigenome.usc.edu/services/nextgen/making_libraries.html)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1000 |
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| Data processing |
Basecalls performed using Illumina Casava1.7 software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to hg19 whole genome using tophat with default parameters.
FAIRE Peaks were called using findPeaks from HOMER (http://biowhat.ucsd.edu/homer), using a triangle-based B224distribution with a median length of 150bp with an alpha value of 0.01 (99.0% confidence interval). To identify epigenomic domains for histone modification, the MACS software on histone ChIP-seq data was applied with default settings (Zhang et al, 2008)
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated using makeTagDirectory and makeUCSCfile from homer with following -o auto -res 1 -fsize 5e7; FAIRE peak files were generated using following settings (-alpha 0.01 -subpeaks 0.6) and score represents number of tags found clustered together. ChIPseq peaks were processed by using MACS default settings.
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| Submission date |
Aug 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Suhn K Rhie |
| Organization name |
University of Southern California
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| Street address |
1450 Biggy Street
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089 |
| Country |
USA |
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| Platform ID |
GPL15433 |
| Series (1) |
| GSE49651 |
Nucleosome Positioning and Histone Modifications Define Relationships between Regulatory Elements and Nearby Gene Expression in Breast Epithelial Cells |
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| Relations |
| BioSample |
SAMN02313870 |
| SRA |
SRX332677 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1204473_MDAMB231.H3K4me3_2.hg19.tags.bedGraph.gz |
43.4 Mb |
(ftp)(http) |
BEDGRAPH |
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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