GEO DataSets

(Submitter supplied) The root epidermis of Arabidopsis provides a simple and experimentally useful model for studying the molecular basis of cell fate and differentiation. The goal of this study was to define the larger gene regulatory network that governs the differentiation of the root hair and non-hair cell types of the Arabidopsis root epidermis. Transcript levels in the root epidermis of wild-type and mutant lines were assessed by purifying populations of root epidermal cells using fluorescence-based cell-sorting. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL13838

75 Samples

Download data: CEL

(Submitter supplied) GLABRA3 (GL3) and GLABRA1 (GL1) function as selector genes that control the differentiation of a group of protodermal cells into trichomes in Arabidopsis thaliana. We performed genome-wide location (ChIP-chip) analyses by using transgenic Arabidopsis plants carrying GL3-YFP or GL1-YFP-MYC1 mini genes. These analyses identified statistically significant enriched DNA associated with GL1 and GL3. A total ~540 and ~700 genes were identified as located proximal and downstream to the GL1 and GL3 binding regions, respectively. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10977

2 Samples

Download data: BAR, CEL

(Submitter supplied) The development of trichomes (leaf hairs) from pluripotent epidermal cells in Arabidopsis provides a powerful system to investigate the regulatory motifs involved in plant cell differentiation. Genetic studies have revealed that a bHLH transcription factor, GL3, activates downstream genes required for trichome initiation by interacting with a R2R3-MYB protein, GL1. In order to investigate genome-wide regulatory functions of GL1 and GL3, we performed genome-wide expression analyses using GR inducible systems of GL1 and GL3.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

22 Samples

Download data: CEL

(Submitter supplied) The development of trichomes (leaf hairs) from pluripotent epidermal cells in Arabidopsis provides a powerful system to investigate the regulatory motifs involved in plant cell differentiation. Genetic studies have revealed that a bHLH transcription factor, GL3, activates downstream genes required for trichome initiation by interacting with a R2R3-MYB protein, GL1. We have taken advantage of several mutants in the trichome developmental pathway and gene expression analyses to identify a set of genes expressed predominantly in Arabidopsis trichomes.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

4 Samples

Download data: CEL

(Submitter supplied) The root epidermis of Arabidopsis provides a simple and experimentally useful model for studying the molecular basis of cell fate and differentiation. The goal of this study was to define the transcript changes in the root epidermis of mutants associated with root epidermis cell specification, including mutants that lack a visible phenotypic alteration (try, egl3, myb23, and ttg2). Transcript levels were assessed by purifying populations of root epidermal cells using fluorescence-based cell-sorting with the WER::GFP transgene. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL13838

24 Samples

Download data: CEL

(Submitter supplied) We performed a chromatin immunoprecipitation-based microarray experiment (ChIP chip) in order to identify GTL1 and DF1 direct target genes

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10326

8 Samples

Download data: TXT

(Submitter supplied) How plants determine the final size of growing cells is an important, yet unanswered question. Root hairs provide an excellent model system to study this question since their final cell size is remarkably constant under given environmental conditions. In this study we demonstrate that a trihelix transcription factor GT-2-LIKE1 (GTL1) and its homolog DF1 repress root hair growth in Arabidopsis. Our transcriptional data, combined with genome-wide chromatin binding data, show that GTL1 and DF1 directly bind the RSL4 promoter and regulate its expression to repress root hair growth. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

18 Samples

Download data: CEL

(Submitter supplied) Optimal plant growth is hampered by limiting amounts of the essential macronutrient phosphate in most soils. As a response, plant roots produce root hairs to capture this immobile nutrient. Although vital to high-yielding crops, this response remains poorly understood. By generating and exploiting a high spatial and temporal resolution single cell atlas of the Arabidopsis root, we show a remarkable enrichment of TMO5/LHW target genes in root hair epidermal cells. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21785

3 Samples

Download data: H5

(Submitter supplied) We investigated root hair-specific transcriptome using RNA-seq in maize. ZmLRL5 was further identified as a key regulator of maize root hair elongation.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17628

14 Samples

Download data: TXT

(Submitter supplied) The expression levels of Arabidopsis thaliana (Col-0) genes in several developmental stages during the seed-to-seedling transition were measured by using high-density Affymetrix® arrays (Aragene.st1.1). We used a time-series of microarrays to gain temporal resolution and identify relevant genes in the seed-to-seedling transition.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL19371

21 Samples

Download data: CEL

(Submitter supplied) We report both raw and processed scRNA-seq data profiling brassinosteroid response and related mutants in Arabidopsis roots

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

30 Samples

Download data: RDS

(Submitter supplied) In plants, formation of functional stomatal guard cells is a highly regulated event so that this cell differentiation model constitutes an interesting genetic system to explore cell differentiation in response to cell cycle controllers or cell fate determinants such as transcription factors. The latest acting bHLH in the stomatal lineage circuit is FAMA that appears to be absolutely required to promote stomatal development by controlling the GMC to GC transition. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

15 Samples

Download data: CEL

(Submitter supplied) In plants, basic helix-loop-helix (bHLH) transcription factors play important roles in the control of cell elongation. Two bHLH proteins, PACLOBTRAZOL RESISTANCE1 (PRE1) and Arabidopsis ILI1 binding bHLH1 (IBH1), antagonistically regulate cell elongation in response to brassinosteroid and gibberellin signaling, but the detailed molecular mechanisms by which these factors regulate cell elongation remain unclear. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL7299

3 Samples

Download data: TXT

(Submitter supplied) Auxin-dependent transcript abundance was assayed by transferring 6 day old Arabidopsis grown on a a nylon mesh to IAA-containing or control media

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

48 Samples

Download data: CEL

(Submitter supplied) Purpose: Identify novel genes and relationships of a temporal transcriptional landscape in Arabidopsis epidermal root cells under iron deficiency stress Results: We identified 1,709 novel iron responsive genes which would have been missed had we identified DEGs with respect to the 0hr time point using the whole root or epidermis data. Conclusion: Gene set comparisons allowed us to identify organ-level response versus cell-specific and to parse out developmental from iron deficiency-induced response. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

39 Samples

Download data: CSV, XLSX

(Submitter supplied) We found that histone acetylation relays positional information and that a mutant altered in the histone deacetylase (HDAC) gene family member HDA18 exhibits altered H and N epidermal cell patterning. We then performed genome-wide location (ChIP-chip) analyses by using antibody against HDA18 in transgenic HDA18 overexpression Arabidopsis plants. These analyses identified statistically significant enriched DNA associated with HDA18. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10977

1 Sample

Download data: BED, CEL, TXT

(Submitter supplied) Transcriptional profiling of WT and rss3 root tips, grown in the presense or absense of 100 mM NaCl for 3 days.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL6864

12 Samples

Download data: TXT

(Submitter supplied) Phosphate (Pi) deficiency triggers the differential expression of a large set of genes, which communally adapt the plant to low Pi bioavailability. To infer functional modules in early transcriptional responses to Pi deficiency, we conducted time-course microarray experiments and subsequent coexpression-based clustering of Pi-responsive genes by pairwise comparison of a large number of genes against a customized data base.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Dataset:

GDS3896

Platform:

GPL198

24 Samples

Download data: CEL, TXT

Analysis of roots from plants grown in the absence of phosphate (Pi) for up to 24 hrs. Pi deficiency-induces the formation of root hairs with increased length and density. Results provide insight into molecular mechanisms involved in acclimating plants to low Pi availability.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array, transformed count, 2 growth protocol, 4 time sets

Platform:

GPL198

Series:

GSE25171

24 Samples

Download data: CEL

(Submitter supplied) Purpose: The root hair is a model for understanding evolution of individual cell differentiation programs in plants. We compare the expression of the genes that participate in root hair development between Arabidopsis and other vascular plants to assess the conservation/diversification of the root hair development programs in vascular plants. Methods: We used RNA-Seq, in triplicates, to measure the genome-wide transcription activity of the root-hair cells isolated by Fluorescence-activated cell sorting (FACS) in Arabidopsis (COBL9::GFP transgeneic line, AtRH) and rice (EXPA30::GFP transgenic line, OsRH). more...

Organism:

Arabidopsis thaliana; Solanum lycopersicum; Zea mays; Oryza sativa; Cucumis sativus; Glycine max

Type:

Expression profiling by high throughput sequencing

8 related Platforms

30 Samples

Download data: XLS, XLSX