GEO DataSets

(Submitter supplied) In plants, the plant-specific RNA polymerase V (Pol V) transcripts non-coding RNA and provides a docking platform for the association of accessory proteins in the RNA-directed DNA methylation (RdDM) pathway. Various components were uncovered in the process of DNA methylation, but it is still not clear how the transcription of Pol V is regulated. Here, we found the conserved elongation factor, SPT6L, bound to thousands of intergenic regions in an RNA polymerase II (Pol II) independent manner. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other; Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL26208

41 Samples

Download data: BW

(Submitter supplied) To understand the combined role of SL and KAR signaling pathways in regulating levels and metabolism of other plant hormones, we performed the compare transcriptome profiling d14 kai2 and WT plants. Aligent´s whole Arabidopsis Gene Expression Microarray (G2519F-021169, V4, 4x44K) was used.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL9020

6 Samples

Download data: TXT

(Submitter supplied) Here, we reported transcriptome-wide m6A modification maps within single-base resolution using m6A-SAC-seq in rice and Arabidopsis. Our analysis uncovered a total of 205,691 m6A sites distributed across 22,574 genes in rice, and 188,282 m6A sites across 19,984 genes in Arabidopsis.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL26208

44 Samples

Download data: TSV

(Submitter supplied) Purpose: To understand the molecular mechanism between PNET2 and NTLs, we generated 35S:NTL-SRDX in pnet2_ab mutants to suppress NTL gene expression and performed the whole genome transcriptome analysis on 4-week-old plants of WT, pnet2_ab, 35S:NTL6-SRDX pnet2_ab, 35S:NTL9-SRDX pnet2_ab, and 35S:NTL12-SRDX pnet2_ab. Conclusions: PNET2 regulates diverse responses by associating with a family of membrane-bound transcriptional factors.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

10 Samples

Download data: TXT

(Submitter supplied) We investigated the root growth of several knockout mutants of heat shock protein family genes and found that heat stress response was compromised in these mutants compared to wild type plants. It suggested that heat shock protein genes including heat shock protein genes including HSP17s, HSP23s, HSP101, and HSFA2 proteins are deployed upon exposure to Cs for plant stress tolerance. Our study provided novel insights into the molecular events occurring in Cs-stressed plants.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

6 Samples

Download data: TXT

(Submitter supplied) TREX (transcription and export) is a multi-subunit complex that links synthesis, processing and export of mRNAs. It interacts with the RNA helicase UAP56 and export factors such as MOS11 and ALYs to facilitate nucleocytosolic transport of mRNAs. Plant MOS11 is a conserved, but sparsely researched RNA-binding export factor, related to yeast Tho1 and metazoan CIP29/SARNP. Using biochemical approaches, the domains of MOS11 required for interaction with UAP56 and RNA-binding were identified. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30821

28 Samples

Download data: TSV

(Submitter supplied) VND1 is a member of NAC-type family transcription factors and has a important role in xylem differentiation. However, how VND1 regulates vascular differentiation is not well known. Here, we identified specific genes downstream of VND1 with transformed suspension culture cells in microarray experiments.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL17416

6 Samples

Download data: CEL, CHP

(Submitter supplied) This study investigates the multifaceted defense mechanisms of plants in response to beneficial fungi Trichoderma atroviride. The researchers focus on a small RNA, Ta_sRNA1, produced by T. atroviride during its interaction with Arabidopsis thaliana.

Organism:

Arabidopsis thaliana; Trichoderma atroviride

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL17970 GPL34134

10 Samples

Download data: TSV

(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:

GPL19580

22 Samples

Download data: BEDGRAPH, CSV

(Submitter supplied) Plants respond to environmental challenges via a network of signalling pathways. Early responses prevent damage if the stress persists but delay growth in fluctuating conditions. Optimizing these trade-offs requires tunability of plant responsiveness to environmental signals. We have previously shown that Histone Deacetylation Complex 1 (HDC1), which interacts with multiple proteins in histone deacetylation complexes, regulates the sensitivity of Arabidopsis seedlings to salt and ABA, but the underlying mechanism remained elusive. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19580

4 Samples

Download data: BEDGRAPH

(Submitter supplied) Plants respond to environmental challenges via a network of signalling pathways. Early responses prevent damage if the stress persists but delay growth in fluctuating conditions. Optimizing these trade-offs requires tunability of plant responsiveness to environmental signals. We have previously shown that Histone Deacetylation Complex 1 (HDC1), which interacts with multiple proteins in histone deacetylation complexes, regulates the sensitivity of Arabidopsis seedlings to salt and ABA, but the underlying mechanism remained elusive. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19580

18 Samples

Download data: CSV

(Submitter supplied) We analyzed transcriptome changes from germinating cyp79B2 cyp79B3, qko, and pad3 mutant Arabidopsis seeds. Here were used mutant lines in Col-0 genetic background: a cyp79B2 cyp79B3 double mutant defective in indolic glucosinolate (cyp79B2/B3), a cyp79B2 cyp79B3 myb28 myb29 quadruple mutant defective in indolic and aliphatic glucosinolates (qko), and a camalexin deficient mutant (pad3). Differentially expressed genes were identified at 3, 6 and 10 days after sowing from both the mutant line seeds and from Alternaria brassicicola when inoculated seeds were analyzed.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28290

42 Samples

Download data: CSV

(Submitter supplied) In plants, the genomic structure of hybrids changed compared with their parents. However, the effects of genomic structure changes on heterotic expression in hybrids remain elusive. By comparing interspecific hybrids between Col×C24 and their backcross C24×Col in Arabidopsis with Hi-C analysis, we found that the three-dimensional (3D) chromatin organization had more long-distance interactions relative to parents. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

12 Samples

Download data: TXT

(Submitter supplied) In plants, the genomic structure of hybrids changed compared with their parents. However, the effects of genomic structure changes on heterotic expression in hybrids remain elusive. By comparing interspecific hybrids between Col×C24 and their backcross C24×Col in Arabidopsis with Hi-C analysis, we found that the three-dimensional (3D) chromatin organization had more long-distance interactions relative to parents. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

12 Samples

Download data: TXT

(Submitter supplied) The endosperm is a reproductive tissue supporting embryo development. In most 30 flowering plants, the initial divisions of endosperm nuclei are not succeeded by 31 cellularization; this process occurs only after a specific number of mitotic cycles have 32 taken place. The timing of cellularization significantly influences seed viability and size. 33 Previous research implicated auxin as a key factor in initiating nuclear divisions and 34 determining the timing of cellularization. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

17 Samples

Download data: TXT

(Submitter supplied) Several fungi have been reported to form intimate bonds with plants. These close mutual relationships can provide physiological benefits to the interacting organisms, including the improvement of nutrient assimilation or enhanced stress tolerance. The root-colonizing fungus Fusarium sp. strain K-23 is known to successfully colonize tomato roots. Previous studies highlighted the promotion of plant biomass production and stress tolerance of tomato plants infected with the K-23. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

24 Samples

Download data: TXT

(Submitter supplied) To investigate the function of CPL2 in flowering time control, we collected 9-day-old wild type and cpl2-2 seedlings to perform RNA-seq.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

6 Samples

Download data: TXT

(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

Platforms:

GPL26208 GPL23157

27 Samples

Download data: BROADPEAK, BW

(Submitter supplied) When exposed to low temperatures, plants undergo a drastic reprogramming of their transcriptome in order to adapt to their new environmental conditions, which primes them for potential freezing temperatures. While the involvement of transcription factors in this process, termed cold acclimation, has been deeply investigated, the potential contribution of chromatin regulation remains unelucidated. A large proportion of cold-inducible genes carries the repressive mark histone 3 lysine 27 trimethylation (H3K27me3), which has been hypothesized as maintaining them in a silenced state in the absence of stress, but which would need to be removed or counteracted upon stress perception. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23157

18 Samples

Download data: BROADPEAK, BW

(Submitter supplied) When exposed to low temperatures, plants undergo a drastic reprogramming of their transcriptome in order to adapt to their new environmental conditions, which primes them for potential freezing temperatures. While the involvement of transcription factors in this process, termed cold acclimation, has been deeply investigated, the potential contribution of chromatin regulation remains unelucidated. A large proportion of cold-inducible genes carries the repressive mark histone 3 lysine 27 trimethylation (H3K27me3), which has been hypothesized as maintaining them in a silenced state in the absence of stress, but which would need to be removed or counteracted upon stress perception. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

9 Samples

Download data: TXT