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| Status |
Public on Nov 23, 2018 |
| Title |
HEK293_DNase |
| Sample type |
SRA |
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| Source name |
HEK293_DNase
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNase-seq was conducted on 50 million cells as previously described (Song and Crawford, 2010), with the minor modification of using 5’ phosphorylated oligo 1b. Samples digested with 12U, 4U and 1.2U total DNase I were pooled.
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| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The reads were trimmed to the first 20 bases. Trimmed reads were aligned to the hg19 build of the human genome, using the Burrows-Wheeler aligner (BWA) (Li and Durbin, 2009), tolerating up to two mismatches. Sequences aligning to more than four locations were discarded. Further processing was performed to filter out unwanted chromosomes and alpha satellites. In order to remove PCR artifacts, reads that piled up (>=10 reads) at a single base were discarded, if they constituted at least 70 percent of all reads in the surrounding 30 base pair window. Signal bedGraph files were generated with the SignalGenerator.sh script from JAMM (Ibrahim et al., 2014), with the parameters -f 1 and -n depth. BedGraph files were converted to the binary bigWig format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain library depth normalized signal in 10 base pair bins genome-wide. These are the binary versions of bedGraph files which contain 4 columns: chromosome, start, end, signal.
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| Submission date |
Dec 26, 2017 |
| Last update date |
Nov 25, 2018 |
| Contact name |
Aslihan Karabacak |
| E-mail(s) |
aslihan.karabacak@gmail.com
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| Organization name |
Max Delbrück Center for Molecular Medicine
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| Department |
Berlin Institute for Medical Systems Biology
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| Lab |
Uwe Ohler
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| Street address |
Robert-Rössle-Straße 10
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| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE108513 |
Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets via protocol-specific bias modeling |
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| Relations |
| BioSample |
SAMN08243310 |
| SRA |
SRX3511101 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2902639_HEK293_DNase.bw |
1.0 Gb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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