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Sample GSM2902639 Query DataSets for GSM2902639
Status Public on Nov 23, 2018
Title HEK293_DNase
Sample type SRA
 
Source name HEK293_DNase
Organism Homo sapiens
Characteristics cell line: HEK293
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.
 
Library strategy DNase-Hypersensitivity
Library source genomic
Library selection DNAse
Instrument model Illumina HiSeq 2500
 
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.
 
Submission date Dec 26, 2017
Last update date Nov 25, 2018
Contact name Aslihan Karabacak
E-mail(s) aslihan.karabacak@gmail.com
Organization name Max Delbrück Center for Molecular Medicine
Department Berlin Institute for Medical Systems Biology
Lab Uwe Ohler
Street address Robert-Rössle-Straße 10
City Berlin
ZIP/Postal code 13125
Country Germany
 
Platform ID GPL16791
Series (1)
GSE108513 Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets via protocol-specific bias modeling
Relations
BioSample SAMN08243310
SRA SRX3511101

Supplementary file Size Download File type/resource
GSM2902639_HEK293_DNase.bw 1.0 Gb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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