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Links from GEO DataSets

Items: 20

1.

In vitro, genomic context identification of transcription factor binding sites

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Zea mays; Arabidopsis thaliana
Type:
Other; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL17628 GPL17639
941 Samples
Download data: NARROWPEAK
Series
Accession:
GSE60143
ID:
200060143

PubMed Full text in PMC Similar studies

2.

The DNA affinity purification DAP-Seq assay [ChIP-seq]

(Submitter supplied) As 5-15% of higher eukaryotes genes are transcription factors (TFs), the lack of transcription factor binding site (TFBS) information for most factors in most organisms limits the study of gene regulation. Here we describe a next-generation sequencing method, DNA affinity purification (DAP-Seq), an in vitro gDNA/TF interaction assay that produces whole-genome TFBS annotation for any factor from any organism. more...
Organism:
Arabidopsis thaliana
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17639
6 Samples
Download data: NARROWPEAK
Series
Accession:
GSE60142
ID:
200060142

PubMed Full text in PMC Similar studies SRA Run Selector

3.

A Comprehensive Atlas of Arabidopsis Regulatory DNA [DAP-seq]

(Submitter supplied) We have developed a high throughput, next-generation DNA sequencing assay for rapid transcription factor binding site (TFBS) discovery in a genomic context. DNA affinity purification sequencing (DAP-seq), which uses affinity-purified transcription factors (TFs) to capture genomic DNA fragments, was applied to all 1,725 Arabidopsis thaliana TFs. High confidence TFBS motifs for 529 TFs and genome-wide enrichment maps for 349 factors were identified. more...
Organism:
Zea mays; Arabidopsis thaliana
Type:
Other
Platforms:
GPL17639 GPL17628
936 Samples
Download data: NARROWPEAK
Series
Accession:
GSE60141
ID:
200060141

PubMed Full text in PMC Similar studies SRA Run Selector

4.

Identification of genes regulated by the MADS transcription factor (TF), SEPALLATA3, in the context of the double sep1sep2 and triple sep1sep2sep3 mutant background, by RNA-Seq analysis

(Submitter supplied) These analyses allowed the identification of more than 2000 genes regulated by the MADS TF, SEPALLATA3 (SEP3). Although the involvement of SEP3 in all flower organ development is well established, the single sep3 mutant shows no flower phenotype, due to redundancy with other SEPALLATA genes. The triple mutant, sep1sep2sep3, shows no floral organ development except sepals, while the sep1sep2 mutant showed characteristic WT flower with, from the outer to the inner whorl of the flower, 4 sepals, 4 petals, 6 stamens and one gynoecium. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21785
6 Samples
Download data: TXT
Series
Accession:
GSE150605
ID:
200150605

PubMed Full text in PMC Similar studies SRA Run Selector

5.

Genome-wide binding of SEPALLATA3 (SEP3) and AGAMOUS (AG) complexes determined by sequential DNA-affinity purification sequencing

(Submitter supplied) In this study, we compare the DNA binding specifify and affinity of SEPALLATA3 and AGAMOUS complexes The MADS transcription factors, SEPALLATA3 (SEP3) and AGAMOUS (AG), are required for floral organ identity and determinacy of the floral meristem in Arabidopsis. Dimerization is obligatory for their DNA binding, however SEP3 and SEP3-AG also form tetrameric complexes. The goal of this study is to understand how homo and hetero-dimerization and tetramerization of MADS TFs affect genome-wide DNA-binding patterns. more...
Organism:
Arabidopsis thaliana
Type:
Other
Platform:
GPL17970
10 Samples
Download data: BEDGRAPH, NARROWPEAK
Series
Accession:
GSE150528
ID:
200150528

PubMed Full text in PMC Similar studies SRA Run Selector

6.

In vitro, genomic context identification of transcription factor binding sites for bZIP C/S1 homodimers and heterodimers

(Submitter supplied) In eukaryotes, many transcription factors (TF) usually form dimers or oligomers with itself or other TFs to regulate gene expression. To study how homo- and heterodimerization of TFs affect DNA binding specificity, we developed a double DNA Affinity Purification sequencing (double DAP-seq; dDAP-seq) technique that maps heterodimer binding sites in endogenous genome context and applied it to elucidate the binding profiles of homo- and heterodimers of the Group C and S1 basic leucine zipper (bZIP) transcription factors in Arabidopsis. more...
Organism:
Arabidopsis thaliana
Type:
Other
Platform:
GPL19580
86 Samples
Download data: NARROWPEAK
Series
Accession:
GSE198873
ID:
200198873

PubMed Full text in PMC Similar studies

7.

Epigenomic and genome structural diversity in a worldwide collection of Arabidopsis thaliana

(Submitter supplied) Epigenetic variation can impact gene transcription and may play roles in phenotypic diversity and adaptation. Here we report 1,107 high quality single-base resolution methylomes, and 1,210 transcriptomes from the 1001 Arabidopsis Genomes population. Analyses reveal strong effects of geographic origin on average DNA methylation levels, alterations of gene expression by epialleles and a highly complex genetic basis for DNA methylation. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL17639 GPL21785
728 Samples
Download data: TSV, TXT
Series
Accession:
GSE80744
ID:
200080744

PubMed Full text in PMC Similar studies SRA Run Selector

8.

Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (Methyl-Seq)

(Submitter supplied) Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to phenotypic diversity, its interaction with genetic variation requires further investigation.
Organism:
Arabidopsis thaliana
Type:
Methylation profiling by high throughput sequencing
Platforms:
GPL17639 GPL11221
927 Samples
Download data: TSV
Series
Accession:
GSE43857
ID:
200043857

PubMed Full text in PMC Similar studies SRA Run Selector

9.

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(Submitter supplied) The DNA sequence preferences of the vast majority of eukaryotic transcription factors (TFs) are unknown. Using an approach designed to broadly sample both DNA-binding domain types and eukaryotic clades, we have determined DNA-binding motifs for 1,033 TFs from 131 diverse eukaryotes, encompassing 54 domain types. Closely related orthologs and paralogs typically have very similar sequence preferences; this property allows inference of motifs for roughly one third of the 166,851 known or predicted eukaryotic TFs. more...
Organism:
synthetic construct
Type:
Other
Platform:
GPL11260
2064 Samples
Download data: TXT
Series
Accession:
GSE53348
ID:
200053348

PubMed Full text in PMC Similar studies Analyze with GEO2R

10.

Mature Arabidopsis leaves: RAP2.6L overexpressing vs wild-type (Ws)

(Submitter supplied) Transcriptional profiling of Arabidopsis thaliana, comparing control wild-type (ecotype Wassilewskija, Ws) leaves with leaves from transgenic plants overexpressing the transcription factor RAP2.6L under control of the cauliflower mosaic virus 35S promoter (RAP2.6L-OX; this line was originally described in Krishnaswamy et al (2010)).
Organism:
Arabidopsis thaliana
Type:
Expression profiling by array
Platform:
GPL16132
6 Samples
Download data: TXT
Series
Accession:
GSE90601
ID:
200090601

PubMed Full text in PMC Similar studies Analyze with GEO2R

11.

ChIP-Seq and RNA-Seq of abscisic acid-reponsive transcription factors

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17639
165 Samples
Download data: BED
Series
Accession:
GSE80568
ID:
200080568

PubMed Full text in PMC Similar studies

12.

RNA-seq of abscisic acid-reponsive transcription factors [DIG]

(Submitter supplied) Abscisic acid (ABA) is an essential hormone that allows plants to respond to environmental stresses such as high salinity, drought and cold. It also plays a pivotal role in seed maturation and germination. Because of its importance, transcriptome changes in response to ABA have been profiled extensively by the plant community. Very few ChIP-chip/seq of ABA-related TFs have been reported to date. To fill the knowledge gap about how ABA works at the transcriptional level, we carried out ChIP-seq on 21 TFs from 11 different families using both mock- and ABA-treated conditions. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17639
10 Samples
Download data: TXT
Series
Accession:
GSE80567
ID:
200080567

PubMed Full text in PMC Similar studies SRA Run Selector

13.

ChIP-seq of abscisic acid-reponsive transcription factors [DIG]

(Submitter supplied) Abscisic acid (ABA) is an essential hormone that allows plants to respond to environmental stresses such as high salinity, drought and cold. It also plays a pivotal role in seed maturation and germination. Because of its importance, transcriptome changes in response to ABA have been profiled extensively by the plant community. Very few ChIP-chip/seq of ABA-related TFs have been reported to date. To fill the knowledge gap about how ABA works at the transcriptional level, we carried out ChIP-seq on 21 TFs from 11 different families using both mock- and ABA-treated conditions. more...
Organism:
Arabidopsis thaliana
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17639
3 Samples
Download data: BED
Series
Accession:
GSE80566
ID:
200080566

PubMed Full text in PMC Similar studies SRA Run Selector

14.

RNA-seq of abscisic acid-reponsive transcription factors

(Submitter supplied) Abscisic acid (ABA) is an essential hormone that allows plants to respond to environmental stresses such as high salinity, drought and cold. It also plays a pivotal role in seed maturation and germination. Because of its importance, transcriptome changes in response to ABA have been profiled extensively by the plant community. Very few ChIP-chip/seq of ABA-related TFs have been reported to date. To fill the knowledge gap about how ABA works at the transcriptional level, we carried out ChIP-seq on 21 TFs from 11 different families using both mock- and ABA-treated conditions. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17639
28 Samples
Download data: TXT
Series
Accession:
GSE80565
ID:
200080565

PubMed Full text in PMC Similar studies SRA Run Selector

15.

ChIP-seq of abscisic acid-reponsive transcription factors

(Submitter supplied) Abscisic acid (ABA) is an essential hormone that allows plants to respond to environmental stresses such as high salinity, drought and cold. It also plays a pivotal role in seed maturation and germination. Because of its importance, transcriptome changes in response to ABA have been profiled extensively by the plant community. Very few ChIP-chip/seq of ABA-related TFs have been reported to date. To fill the knowledge gap about how ABA works at the transcriptional level, we carried out ChIP-seq on 21 TFs from 11 different families using both mock- and ABA-treated conditions. more...
Organism:
Arabidopsis thaliana
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17639
124 Samples
Download data: BED
Series
Accession:
GSE80564
ID:
200080564

PubMed Full text in PMC Similar studies SRA Run Selector

16.

Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17639
6 Samples
Download data: BED, NARROWPEAK
Series
Accession:
GSE122772
ID:
200122772

PubMed Full text in PMC Similar studies

17.

ATAC-seq on 14-d-old WT col-0 Arabidopsis thaliana roots carrying INTACT

(Submitter supplied) Background: There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is the binding of transcription factors to specific DNA sequence motifs across the genome. more...
Organism:
Arabidopsis thaliana
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17639
3 Samples
Download data: BED, NARROWPEAK
Series
Accession:
GSE122771
ID:
200122771

PubMed Full text in PMC Similar studies SRA Run Selector

18.

RNA-seq from roots of 14 day old col-0 Arabidopsis thaliana carrying INTACT

(Submitter supplied) Background: There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is the binding of transcription factors to specific DNA sequence motifs across the genome. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17639
3 Samples
Download data: TXT
Series
Accession:
GSE122770
ID:
200122770

PubMed Full text in PMC Similar studies SRA Run Selector

19.

ChIP-seq for Polycomb repressive complex 2 in wild type and mutants in Arabidopsis

(Submitter supplied) We performed ChIP-seq for the Polycomb protein FIE using anti-FIE antiserum in germinated wild-type and double class I BPC and C1-2iD transcruption factor family knockdown seedlings of Arabidopsis thaliana.
Organism:
Arabidopsis thaliana
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19580
9 Samples
Download data: BED, BW
Series
Accession:
GSE95562
ID:
200095562

PubMed Similar studies SRA Run Selector

20.

ChIP-seq for Polycomb and associated transcription factors in Arabidopsis

(Submitter supplied) We performed ChIP-seq for H3K27me3, the Polycomb protein FIE, and two associated transcription factor (AZF1 and BPC1) using epitope tags expressed in germinated seedlings of Arabidopsis thaliana.
Organism:
Arabidopsis thaliana
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19580
21 Samples
Download data: BED, BW
Series
Accession:
GSE84483
ID:
200084483

PubMed Similar studies SRA Run Selector

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