GEO DataSets

(Submitter supplied) Gene expression of fine tissues of developing rice endosperm

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL8852

24 Samples

Download data: TXT

(Submitter supplied) Heat stress occurrence during endosperm development and seed filling forms chalky portion in the limited zone of starchy endosperm of rice grains. In this study, isolation of aleurone, dorsal, central and lateral tissues of developing endosperm by laser-microdissection (LM) coupled with gene expression analysis of 44K microarray was performed to identify key regulatory genes involved in the formation of milky-white (MW) and white-back (WB) chalky grains during heat stress. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL8852

24 Samples

Download data

(Submitter supplied) RNAi mediated suppression of MADS29 severely affects seed set; the surviving seeds are smaller in size with reduced grain filling, abnormal starch grains and aberrant embryo development. To identify the affected pathways due to suppression of this transcription factor in the transgenic seeds, transcriptome analysis using microarray was carried out.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

6 Samples

Download data: CEL

(Submitter supplied) Overexpression of MADS29 results in severely dwarfed phenotype, resulting from a shift in auxin-cytokinin ratio in favor of cytokinins. To see the extent of change in gene expression in the leaves of the transgenic plants, whole genome transcript analysis was carried out using microarray.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

6 Samples

Download data: CEL

(Submitter supplied) Purpose: Analysis of gene expression level. Methods: Retinal mRNA profiles of 7 DAP endosperm of the wild-type (WT) and NF-YC11 knockout mutant were generated by deep sequencing, in triplicate, using Illumina 2000.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13834

6 Samples

Download data: XLSX

(Submitter supplied) Rice NF-YC11 is a transcription factor that plays a key regulatory role in storage substance accumulation during rice grain filling. To reveal the transcription regulatory network of NF-YC11 in rice, we performed genome-wide identification of NF-YC11 targets by immunoprecipitation sequencing (ChIP-seq) analyses in the NF-YC11-overexpression plants.

Organism:

Oryza sativa Japonica Group

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13834

2 Samples

Download data: BED, BW, XLSX

(Submitter supplied) Using whole genome bisulfite sequencing to provide single-base resolution of DNA methylation status in the endosperm of wild-type (ZH11) and ta2-1 rice plants, and identify hypermethylated regions in ta2-1.

Organism:

Oryza sativa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24468

3 Samples

Download data: BEDGRAPH

(Submitter supplied) Aleurone layer differentiation completes by 9 DAF, and most of the nutrient filling occurs between 6-21 DAF, (Wu et al., 2016a, 2016b), so we decided to use 10 DAF time point for collection of pericarp, aleurone, embryo and endosperm tissues for RNA-Seq analysis. Since aleurone is mostly single layer, and it’s almost impossible to separately collect pure pericarp and aleurone layers manually, so firstly we developed a method to collect different tissue types of developing grain through LCM and RNA extraction and Sequencing

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

12 Samples

Download data: XLSX

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

Organism:

Oryza sativa

Type:

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

Platform:

GPL19290

6 Samples

Download data

(Submitter supplied) OsNF-YB1 is a transcription factor that plays important roles during rice grain filling. OsNF-YB1 is specifically expressed in aleurone layer of developing endosperm and OsNF-YB1 RNAi lines showed retardation in grain filling and produced small grains with chalky endosperm as well as the altered starch quality. To reveal the transcriptional regulatory framework of OsNF-YB1, we determined OsNF-YB1 DNA binding targets using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq). more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19290

4 Samples

Download data: BED, TXT

(Submitter supplied) Analysis of gene expression level. The hypothesis tested in the present study was that OsNF-YB1 is specifically expressed in aleurone layer of developing endosperm and suppressed expression of OsNF-YB1 results in a reduced grain-filling rate and small grains. Of the down-regulated genes, the enrichment of transmembrane transport and ATP biosynthetic process is consistent with the decreased grain-filling rate.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

2 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Endosperm is a product of double fertilization, and provides nutrients and signals to the embryo during seed development in flowering plants. Early stages of endosperm development are critical for the development of its storage capacity through synthesis and accumulation of starch and storage proteins. Here we report on the isolation and sequencing of mRNAs from the central portion of the starchy endosperm of Zea mays (maize) B73 at 6 days after pollination. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13977

4 Samples

Download data: TXT

(Submitter supplied) As a species mostly planted in tropical and subtropical regions, rice is sensitive to chilling temperature, especially at reproductive stage. However, the effect of low temperature on seed development has not been well characterized. The transcriptome of two rice cultivars Zhonghua11 and Hanfeng were analyzed to characterize the gene regulatory networks of rice seed during low temperature treatment.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

16 Samples

Download data: CEL

(Submitter supplied) In flowering plants, the male gametophyte, the pollen, develops in the anther. Complex patterns of gene expression in both the gametophytic and sporophytic tissues of the anther regulate this process. The gene expression profiles of the microspore/pollen and the sporophytic tapetum are of particular interest. In this study, a microarray technique combined with laser microdissection (44K LM-microarray) was developed and used to characterize separately the transcriptomes of the microspore/pollen and tapetum in rice. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL6864

33 Samples

Download data: TXT

(Submitter supplied) We aimed to reveal transitions of gene expression profile in developing female gametophytes of rice in this study. The developmental process of rice female gametophyte, from megaspore mother cell at pre-meiotic stage to mature embryo sac, was separated into six stages. Developing ovules at each stage were separated from surrounding sporophyte tissues and collected using LMD. RNA samples extracted from them were subjected to microarray analysis. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL8852

19 Samples

Download data: TXT

(Submitter supplied) Opaque11 (O11) is a bHLH transcription factor that plays important roles in maize endosperm development, nutrient metabolism, and stress response.

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17628

4 Samples

Download data: BED, TXT

(Submitter supplied) Analysis of gene expression level. The hypothesis tested in the present study was that o11 mutant affects nutrient metabolism and stress response.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17628

6 Samples

Download data: TXT

(Submitter supplied) We used microarrays to detail the global programme of gene expression underlying seed developing and lysine metabolism.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

12 Samples

Download data: CEL, CHP

(Submitter supplied) To summarize the impact of high temperature on rice grain filling, we performed the rice 44k oligo microarray analysis.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL6864

6 Samples

Download data: TXT

(Submitter supplied) Durum wheat (Triticum turgidum subsp. durum) is widely grown for pasta production, and more recently, is gaining additional interest due to its resilience to warm, dry climates and its use as an experimental model for wheat research. To enable further research into endosperm development and storage reserve synthesis, we generated a high-quality transcriptomics dataset from developing endosperms of durum variety Kronos, to complement the extensive mutant resources available for this variety. more...

Organism:

Triticum turgidum subsp. durum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28728

24 Samples

Download data: TSV