|
| Status |
Public on Sep 04, 2014 |
| Title |
MCF7_Deproteinized_DNase |
| Sample type |
SRA |
| |
|
| Source name |
cultured MCF7 cells (ATCC HTB-22)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ATCC HTB-22
cell type: MCF7
|
| Growth protocol |
K562 or MCF7 cells were cultured in RPMI-1640 or DMEM media, respectively, + 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Deproteinized genomic DNA was isolated from ~20 million K562 or MCF7 cells using a DNeasy Blood and Tissue kit (Qiagen). Isolated total DNA was then subjected to two phenol-chloroform extractions followed by ethanol precipitation to ensure removal of bound protein.
DNase I digestions were performed in 120μL solution with ~50μg of deproteinized DNA. Digestions were punctuated by addition of 50mM EDTA and 15 min incubation at 75°C. Digestions performed with 1.2U and 2.4U total DNase I were selected based on .8% agarose gel sizing to be similar to typical DNase-seq assay digestions and pooled for the two cell lines separately. Libraries were constructed from pooled digests as described (Song and Crawford 2010; PMID:20150147).
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA v1.8
First 20bp of DNase-seq reads mapped to hg19 with BWA, allowing up to 2 mismatches
Putative PCR artifacts filtered from mapped DNase-seq reads
We counted the number of DNA 6-mers centered at each DNase cleavage site (between the 3rd and 4th bp) and calculated the relative frequency of each 6-mer. These relative frequencies are normalized by the relative frequency of each 6-mer in the human genome and genomic relative frequencies are corrected for regions that are mappable using our DNase-seq protocol.
Genome_build: hg19
Supplementary_files_format_and_content: plain text file with two columns: DNA 6-mer and corresponding cleavage propensity
|
| |
|
| Submission date |
Sep 04, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher L Frank |
| E-mail(s) |
chris.frank21@gmail.com
|
| Organization name |
Duke University
|
| Lab |
Gregory Crawford
|
| Street address |
101 Science Dr.
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE61105 |
Explicit DNase sequence bias modeling enables high resolution transcription factor footprint detection |
|
| Relations |
| BioSample |
SAMN03019528 |
| SRA |
SRX692834 |
