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Links from GEO DataSets

Items: 20

1.

A cis-regulatory atlas of maize single cells

(Submitter supplied) Cis-regulatory elements (CREs) encode the genomic blueprints for coordinating the spatiotemporal regulation of gene transcription programs necessary for highly specialized cellular functions. To identify cis-regulatory elements underlying cell-type specification and developmental transitions, we implemented single-cell sequencing of Assay for Transposase Accessible Chromatin (scATAC-seq) in an atlas of Zea mays tissues and organs. more...
Organism:
Zea mays; Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL25410 GPL26208
14 Samples
Download data: TXT
Series
Accession:
GSE155178
ID:
200155178

PubMed Similar studies SRA Run Selector

2.

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

PubMed Full text in PMC Similar studies SRA Run Selector

3.

Single-cell RNA-seq data of Arabidopsis root

(Submitter supplied) We report both raw and processed scRNA-seq data that are used to build transcriptomic atlas of Arabidopsis root.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing; Third-party reanalysis
Platform:
GPL26208
19 Samples
Download data: RDS, TAR
Series
Accession:
GSE152766
ID:
200152766

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4.

ImmGen ULI: Systemwide RNA-seq profiles (#1)

(Submitter supplied) Primary RNAseq data for 127 highly purified immunocyte populations representing all lineages and several differentiation cascades, profiled using the ImmGen ULI pipeline.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
274 Samples
Download data: CSV, TSV, TXT
Series
Accession:
GSE109125
ID:
200109125

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5.

ImmGen ATAC-seq data

(Submitter supplied) Immunological Genome Project chromatin accessibility maps for 86 different immunocytes (ATAC-seq). Immune cell populations were isolated in high-purity by flow cytometry.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
185 Samples
Download data: BW
Series
Accession:
GSE100738
ID:
200100738

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6.

Mapping and dynamics of regulatory DNA in A. thaliana tissues and cell types across developmental transitions

(Submitter supplied) We performed DNase-seq on root tissue, root epidermal cell types, seed coat epidermal cells at two developmental stages, and open and closed flowers.
Organism:
Arabidopsis thaliana
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13222
17 Samples
Download data: BED, BW, TXT
Series
Accession:
GSE53324
ID:
200053324

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7.

Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana

(Submitter supplied) We mapped DNaseI hypersensitive sites (DHSs) and applied genomic footprinting to define in vivo transcription factor (TF) occupancy at nucleotide resolution across the A. thaliana genome in whole seedlings during heat- and light-response states. We find that trait-associated variation localizes within DHSs, and that extensive TF occupancy within protein-coding exons has shaped A. thaliana codon usage. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13222
20 Samples
Download data: BW, TXT
Series
Accession:
GSE53322
ID:
200053322

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8.

Coupled single-cell CRISPR screening and epigenomic profiling reveals causal gene regulatory networks

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL18573 GPL15520
8711 Samples
Download data
Series
Accession:
GSE116297
ID:
200116297

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9.

Coupled single-cell epigenome editing and profiling reveals causal gene regulatory networks [Perturb-ATAC (GBC/sgRNA)]

(Submitter supplied) Here we present Perturb-ATAC, a method which combines multiplexed CRISPR interference or knockout with genome-wide chromatin accessibility profiling in single cells, based on the simultaneous detection of CRISPR guide RNAs and open chromatin sites by Assay of Transposase-accessible Chromatin with sequencing (ATAC-seq). We applied Perturb-ATAC to transcription factors (TFs), chromatin-modifying factors, and noncoding RNAs (ncRNAs) in ~3,700 single cells, encompassing more than 75 unique genotype-phenotype relationships.
Organism:
Homo sapiens
Type:
Other
Platform:
GPL15520
4208 Samples
Download data: TXT
Series
Accession:
GSE116285
ID:
200116285

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10.

Coupled single-cell epigenome editing and profiling reveals causal gene regulatory networks [Perturb-ATAC (ATAC)]

(Submitter supplied) Here we present Perturb-ATAC, a method which combines multiplexed CRISPR interference or knockout with genome-wide chromatin accessibility profiling in single cells, based on the simultaneous detection of CRISPR guide RNAs and open chromatin sites by Assay of Transposase-accessible Chromatin with sequencing (ATAC-seq). We applied Perturb-ATAC to transcription factors (TFs), chromatin-modifying factors, and noncoding RNAs (ncRNAs) in ~3,700 single cells, encompassing more than 75 unique genotype-phenotype relationships.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL15520 GPL18573
4207 Samples
Download data: TXT
Series
Accession:
GSE116249
ID:
200116249

PubMed Full text in PMC Similar studies

11.

Coupled single-cell epigenome editing and profiling reveals causal gene regulatory networks [scATAC-seq]

(Submitter supplied) Here we present Perturb-ATAC, a method which combines multiplexed CRISPR interference or knockout with genome-wide chromatin accessibility profiling in single cells, based on the simultaneous detection of CRISPR guide RNAs and open chromatin sites by Assay of Transposase-accessible Chromatin with sequencing (ATAC-seq). We applied Perturb-ATAC to transcription factors (TFs), chromatin-modifying factors, and noncoding RNAs (ncRNAs) in ~3,700 single cells, encompassing more than 75 unique genotype-phenotype relationships.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
288 Samples
Download data: TXT
Series
Accession:
GSE116248
ID:
200116248

PubMed Full text in PMC Similar studies

12.

Coupled single-cell epigenome editing and profiling reveals causal gene regulatory networks [Bulk ATAC-seq]

(Submitter supplied) Here we present Perturb-ATAC, a method which combines multiplexed CRISPR interference or knockout with genome-wide chromatin accessibility profiling in single cells, based on the simultaneous detection of CRISPR guide RNAs and open chromatin sites by Assay of Transposase-accessible Chromatin with sequencing (ATAC-seq). We applied Perturb-ATAC to transcription factors (TFs), chromatin-modifying factors, and noncoding RNAs (ncRNAs) in ~3,700 single cells, encompassing more than 75 unique genotype-phenotype relationships.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
8 Samples
Download data: TXT
Series
Accession:
GSE116247
ID:
200116247

PubMed Full text in PMC Similar studies

13.

Enhancer connectome in primary human cells reveals target genes of disease-associated DNA elements

(Submitter supplied) The imprecision of linking intergenic mutations to target genes has limited molecular understanding of diverse human diseases. Here, we show H3K27ac HiChIP generates high-resolution contact maps of active enhancers and target genes in rare primary human T cell subtypes and coronary artery smooth muscle cells. Differentiation of naïve T cells to either T helper 17 cells or regulatory T cells create subtype-specific enhancer-promoter interactions, specifically at regions of shared DNA accessibility. more...
Organism:
Homo sapiens; Mus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL18573 GPL23787 GPL20301
58 Samples
Download data: BED, TXT
Series
Accession:
GSE101498
ID:
200101498

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14.

ConnecTF: A platform to integrate validated transcription factor-target interactions to build and refine gene regulatory networks

(Submitter supplied) The direct targets of 16 TFs were identified using the TARGET system. Arabidopsis plants were grown on 1/2X MS media and after 10 days protoplasts were generated from root tissue, Cells were transfected with a vector containing the GR-TF fusion and incubated overnight. Each experiment also included a GR-only empty vector control. In the morning, samples were pre-treated with cycloheximide for 20 minutes, before TF entry into the nucleus was induced with dexamethasone. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19580
56 Samples
Download data: CSV
Series
Accession:
GSE152405
ID:
200152405

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15.

ATAC-seq profiling of open chromatin in the root tips of four plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) and two Arabidopsis thaliana cell types (root hair and non-hair epidermal cells)

(Submitter supplied) The transcriptional regulatory structure of plant genomes remains poorly defined relative to that of animals. It has been unclear how many cis-regulatory elements generally exist in plant genomes, where these elements lie in relation to their target promoters, and how these features are conserved across species. We employed the Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) in four different plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome. more...
Organism:
Arabidopsis thaliana; Solanum lycopersicum; Oryza sativa; Medicago truncatula
Type:
Genome binding/occupancy profiling by high throughput sequencing
5 related Platforms
15 Samples
Download data: BED
Series
Accession:
GSE101482
ID:
200101482

PubMed Full text in PMC Similar studies SRA Run Selector

16.

Fine scale time-series RNA-Seq of shoot and root responses to Nitrogen supply

(Submitter supplied) Arabidopsis plants grown in a hydroponic media with sufficient Nitrogen were given a 60mM supply of Nitrogen. Triplicate sets of plants were sampled at time points 0,5,10,15,20,30,45,60,90 and 120 minutes after supply from treated and control plants (20mM KCl). The samples were flash frozen in liquid N and used to construct RNA-Seq libraries to assay transcriptional changes in the shoots and roots, separately, in response to Nitrogen.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13222
114 Samples
Download data: TXT
Series
Accession:
GSE97500
ID:
200097500

PubMed Full text in PMC Similar studies SRA Run Selector

17.

Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [plasmid libraries subassembly, v2]

(Submitter supplied) The inability to scalably and precisely measure the activity of developmental enhancers in multicellular systems is a bottleneck in genomics. Here, we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. more...
Organism:
Escherichia coli
Type:
Other
Platforms:
GPL32081 GPL21222 GPL28771
42 Samples
Download data: TXT
Series
Accession:
GSE245260
ID:
200245260

PubMed Full text in PMC Similar studies

18.

Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [bulkMPRA(promoters, cells v2)]

(Submitter supplied) The inability to scalably and precisely measure the activity of developmental enhancers in multicellular systems is a bottleneck in genomics. Here, we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30173
48 Samples
Download data: TXT
Series
Accession:
GSE245191
ID:
200245191

PubMed Full text in PMC Similar studies

19.

Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [bulkMPRA (devCRE, mEB, v2)]

(Submitter supplied) The inability to scalably and precisely measure the activity of developmental enhancers in multicellular systems is a bottleneck in genomics. Here, we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30172
120 Samples
Download data: TXT
Series
Accession:
GSE245190
ID:
200245190

PubMed Full text in PMC Similar studies

20.

Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [scQer_mEB, v2)]

(Submitter supplied) The inability to scalably and precisely measure the activity of developmental enhancers in multicellular systems is a bottleneck in genomics. Here, we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL19057 GPL30172
12 Samples
Download data: RDS, TXT
Series
Accession:
GSE245189
ID:
200245189

PubMed Full text in PMC Similar studies

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