GEO DataSets

(Submitter supplied) Transcription factors (TF) binding is key to understanding and characterizing the effect of genetic variability on phenotypic differences. Here, we used a novel scalable ChIP-seq approach to annotate the regulatory landscape of the maize genome with binding data from 104 leaf TFs. TF binding regions co-localized with open chromatin regions, with ~70% of TF binding nearby genes. TF binding sites are evolutionarily conserved and show enrichment for GWAS-hits, cis-expression QTLs. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25842

217 Samples

Download data: BW, TXT

(Submitter supplied) Opaque11 (O11) is a bHLH transcription factor that plays important roles in maize endosperm development, nutrient metabolism, and stress response.

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17628

4 Samples

Download data: BED, TXT

(Submitter supplied) Analysis of gene expression level. The hypothesis tested in the present study was that o11 mutant affects nutrient metabolism and stress response.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17628

6 Samples

Download data: TXT

(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

(Submitter supplied) To invesigate the physiology roles of mir-122 in liver, we performed expression profiling of mir-122 knockout mice and the control B6/129 mice.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

7 Samples

Download data: CEL, CHP

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

Organism:

Zea mays

Type:

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

Platform:

GPL20156

21 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) DAP-seq was used to generate genome-wide DNA:TF interaction maps for fourteen maize ARFs from the evolutionarily conserved class A ‘activator’ and class B ‘repressor’ clades. Among the distinct binding sites that were identified, we observed a high degree of overlap for ARFs of the same class, but found substantial differences in motif sequence, spacing, site preference, and association with auxin induced genes among clade A and clade B ARFs.

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20156

15 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) DAP-seq was used to generate genome-wide DNA:TF interaction maps for fourteen maize ARFs from the evolutionarily conserved class A ‘activator’ and class B ‘repressor’ clades. Among the distinct binding sites that were identified, we observed a high degree of overlap for ARFs of the same class, but found substantial differences in motif sequence, spacing, site preference, and association with auxin induced genes among clade A and clade B ARFs.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20156

6 Samples

Download data: TXT

(Submitter supplied) Analysis of gene expression level. The hypothesis tested in the present study was that zmbzip22 mutant affects nutrient metabolism and stress response.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17628

6 Samples

Download data: XLSX

(Submitter supplied) A new factor binds to the 27-kD γ-zein gene promoter was identified through probe affinity purification and mass spectrometry analysis. This new factor belongs to bZIP type TF (hence named as ZmbZIP22). Chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq) analysis with two biological replicates was performed to determine the DNA binding targets of ZmbZIP22. ChIP-Seq analysis detected 1,550 DNA binding sites distributed over 514 genes. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17628

4 Samples

Download data: BED, TXT

(Submitter supplied) Opaque2 (O2) is a transcription factor that plays important roles during maize endosperm development. Mutation of the O2 gene improves the nutritional value of maize seeds, but also confers pleiotropic effects that result in reduced agronomic quality. To reveal the transcriptional regulatory framework of O2, we determined O2 DNA binding targets using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq). more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15463

2 Samples

Download data: BED, TXT

(Submitter supplied) Analysis of gene expression level. The hypothesis tested in the present study was that opaque2 mutant influence the expression of storage proteins. Results provide important information of the gene expression level regulation of storage proteins and other biological processes.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17628

2 Samples

Download data: TXT

(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:

Arabidopsis thaliana; Zea mays

Type:

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

Platforms:

GPL26208 GPL25410

14 Samples

Download data: TXT

(Submitter supplied) We report the ER alpha regulatory network of Tamoxifen resistance MCF7 cell line using the Chromatin immunoprecipitated high-throughput sequencing technology (ChIP-seq). By Integrating the gene expression data (previously reported) with the ChIP-seq data, we generated ER alpha regulatory network and pathways. For ER alpha regulatory network, hub TFs with enriched motifs were identified from ER alpha peak together with PolII peaks. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9052

4 Samples

Download data: BED

(Submitter supplied) We report the development of a deep learning-based tool, DeepTFactor, that predicts whether a protein of question is a transcription factor. DeepTFactor uses a convolutional neural network to extract features of protein sequences. We characterized the genome-wide binding sites of three TFs (i.e., YqhC, YiaU, and YahB), which are predicted by DeepTFactor

Organism:

Escherichia coli

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18133

6 Samples

Download data: GFF