About: Data Types

DNaseI Hypersensitive Sites (DHSs)

DNaseI has long been used to map general chromatin accessibility and DNaseI hypersensitivity is a universal feature of active cis-regulatory sequences. The use of this method has led to the discovery of functional regulatory elements that include enhancers, insulators, promoters, locus control regions and novel elements. For each experiment (cell type) this track shows DNaseI sensitivity as a continuous function using sequencing tag density (Raw Signal), and discrete loci of DNaseI sensitive zones (HotSpots) and hypersensitive sites (Peaks).

Digital Genomic Footprinting

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. Sequencing these next-generation-sequencing DNase samples to significantly higher depths of 300-fold or greater 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

RNA-Seq

RNA-Seq is a method for mapping and quantifying the transcriptome of any organism that has a genomic DNA sequence assembly. RNA-Seq was performed by reverse-transcribing an RNA sample into cDNA, followed by high throughput DNA sequencing on an Illumina Genome Analyser.

Exon Arrays

Samples are hybridized to the Affymetrix Human Exon 1.0 GeneChip. In contrast to traditional microarrays, which are designed to measure overall gene expression, the Affymetrix exon arrays contain separate probesets for each exon. This allows large-scale measurement of alternative splicing, alternative polyadenylation, and alternative promoter usage. Additionally, analysis of the constitutive exons (those included in all transcripts) offer accurate measurement of overall gene expression levels.

Whole Genome Shotgun

This method is used to sequence genomes. The genomic DNA is isolated from a source tissue or cell type, randomly shared in to fragments of defined size and used to construct next-gen Illumina library. The library is sequenced on HiSeq 2000 to produce desired depth of sequence coverage.

ChIP-Input

Randomly shared crosslinked DNA is processed as Chip-Seq sample without precipitation with an antibody. The method provides background signal specific to a given cell or tissue.

CTCF

This type maps genome-wide binding of the CTCF transcription factor in different cell lines using ChIP-seq high-throughput sequencing.

H3K4me3 Signal

Chemical modifications (e.g. methylation and acylation) to the histone proteins present in chromatin influence gene expression by changing how accessible the chromatin is to transcription. A specific modification of a specific histone protein is called a histone mark. This type shows the levels of enrichment of the H3K4Me3 histone mark across the genome as determined by a ChIP-seq assay.

H3K27me3 Signal

Chemical modifications (e.g. methylation and acylation) to the histone proteins present in chromatin influence gene expression by changing how accessible the chromatin is to transcription. A specific modification of a specific histone protein is called a histone mark. This type shows the levels of enrichment of the H3K27Me3 histone mark across the genome as determined by a ChIP-seq assay.

H3K36me3 Signal

Chemical modifications (e.g. methylation and acylation) to the histone proteins present in chromatin influence gene expression by changing how accessible the chromatin is to transcription. A specific modification of a specific histone protein is called a histone mark. This type shows the levels of enrichment of the H3K36Me3 histone mark across the genome as determined by a ChIP-seq assay.