GEO DataSets

(Submitter supplied) Chromatin accessibility and modification is a hallmark of regulatory DNA, which has led to the discovery of cis-regulatory elements (CREs). Here, we characterize chromatin accessibility, histone modifications and sequence conservation in 13 plant species. We identified thousands of putative CREs and revealed that distal CREs are prevalent in plants especially in species with large and complex genomes. more...

Organism:

Populus trichocarpa; Glycine max; Hordeum vulgare; Setaria viridis; Asparagus officinalis; Oryza sativa; Brachypodium distachyon; Eutrema salsugineum; Arabidopsis thaliana; Phaseolus vulgaris; Sorghum bicolor; Zea mays; Spirodela polyrhiza

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

13 related Platforms

170 Samples

Download data: BW

(Submitter supplied) With the creation of accurate, chromosome-scale genomes, the next challenge facing the genomics community is the accurate idenfication of transcriptional units, distinguishing them from aberrant transcriptional noise. This has proven to be a challenge as annotation by traditional means, such as short read RNA-seq followed by transcriptome assembly, which is prone to the generation of in-silico artifacts. more...

Organism:

Glycine max; Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

6 Samples

Download data: BED

(Submitter supplied) The genomic sequences of diverse varieties of many crop species continue to be produced at a frenetic pace. However, it remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Here, we explore the potential to use DNA methylation profiles to develop more complete and refined annotations. Using leaf tissue in maize, we define ~100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs (1.3% of the genome) are found greater than 2 kilobase pairs from genes. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20156

2 Samples

Download data: BED, TXT

(Submitter supplied) The genomic sequences of diverse varieties of many crop species continue to be produced at a frenetic pace. However, it remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Here, we explore the potential to use DNA methylation profiles to develop more complete and refined annotations. Using leaf tissue in maize, we define ~100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs (1.3% of the genome) are found greater than 2 kilobase pairs from genes. more...

Organism:

Zea mays

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17628

6 Samples

Download data: TXT

(Submitter supplied) Genetic mapping studies on crops suggest that agronomic traits can be controlled by loci within the gene-distal intergenic space. Despite the biological importance and the potential agronomic utility of these intergenic loci, they remain virtually uncharacterized in all crop species to date. Here, we provide genetic, epigenomic, and functional molecular evidence supporting the widespread existence of gene-distal (hereafter, distal) loci which act as long-range transcriptional cis-regulatory elements (CREs) in the maize genome. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Other

Platforms:

GPL20156 GPL17628

81 Samples

Download data: BED, TSV, TXT

(Submitter supplied) Gene expression is controlled by the complex interaction of transcription factors binding to promoters and other regulatory DNA elements. One common characteristic of the genomic regions associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We reported genome-wide high resolution maps of DNase I hypersensitive (DH) sites from both seedling and flower tissues of Arabidopsis from the Columbia (Col) ecotype and the corresponding ddm1 (deficient in DNA methylation 1) mutant. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9302

14 Samples

Download data: BAM, BED, TXT

(Submitter supplied) Profiling the methylation and gene expression between vegetative (coleoptile-stage shoots) and reproductive (tassel primordium) tissues with RRBS and RNA-seq

Organism:

Zea mays

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL15463 GPL20156

6 Samples

Download data: CGMAP, TXT

(Submitter supplied) Most cells in a multicellular organism carry the same genetic information; however, they can still differentiate to take up different functions in the organism. This differentiation process involves tight regulation of gene expressions by regulatory sequences including transcriptional enhancers. Enhancers can be located distantly from their target genes; this characteristic makes it difficult to identify enhancers only using experimental approaches. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17628

6 Samples

Download data: BED, BW

(Submitter supplied) Genome-wide prediction of transcriptional enhancers in maize B73 using DNase-seq and H3K9ac ChIP-seq. RNA-seq data was used to associate potential target genes to enhancer candidates.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17628

19 Samples

Download data

(Submitter supplied) Most cells in a multicellular organism carry the same genetic information; however, they can still differentiate to take up different functions in the organism. This differentiation process involves tight regulation of gene expressions by regulatory sequences including transcriptional enhancers. Enhancers can be located distantly from their target genes; this characteristic makes it difficult to identify enhancers only using experimental approaches. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17628

12 Samples

Download data: DIFF

(Submitter supplied) Most cells in a multicellular organism carry the same genetic information; however, they can still differentiate to take up different functions in the organism. This differentiation process involves tight regulation of gene expressions by regulatory sequences including transcriptional enhancers. Enhancers can be located distantly from their target genes; this characteristic makes it difficult to identify enhancers only using experimental approaches. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17628

7 Samples

Download data: BED, BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL19041 GPL19042

34 Samples

Download data: PAIR

(Submitter supplied) The eukaryotic nuclear genome is organized into the fundamental units of chromatin, nucleosomes. The positions and biochemical states of nucleosomes on DNA can regulate protein-DNA interactions, and in turn influence DNA-templated events. Despite the increasing number of genome-wide maps of nucleosome position, how global changes in nucleosome position relate to changes in gene expression is poorly understood. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL19042

24 Samples

Download data: PAIR, TSV

(Submitter supplied) The eukaryotic nuclear genome is organized into the fundamental units of chromatin, nucleosomes. The positions and biochemical states of nucleosomes on DNA can regulate protein-DNA interactions, and in turn influence DNA-templated events. Despite the increasing number of genome-wide maps of nucleosome position, how global changes in nucleosome position relate to changes in gene expression is poorly understood. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL19041

10 Samples

Download data: PAIR, TSV

(Submitter supplied) Plants have developed complex mechanisms to respond and adapt to abiotic stresses, coupling elaborate modulation of gene expression together with the preservation of genome stability. Epigenetic mechanisms - DNA methylation, chromatin modifications and non coding RNAs - were shown to play a fundamental role in stress-induced gene regulation and may also result in genome destabilization, with the activation and/or the transcription of silenced transposons and retroelements, causing genome rearrangements and novel gene expression patterns. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

32 Samples

Download data: GTF, TXT

(Submitter supplied) This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Richard Sandstrom mailto:sull@u.washington.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). This track was produced as part of the ENCODE Project. This track displays genome-wide maps of histone modifications in different cell lines (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=cellType) using ChIP-seq high-throughput sequencing. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9052

171 Samples

Download data: BIGWIG, BROADPEAK, NARROWPEAK

(Submitter supplied) This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Terry Furey mailto:tsfurey@duke.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). These tracks display DNaseI hypersensitivity (HS) evidence as part of the four Open Chromatin track sets. DNaseI is an enzyme that has long been used to map general chromatin accessibility, and DNaseI "hypersensitivity" is a feature of active cis-regulatory sequences. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9052

97 Samples

Download data: BIGWIG, NARROWPEAK, TXT

(Submitter supplied) This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Richard Sandstrom mailto:sull@u.washington.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). This track is produced as part of the ENCODE Project. This track shows DNaseI sensitivity measured genome-wide in different cell lines using the Digital DNaseI methodology (see below), and DNaseI hypersensitive sites. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9052 GPL9115

208 Samples

Download data: BAM, BIGWIG, BROADPEAK, NARROWPEAK

(Submitter supplied) This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Richard Sandstrom mailto:sull@u.washington.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). At cell harvest, a subset of cells was stored at -20oC in RNALater. Total RNA from 5 X 106 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

182 Samples

Download data: BED, BROADPEAK, CEL

(Submitter supplied) These samples are part of the ENCODE consortium’s proposed time-limited Pilot Study for confirmation of the utility of RNA abundance measurements as a standard reference phenotyping tool. Keywords: cell type comparison For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

26 Samples

Download data: CEL, CHP