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Series GSE40869 Query DataSets for GSE40869
Status Public on Sep 19, 2012
Title DNaseI Digital Genomic Footprinting from ENCODE/University of Washington [Mouse]
Project Mouse ENCODE
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Richard Sandstrom If you have questions about the Genome Browser track associated with this data, contact ENCODE (
This track, produced as part of the mouse ENCODE Project, contains deep sequencing DNase data that will be used to identify sites where regulatory factors bind to the genome (footprints).
Footprinting is a technique used to define the DNA sequences that interact with and bind DNA-binding proteins, such as transcription factors, zinc-finger proteins, hormone-receptor complexes, and other chromatin-modulating factors like CTCF. The technique depends upon the strength and tight nature of protein-DNA interactions. In their native chromatin state, DNA sequences that interact directly with DNA-binding proteins are relatively protected from DNA degrading endonucleases, while the exposed/unbound portions are readily degraded by such endonucleases. A massively parallel next-generation sequencing technique to define the DNase hypersensitive sites in the genome was adopted. The DNase samples were sequenced using next-generation sequencing machines to significantly higher depths of 300-fold or greater. This produces a base-pair level resolution of the DNase susceptibility maps of the native chromatin state. These base-pair resolution maps represent and are dependent upon the nature and the specificity of interaction of the DNA with the regulatory/modulatory proteins binding at specific loci in the genome; thus they represent the native chromatin state of the genome under investigation. The deep sequencing approach has been used to define the footprint landscape of the genome by identifying DNA motifs that interact with known or novel DNA binding proteins.
Overall design Cells were grown according to the approved ENCODE cell culture protocols ( Digital DNaseI was performed by DNaseI digestion of intact nuclei, followed by isolating DNaseI "double-hit" fragments (Sabo et al., 2006), and direct sequencing of fragment ends (which correspond to in vivo DNaseI cleavage sites) using the Solexa platform (27 bp reads). High-quality reads were mapped to the NCBI37/mm9 mouse genome using Bowtie 0.12.5; only unique mappings were kept. DNaseI sensitivity is directly reflected in raw tag density (Raw Signal), which is shown in the track as density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). DNaseI hypersensitive zones (HotSpots) were identified using the HotSpot algorithm (Sabo et al., 2004). False discovery rate thresholds of 1.0% (FDR 0.01) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 36-mers. DNaseI hypersensitive sites (DHSs or Peaks) were identified as signal peaks within 1.0% (FDR 0.01) hypersensitive zones using a peak-finding algorithm. Only DNase Solexa libraries from unique cell types producing the highest quality data, as defined by Percent Tags in Hotspots (PTIH ~40%), were designated for deep sequencing to a depth of over 200 million tags.
Results were validated by conventional DNaseI hypersensitivity assays using end-labeling/Southern blotting methods.
Web link
Contributor(s) Sandstrom R
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BioProject PRJNA63471
Submission date Sep 13, 2012
Last update date May 15, 2019
Contact name ENCODE DCC
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (22)
GSM1003813 UW_DnaseDgf_B-cell_(CD43-)_adult-8wks
GSM1003814 UW_DnaseDgf_B-cell_(CD19+)_adult-8wks
GSM1003815 UW_DnaseDgf_416B_immortalized
SRA SRP015813

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE40869_RAW.tar 21.9 Gb (http)(custom) TAR (of BIGWIG, BROADPEAK, NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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