GEO DataSets

(Submitter supplied) HB21 is a homeodomain leucine zipper transcription factor involved in the establishment of bud axillary dormancy. In this work we have characterized the role of HB21 in the control of the inflorescence arrest at the end of flowering. HB21, together with HB40 and HB53, are upregulated in the inflorescence apex at the end of the flowering phase promoting the floral bud arrest associated with the process. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

6 Samples

Download data: TSV

(Submitter supplied) To investigate the genes which relay on XBAT31 under high temperature and are induced by high temperature.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

12 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

Platform:

GPL26208

24 Samples

Download data: BW, TXT

(Submitter supplied) To investigate the functional conservation of H2A.Z histones during eukaryotic evolution we transformed h2a.z deficient plants with three human H2A.Z proteins to assess their ability to rescue the mutant defects. We discovered that human H2A.Z.1 and H2A.Z.2.1 fully complement the phenotypic abnormalities of h2a.z plants even though Arabidopsis and human H2A.Z N-terminal tail sequences are divergent, while the brain-specific splice variant H2A.Z.2.2 has a dominant-negative effect in wild-type plants. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26208

9 Samples

Download data: BW, TXT

(Submitter supplied) To investigate the functional conservation of H2A.Z histones during eukaryotic evolution we transformed h2a.z deficient plants with three human H2A.Z proteins to assess their ability to rescue the mutant defects. We discovered that human H2A.Z.1 and H2A.Z.2.1 fully complement the phenotypic abnormalities of h2a.z plants even though Arabidopsis and human H2A.Z N-terminal tail sequences are divergent, while the brain-specific splice variant H2A.Z.2.2 has a dominant-negative effect in wild-type plants. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

6 Samples

Download data: TXT

(Submitter supplied) To investigate the functional conservation of H2A.Z histones during eukaryotic evolution we transformed h2a.z deficient plants with three human H2A.Z proteins to assess their ability to rescue the mutant defects. We discovered that human H2A.Z.1 and H2A.Z.2.1 fully complement the phenotypic abnormalities of h2a.z plants even though Arabidopsis and human H2A.Z N-terminal tail sequences are divergent, while the brain-specific splice variant H2A.Z.2.2 has a dominant-negative effect in wild-type plants. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

9 Samples

Download data: TXT

(Submitter supplied) Heterochromatin constitutes a fundamental aspect of genomes that is crucial for maintaining genome stability. In flowering plants, maintenance of heterochromatin relies on a positive feedback loop involving the histone 3 lysine nine methyltransferase (H3K9), KRYPTONITE (KYP), and the DNA methyltransferase, CHROMOMETHYLASE3 (CMT3). An H3K9 demethylase, INCREASED IN BONSAI METHYLATION 1 (IBM1), has evolved to modulate the activity of KYP-CMT3 within transcribed genes. more...

Organism:

Arabidopsis thaliana; Raphanus raphanistrum; Isatis lusitanica

Type:

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

Platforms:

GPL34074 GPL26208 GPL34073

12 Samples

Download data: TSV

(Submitter supplied) We show that an abrupt waterlogging treatment of Arabidopsis thaliana plants triggers a systemic ROS and calcium wave response, and that the waterlogging-triggered ROS wave response is dependent on RBOHD, calcium-permeable channels GLR3.3 and GLR3.6, and aquaporin PIP2;1 proteins. We further show that waterlogging stress is accompanied by a rapid systemic transcriptomic response that is evident as early as 10 min following waterlogging initiation and is partially dependent on RBOHD. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

30 Samples

Download data: CSV

(Submitter supplied) The nuclear lamina, a crucial sub-nuclear protein matrix, maintains nuclear structure and genomic function. Our study centers on the Arabidopsis lamina component CROWDED NUCLEIs (CRWNs), unveiling their extensive role in the development of the reproductive system with a specific focus on the endosperm, which is pivotal in seed development. We showed that quadruple crwn null gametophytes exhibit limited viability, and crwn1 crwn2 (crwn1/2) mutations lead to defective seeds often having enlarged chalazal cysts and variable timing of endosperm cellularization. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL26208

56 Samples

Download data: BED, CSV

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

Organism:

Populus; Solanum tuberosum; Oryza sativa; Saccharum officinarum; Dianthus caryophyllus; Arabidopsis thaliana; Solanum lycopersicum; Citrus sinensis; Zea mays; Brassica napus; Glycine max

Type:

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

11 related Platforms

160 Samples

Download data: BROADPEAK, NARROWPEAK

(Submitter supplied) Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a powerful method for profiling histone modifications and transcription factors binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits, tubers and flowers is challenging due to their sturdy cell walls and complex constituents. Here, we present advanced ChIP (aChIP), an optimized ChIP-seq strategy that efficiently isolates chromatin from plant tissues while simultaneously removing plant cell walls and cellular constituents. more...

Organism:

Citrus sinensis; Populus; Oryza sativa; Glycine max; Dianthus caryophyllus; Solanum lycopersicum; Zea mays; Arabidopsis thaliana; Brassica napus; Solanum tuberosum; Saccharum officinarum

Type:

Genome binding/occupancy profiling by high throughput sequencing

11 related Platforms

152 Samples

Download data: BROADPEAK, NARROWPEAK

(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 GPL30471

12 Samples

Download data: BED, BW, MTX, TSV, XLS

(Submitter supplied) Cell-specific transcriptional regulatory networks (TRNs) play vital roles in plant development and response to environmental stresses. However, traditional single-cell mono-omics techniques are unable to fully capture the relationships and dynamics of molecular information within cells. While data integration algorithm facilitates the merging of single-cell RNA-seq and single-cell ATAC-seq data, ensuring the accuracy of the integration process remains a challenge, particularly when investigating cell-type-specific TRNs. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

4 Samples

Download data: MTX, TSV

(Submitter supplied) Cell-specific transcriptional regulatory networks (TRNs) play vital roles in plant development and response to environmental stresses. However, traditional single-cell mono-omics techniques are unable to fully capture the relationships and dynamics of molecular information within cells. While data integration algorithm facilitates the merging of single-cell RNA-seq and single-cell ATAC-seq data, ensuring the accuracy of the integration process remains a challenge, particularly when investigating cell-type-specific TRNs. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26208

4 Samples

Download data: BED, MTX, TSV

(Submitter supplied) During the embryonic-to-vegetative transition in plants, many genes that were active in seeds become transcriptionally turned off. Recently, we reported a new transcriptional corepressor of the embryonic program, SEED DORMANCY 4-LIKE (AtSDR4L). Multiple lines of evidence suggest that AtSDR4L plays an essential role in regulating the transition from seed to seedling, possibly by collaborating with components of Polycomb Repressive Complexes (PRCs) and PRC-associated proteins VIVIPAROUS1/ABI3-LIKE (VAL) proteins. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26208

18 Samples

Download data: BROADPEAK, NARROWPEAK, TDF

(Submitter supplied) Light signaling precisely controls the photomorphogenic development in plants. In this study, we report COP1 SUPPRESSOR 6 (CSU6) function as positive regulator of light signaling. Loss of CSU6 function largely rescued the cop1-6 constitutively photomorphogenic phenotype. The hypocotyl length of csu6 mutant seedlings was shorter in the dark, but longer than that of wide-type in the light. CSU6 not only associated with the promoter regions of PIF4 and PIF5 to inhibit their expression during the day, but also directly interacts with both PIF4 and PIF5 to repress their transcriptional activity. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

6 Samples

Download data: TXT

(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) 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) 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) 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