GEO DataSets

(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

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(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) 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

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(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) 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) 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 Japonica Group

Type:

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

Platform:

GPL13834

38 Samples

Download data: BW

(Submitter supplied) ONAC127 and ONAC129 are NAC transcription factors that involved in abiotic stress response and play key regulatory roles in apoplasmic transportation during rice caryopsis filling. To reveal the transcription regulatory network of ONAC127 and ONAC129 in rice caryopsis, we identified significantly differentially expressed genes by RNA-Seq analysis using the caryopses of the CRISPR-mutants(CR) and overexpression lines(OX) of ONAC127 and ONAC129 under natural heat stress(H) and normal cultivation condition(N).

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13834

30 Samples

Download data: XLSX

(Submitter supplied) ONAC127 and ONAC129 are NAC transcription factors that involved in abiotic stress response and play key regulatory roles in apoplasmic transportation during rice caryopsis filling. To reveal the transcription regulatory network of ONAC127 and ONAC129 in rice caryopsis, we performed genome-wide identification of ONAC127 and ONAC129 targets by immunoprecipitation sequencing (ChIP-seq) analyses in the overexpression lines of ONAC127 and ONAC129 under natural heat stress(H) and normal cultivation condition(N) with three technical replicates.

Organism:

Oryza sativa Japonica Group

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13834

8 Samples

Download data: BW

(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) 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) Popular rice mega varieties lack sufficient key micronutrients (e.g., Fe, Zn), vitamins and a balanced amino acid composition that are essential for a healthy diet. The major bottleneck for improving the nutritional quality of popular rice varieties through conventional breeding or gene technology is our lack of an integrated understanding of the biochemical and molecular processes that occur during rice grain filling (and their determining genes or loci). more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18525

28 Samples

Download data: XLSX