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:

GPL28290

12 Samples

Download data: CSV

(Submitter supplied) mRNA abundances are regulated by the opposing forces of transcription and decay, and yet how decay contributes to mRNA abundance regulation is largely unexplored. We addressed this question using genome-wide data on mRNA rates of abundance change, half-lives, and transcription rates of leaf cells responding to a transdifferentiation stimulusulus. Half-life regulation was common (22% of mRNAs underwent changes in half-life), but RNA abundance regulation by decay alone or by decay that supported transcriptional regulation was rare. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

24 Samples

Download data: CSV

(Submitter supplied) mRNA abundances are regulated by the opposing forces of transcription and decay, and yet how decay contributes to mRNA abundance regulation is largely unexplored. We addressed this question using genome-wide data on mRNA rates of abundance change, half-lives, and transcription rates of leaf cells responding to a transdifferentiation stimulusulus. Half-life regulation was common (22% of mRNAs underwent changes in half-life), but RNA abundance regulation by decay alone or by decay that supported transcriptional regulation was rare. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

30 Samples

Download data: TXT

(Submitter supplied) Using ChIP-seq to study the enrichment of AtMBD9 in Col-0 control plants and AtMBD9-3xMYC/atmbd9-2 transgenic line

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17639

8 Samples

Download data: BEDGRAPH

(Submitter supplied) Using whole genome bisulfite sequencing to provide single-base resolution of DNA methylation status in arp6-5 and pie1-7 mutant

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17639

2 Samples

Download data: TXT

(Submitter supplied) Using whole genome bisulfite sequencing to provide single-base resolution of DNA methylation status in hdp1-1 and hdp2-1 mutants

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: WIG

(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

Platform:

GPL17639

11 Samples

Download data: WIG

(Submitter supplied) Using ChIP-seq to study the deposition of H2A.Z in different anti-silencing mutants

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17639

5 Samples

Download data: WIG

(Submitter supplied) Using MethylC-Seq to provide single-base resolution of DNA methylation status in 35S-SUC2 WT and anti-silencing mutants( arp6-5, pie1-7, h2a.z-2, idm1-9 and ros1-14）

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17639

6 Samples

Download data: WIG

(Submitter supplied) We present here a transcriptome dataset of millet seedling leaves based on RNA-seq technology. The purpose of this study was to mine the salt and alkali tolerance genes of millet and further explore the mechanism of salt and alkali tolerance of millet. We selected 18 representative samples and conducted in-depth sequencing using the latest sequencing platform to ensure the accuracy and reliability of the data.

Organism:

Setaria italica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32680

18 Samples

Download data: TXT

(Submitter supplied) Innovative strategies for increasing the yield of rice, the staple food for more than half of the global population, are needed to keep pace with the expected worldwide population increase, and sustainably forefront the challenges posed by climate change. Traditionally, in Southern-East Asian countries, rice farming benefits from the use of Azolla spp., either as green manure or as co-cultivated plants, for the supply of nitrogen. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

6 Samples

Download data: XLSX

(Submitter supplied) The SWI/SNF complexes play crucial roles in chromatin remodeling, with the protein BDH emerging as a key component in Arabidopsis. Through evolutionary analysis, we demonstrate the conservation of BDH function across mammals, yeast, and plants. Our study reveals that BDH is integral to the stability of the catalytic subcomplex within SWI/SNF assemblies. Furthermore, we elucidate the biological and molecular implications of BDH in Arabidopsis, highlighting its involvement in nucleosomal occupancy regulation. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28290

6 Samples

Download data: TXT

(Submitter supplied) The SWI/SNF complexes play crucial roles in chromatin remodeling, with the protein BDH emerging as a key component in Arabidopsis. Through evolutionary analysis, we demonstrate the conservation of BDH function across mammals, yeast, and plants. Our study reveals that BDH is integral to the stability of the catalytic subcomplex within SWI/SNF assemblies. Furthermore, we elucidate the biological and molecular implications of BDH in Arabidopsis, highlighting its involvement in nucleosomal occupancy regulation. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17639

3 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Purpose:Comparative transcriptome analyses was applied to characterize gene expression after overexpression GaTOP6B in Arabidopsis thaliana. Methods:The fresh leaves were collected from 4-week-old WT plants and transgenic Arabidopsis lines under drought treatments. The total RNA was first extracted using TRIzol Reagent (TaKaRa, Tokyo, Japan), and treated with RNase-free DNase I (TaKaRa), and then followed with mRNA purification using the Magnetic Oligo (dT) Beads (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

6 Samples

Download data: XLSX

(Submitter supplied) The mRNA expression profiles of the WT and b''ab''b were analyzed in 1 hour 8 μmol/m2s red-light exposure and darkness after 4-day dark-grown. The gene expression changes was analyzed and compared between dark and red-light treated samples.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

12 Samples

Download data: TXT

(Submitter supplied) Throughout evolution, the duplication and functional divergence of transcription factors (TFs) has driven cellular and organismal complexity. Mechanisms by which paralogous TFs functionally diverge are thus of broad interest yet remain poorly understood. One well-established mechanism underlying TF divergence is the occupation and regulation of distinct sets of genes. Here we test for new mechanisms using CORONA (CNA) and PHABULOSA (PHB), two representative members of the CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) family of plant TFs. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30821

48 Samples

Download data: TAB

(Submitter supplied) Throughout evolution, the duplication and functional divergence of transcription factors (TFs) has driven cellular and organismal complexity. Mechanisms by which paralogous TFs functionally diverge are thus of broad interest yet remain poorly understood. One well-established mechanism underlying TF divergence is the occupation and regulation of distinct sets of genes. Here we test for new mechanisms using CORONA (CNA) and PHABULOSA (PHB), two representative members of the CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) family of plant TFs. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24270

31 Samples

Download data: BIGWIG

(Submitter supplied) Identification of open chromatin in wheat spikes and seedlings using MH-seq

Organism:

Triticum aestivum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25409

2 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Root-synthesized secondary metabolites are critical quality-conferring compounds of foods, plant-derived medicines, and beverages. However, information at a single-cell level on root-specific secondary metabolism remains largely unexplored. L-theanine, an important quality component of tea, is primarily synthesized in roots, from which it is then transported to new tea shoots. In this study, we present a single-cell RNA sequencing (scRNA-seq)-derived map for the tea plant root, which enabled cell-type-specific analysis of glutamate and ethylamine (two precursors of theanine biosynthesis) metabolism, and theanine biosynthesis, storage, and transport. more...

Organism:

Camellia sinensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32046

1 Sample

Download data: MTX, 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

Platforms:

GPL30821 GPL24270

79 Samples

Download data: BIGWIG, TAB