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Links from GEO DataSets

Items: 20

1.

The prevalence, evolution and chromatin signatures of plant regulatory elements

(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
Series
Accession:
GSE128434
ID:
200128434
2.

Leveraging histone modifications to improve genome annotation

(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
Series
Accession:
GSE160944
ID:
200160944
3.

Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

(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
Series
Accession:
GSE152046
ID:
200152046
4.

Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

(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
Series
Accession:
GSE150929
ID:
200150929
5.

Widespread Long-range Cis-Regulatory Elements in the Maize Genome

(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
Series
Accession:
GSE120304
ID:
200120304
6.

Mapping regulatory elements using signatures of open chromatin in Arabidopsis thaliana

(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
Series
Accession:
GSE34318
ID:
200034318
7.

RRBS and RNA-seq profiling of maize shoot and tassel primordium

(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
Series
Accession:
GSE84490
ID:
200084490
8.

Genome-wide chromatin accessibility profiling in maize using DNase-seq on two different tissues: inner stem tissue of V2 seedlings and husk

(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
Series
Accession:
GSE94291
ID:
200094291
9.

Inner stem tissue of V2 seedlings and husks (maize B73)

(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
Series
Accession:
GSE94254
ID:
200094254
10.

Genome-wide gene expression profile in inner stem tissue of V2 seedlings and husks (maize B73) [RNA-Seq]

(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
Series
Accession:
GSE94252
ID:
200094252
11.

Genome-wide identification of H3K9ac enriched regions in inner stem tissue of V2 seedlings and husks (maize B73) [ChIP-Seq]

(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
Series
Accession:
GSE94251
ID:
200094251
12.

MNase-chip of maize B73

(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
Series
Accession:
GSE60092
ID:
200060092
13.

MNase-chip of maize B73 immature ears and seedlings

(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
Series
Accession:
GSE60090
ID:
200060090
14.

MNase-chip of maize B73 immature ears, seedling shoots, and seedling roots

(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
Series
Accession:
GSE60089
ID:
200060089
15.

Maize (Zea mays) leaf transcriptome analysis under abiotic stress in wild type and RNA Polymerase IV mutant

(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
Series
Accession:
GSE71046
ID:
200071046
16.

Histone Modifications by ChIP-seq from ENCODE/University of Washington

(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
Series
Accession:
GSE35583
ID:
200035583
17.

Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University)

(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
Series
Accession:
GSE32970
ID:
200032970
18.

DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington

(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
Series
Accession:
GSE29692
ID:
200029692
19.

Exon arrays of ENCODE tier 1, tier 2 and tier 3 cell types

(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
Series
Accession:
GSE19090
ID:
200019090
20.

ENCODE Tier2 cell phenotyping study

(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
Series
Accession:
GSE17778
ID:
200017778
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