GEO DataSets

(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) 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) Aims to look at the targets of the bHLH transcription factor in Arabidopsis roots.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL

(Submitter supplied) Root hairs are an extensive structure of root epidermal cells and are critical for nutrient acquisition, soil anchorage, and environ- mental interactions in sessile plants. The phytohormone ethylene (ET) promotes root hair growth and also mediates the effects of different signals that stimulate hair cell development. However, the molecular basis of ET-induced root hair growth remains poorly understood. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

16 Samples

Download data: XLS

(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) In addition to apical growth, plants undergo radial growth to increase girth, a particularly prominent feature in trees. During both apical and radial growth the phytohormones auxin and cytokinins form symmetries that govern further growth patterns. But whereas the gene regulatory networks interpreting the hormonal fields during apical growth are well established, such networks are not known for the radial growth. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL17133

25 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 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) PMID: 15539473. We compared the gene expression in roots between WT and fit mutant under +Fe and -Fe conditions using ATH1 microarray analysis to explore which genes are affected by the loss of FIT function.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

8 Samples

Download data: CEL

(Submitter supplied) The Oscillation Zone (OZ) of unsynchronized roots was disected and divided into an upper (OZ2) and lower (OZ1) half . Samples were ordered according to DR5:GUS expression as analyzed by real time PCR to find periodic expression patterns

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

39 Samples

Download data: CEL, CHP, EXP

(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) We report the transcriptome composition of gtl1-2 compared to Columbia wild-type plant without treatment and after flg22-application

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21785

10 Samples

Download data: TXT

(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) Iron-deficiency repsonses in Arabidopsis are controlled by several bHLH transcription factors. FIT, for example has been shown to direct iron-uptake responses. However, the role of shoot and root expressed genes bHLH100 and bHLH101 has not be clarified. We used microarray to study what genes might be miss-regulated in the double mutant bhlh100/bhlh101 background

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

24 Samples

Download data: CEL, TXT

(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) Purpose: Investigate transcriptional changes by genetic perturbation of specific transcription factors under sufficient and limiting nitrate conditions. Methods: 9 day old roots were harvested between 1-2pm (get hours after “sunrise”) and frozen in liquid N2. RNA-seq libraries were prepared following the BRAD-Seq DGE protocol (four biological replicates per genotype and treatment). Libraries were sequenced using the Ilummina HiSeq 3000 in SR50 mode. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21179

208 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10977 GPL198

7 Samples

Download data: BAR, BED, CEL, TXT

(Submitter supplied) To understand how GTL1 regulates cell growth, we first identified its potential direct targets by the chromatin immunoprecipitation followed by the hybridization on an Affymetrix Arabidopsis Tiling 1.0R array (ChIP-chip). To enrich the genomic region bound by GTL1 in vivo, we harvested whole aerial parts of 12-day-old gtl1-1 plants complemented with the pGTL:GTL1:GFP constructs and immunoprecipitated the chromatin fragments associated with GTL1-GFP proteins using antibodies against GFP. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10977

1 Sample

Download data: BAR, BED, CEL, TXT

(Submitter supplied) Total RNA from trichomes of fifth and sixth rosette leaves of three-week-old wild-type and gtl1-1 mutants (Figure 3B) were extracted. We found a total number of 1,759 genes, corresponding to 1,694 probes on the ATH1 chip, that show differential expression of at least 1.3-fold. Out of these 1,694 genes, 47.2% are positively regulated and 52.8% are negatively regulated by GTL1.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL

(Submitter supplied) The Arabidopsis thaliana root epidermis is comprised of two cell types, hair and nonhair cells, which differentiate from the same precursor. Although the transcriptional programs regulating these events are well studied, post-transcriptional factors functioning in this cell fate decision are mostly unknown. Here, we globally identify RNA-protein interactions and RNA secondary structure in hair and nonhair cell nuclei. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

16 Samples

Download data: BED, TXT

(Submitter supplied) The final size and arrangement of the plant vasculature requires precise adjustment of cell proliferation. In particular, radial growth of vascular bundles is to a large extent controlled by a bHLH transcription factor heterodimer formed by TARGET OF MONOPTEROS5 (TMO5) and LONESOME HIGHWAY (LHW). Excess activity of this TMO5/LHW dimer causes excessive proliferation of vascular cell divisions and thus suggests the existence of a molecular mechanism that restricts its activity in space and time. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL9020

12 Samples

Download data: TXT