GEO DataSets

(Submitter supplied) Whether and how organisms can inherit environmental information from their parents is a major question in evolutionary theory. Plants have evolved to link reproductive development to seasonal environmental cues and seed dormancy is highly contingent on the environmental temperature during seed set, although the mechanism by which seeds acquire seasonal timing information is unclear. Here we show that loss of maternal like heterochromatin protein 1 (LHP1) causes an inability of progeny seeds to sense temperature and that this is linked mechanistically to reduced ABA levels in seeds and hyperaccumulation of free nitrate. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34608

6 Samples

Download data: MTX, TSV

(Submitter supplied) The colonization of land by plants relies on numerous evolutionary innovations crucial for terrestrial adaptation. These include advances in sexual reproduction and the ability to properly respond to various environmental stresses, which involve precise control of their regulatory genes. A notable genetic innovation in land plants is the emergence of histone lysine methyltransferases ATXR5/6, which specifically catalyse the repressive histone H3 lysine 27 monomethylation (H3K27me1). more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26208

4 Samples

Download data: BW

(Submitter supplied) The colonization of land by plants relies on numerous evolutionary innovations crucial for terrestrial adaptation. These include advances in sexual reproduction and the ability to properly respond to various environmental stresses, which involve precise control of their regulatory genes. A notable genetic innovation in land plants is the emergence of histone lysine methyltransferases ATXR5/6, which specifically catalyse the repressive histone H3 lysine 27 monomethylation (H3K27me1). more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

9 Samples

Download data: TXT

(Submitter supplied) The colonization of land by plants relies on numerous evolutionary innovations crucial for terrestrial adaptation. These include advances in sexual reproduction and the ability to properly respond to various environmental stresses, which involve precise control of their regulatory genes. A notable genetic innovation in land plants is the emergence of histone lysine methyltransferases ATXR5/6, which specifically catalyse the repressive histone H3 lysine 27 monomethylation (H3K27me1). more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

9 Samples

Download data: TXT

(Submitter supplied) The casparian strip serves as a crucial diffusion barrier in the endodermis, playing a vital role in controlling the flow of substances between the root and its external environment. Here, we observed that when the casparian strip is absent, bacteria can accumulate abundantly on the roots. To investigate the impact of this bacterial accumulation on the root indued by casparian strip deficiency , we inoculated Col-0 and sgn3 myb36 roots with CHA0 in a hydroponic system. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

24 Samples

Download data: CSV

(Submitter supplied) Programmed cell death (PCD) is a genetically controlled pathway that plants can use to selectively eliminate redundant or damaged cells.The coordinated and sequential actions of lineage-specific transcription factors and epigenetic regulators are essential for the initiation of PCD. We used CRISPR/Cas9-mediated targeted mutagenesis to generate a series of transgene-free mutant lines either with single or double-null bnafah alleles. more...

Organism:

Brassica napus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15579

27 Samples

Download data: TXT

(Submitter supplied) Changes in temperature during the dormant season, such as the unusual cold or warmth linked to climate change, can affect cold acclimation and endanger the viability of the grape and wine industry. To tackle this problem, we carried out two experiments in a controlled environment to examine the effects of various temperature conditions on the process of cold acclimation in grapevine buds during endodormancy, using transcriptomic monitoring through 3'RNA-seq.

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24368

156 Samples

Download data: CSV

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

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL23157 GPL21785

28 Samples

Download data: BW, CGMAP

(Submitter supplied) Histone deacetylases (HDAs) are evolutionally conserved enzymes and often form a multiprotein complex with histone Lysine-Specific Demethylase 1 (LSD1) to play central roles in epigenetic silencing in yeast and animals. In Arabidopsis, either HDA6 or LSD1-LIKE 1 and 2 (LDL1/2) are known to silence transposable element (TE), but their joint effect remains unexplored. Here, we revealed the individual and joint effects of HDA6 and LDL1/2 carefully by examining the transcriptomes, the genome wide distribution of H3Ac, H3K4me2, and DNA methylation in wildtype and mutants (hda6, ldl1/2 and hda6/ldl1/2). more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21785

12 Samples

Download data: BW

(Submitter supplied) Histone deacetylases (HDAs) are evolutionally conserved enzymes and often form a multiprotein complex with histone Lysine-Specific Demethylase 1 (LSD1) to play central roles in epigenetic silencing in yeast and animals. In Arabidopsis, either HDA6 or LSD1-LIKE 1 and 2 (LDL1/2) are known to silence transposable element (TE), but their joint effect remains unexplored. Here, we revealed the individual and joint effects of HDA6 and LDL1/2 carefully by examining the transcriptomes, the genome wide distribution of H3Ac, H3K4me2, and DNA methylation in wildtype and mutants (hda6, ldl1/2 and hda6/ldl1/2). more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL23157

8 Samples

Download data: CGMAP

(Submitter supplied) Histone deacetylases (HDAs) are evolutionally conserved enzymes and often form a multiprotein complex with histone Lysine-Specific Demethylase 1 (LSD1) to play central roles in epigenetic silencing in yeast and animals. In Arabidopsis, either HDA6 or LSD1-LIKE 1 and 2 (LDL1/2) are known to silence transposable element (TE), but their joint effect remains unexplored. Here, we revealed the individual and joint effects of HDA6 and LDL1/2 carefully by examining the transcriptomes, the genome wide distribution of H3Ac, H3K4me2, and DNA methylation in wildtype and mutants (hda6, ldl1/2 and hda6/ldl1/2). more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23157

8 Samples

Download data: BW

(Submitter supplied) To decipher the mechanisms by which FvALKBH10B regulates fruit ripening, we performed m6A sequencing (m6A-seq) using mRNA from fruits of wild type and Fvalkbh10b mutant. The libraries for sequencing were prepared with 3 replicates, in which the mRNA samples were independently prepared. FvALKBH10B mutation leads to a delay in fruit ripening and causes global m6A hypermethylation of 1859 genes.

Organism:

Fragaria vesca

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL32944

12 Samples

Download data: CSV

(Submitter supplied) To better understand FvSEP3-mediated transcriptional regulation of fruit ripening, we performed DNA affinity purification sequencing (DAP-seq) to uncover FvSEP3 directly binding sites at the genome level. For DAP-seq analysis, the recombinant FvSEP3 fusion protein was used to purify the sheared genomic DNA of strawberry fruits. Two independent biological replicates of DAP-seq and DNA 'input' negative control libraries were prepared and submitted for deep sequencing.

Organism:

Fragaria vesca

Type:

Other

Platform:

GPL32944

3 Samples

Download data: CSV

(Submitter supplied) A period of exposure to high ambient temperatures can damage the process of grain filling in rice, potentially inducing the endosperm to become chalky. Given the established involvement of long non-coding RNAs (lncRNAs) in regulating plant development and its stress response, the purpose here was to reveal the extent to which lncRNA activity contributes to the endosperm chalkiness syndrome. Among 578 lncRNAs identified in spikelets harvested ten days post anthesis from plants exposed to high temperature stress, 14 were found to be more abundant than in control plants, while 45 were less abundant. more...

Organism:

Oryza sativa Japonica Group

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL21812

6 Samples

Download data: TXT, XLSX

(Submitter supplied) Plants have evolved a tightly regulated and inducible immune system to resist pathogen attack. After the initial contact with the pathogen, plants are significantly more resistant to future challenges, even from unrelated pathogens, an event known as systemic acquired resistance (SAR). In plants polyamines are involved in the regulation and establishment of the defense response by modulating their metabolism, specifically their biosynthesis, conjugation and catabolism. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34544

24 Samples

Download data: TAB

(Submitter supplied) Transcriptome profiling of WT, mbd1, pyl5 and mbd1 pyl5 knock-out mutants in response to Abscisic acid (ABA) was done using Affymetrix GenechipTM Arabidopsis ATH1 Genome Array.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

20 Samples

Download data: CEL

(Submitter supplied) Soft rot or Rhizopus rot, caused by the fungal pathogen Rhizopus stolonifer, is an aggressive postharvest disease that affects many fruit and vegetables. We proposed that R. stolonifer displays a necrotrophic behavior when infecting fruit, actively killing the host tissues to complete its life cycle. We tested this hypothesis by identifying R. stolonifer infection strategies when interacting with four fruit hosts (tomato, grape, strawberry, and plum). more...

Organism:

Fragaria x ananassa; Prunus domestica; Solanum lycopersicum; Vitis vinifera; Rhizopus stolonifer

Type:

Expression profiling by high throughput sequencing

5 related Platforms

49 Samples

Download data: CSV

(Submitter supplied) RNA-seq experiment of Col0, sr45, and sap18 mutants

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

6 Samples

Download data: XLSX

(Submitter supplied) Investigation of whole genome gene expression level changes in the youngest expanded leaves of GDDH13 grafted scions either sprayed with reverse osmosis water or acibenzolar-S-methyl (ASM) either exposed to control temperature (21°C/day ; 18°C/night) or three successive heat days (35°C for 4 h during the day ; 18°C/night). The morning of the third heat day, treatment was performed by spraying to runoff (with a pressurized hand sprayer) with the commercial product Bion 50 WG (Syngenta, Basel, Switzerland; 50% of ASM) prepared in reverse osmosis water at a final concentration of 0.4 g/L. more...

Organism:

Malus domestica

Type:

Expression profiling by array

Platform:

GPL25795

16 Samples

Download data: TXT, XLSX

(Submitter supplied) Pathogens infection exerts major effects on gene expression, which is reconfigured to raise the defences of the attacked plant. In the recent years the establishment of an hypoxic environment during Botrytis infection was described. We used the pentuple erfVII mutant to evaluate the contribution of ERFVII members to plant reaction to Botrytis and their effect on gene expression.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

4 Samples

Download data: CEL