GEO DataSets

(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) To identify the downstream genes of OsMADS29, a genome-wide analysis of the gene expression profiles in the nucellar projection cells of ZH11 and A-OsMADS29 was performed. Hybridization with the microarray and subsequent analysis showed that a total of 1318 genes displayed altered expression (at least 2-fold) under suppressed OsMADS29 expression. Among the altered genes, 492 were up-regulated, and 826 were down-regulated.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL8852

6 Samples

Download data: TXT

(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

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) A transcription factor CYTOKININ-RESPONSIVE GATA FACTOR 1 (CGA1) regulates chloroplast development in rice (Oryza sativa) through modifying the expression of important nuclear expressed, chloroplast localized genes. A transcriptome analysis was done in wild type plants and transgenic rice over-expressing this OsCGA1 to identify the set of genes with altered expression.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

6 Samples

Download data: CEL

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL4720

12 Samples

Download data: GPR

(Submitter supplied) Our aim was to identify which stand alone amplification protocol performed best in our lab when the starting amount of total RNA was limited to 50 ng (A typical amount of total RNA we obtained by laser capture microdissection of tissues from silique samples). Since the quality of extracted RNA is very often tissue dependent and will affect the amplification efficiency, we decided to use total RNA extracted from whole siliques; better representing tissues targeted by LCM. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL4720

8 Samples

Download data: GPR

(Submitter supplied) Laser capture microdissection (LCM) provides a useful method for isolating specific cells or tissues from biological samples. Here, we adapted microdissection protocols to allow high-resolution transcript analysis of different tissues from developing Arabidopsis seed. However, to obtain enough RNA for microarray analyses it was necessary to amplify the RNA. Microarray analyses, using endosperm derived RNA amplified by two-round IVT, reproducibly identified endosperm enriched marker genes. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL4720

4 Samples

Download data: GPR

(Submitter supplied) Cellularization is a key event during the development of the endosperm. Our understanding of the developmental regulation of cellularization has been limited for plants other than Arabidopsis. We found that the activation of OsbZIP76 coincided with the initiation of cellularization of rice. Either knockdown or knockout of OsbZIP76 led to precocious cellularization. Many genes involved in endosperm development or starch biosynthesis were prematurely activated in the caryopsis at two days after fertilization. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

7 Samples

Download data: TXT

(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) We report the application of methylacytosine immunoprecipetation combined with Illumina sequencing (MeDIP-seq) for high-throughput profiling of DNA methylation in rice embryo 3, 6, 9 DAP and endosperm 2, 3, 6, 9 DAP. A total number of 12-14 million of 2×49 bp paired-end reads was generated for each sample, and BOWTIE2 was used for read mapping. We generated genome-wide DNA methylation profiles of rice embryo and endosperm. more...

Organism:

Oryza sativa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13160

13 Samples

Download data: TXT

(Submitter supplied) We used microarrays to detail the global programme of gene expression underlying cellularization and identified distinct classes of regulated genes during this process.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

2 Samples

Download data: CEL, CHP

(Submitter supplied) The receptor-like kinases (RLKs) plays critical roles in signal transduction through sensing the extracellular signals and activating the downstream signal transduction by phosphorylating their targets. Up to now, there are only a few RLKs have been functionally identified. In this study, we systemically analyzed the expression pattern of rice genes, especially the RLK coding genes during embryo and endosperm development.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

14 Samples

Download data: CEL

(Submitter supplied) Expression profiles of protein coding genes were characterized using Affymetrix rice genome array to compare with expression profiles of miRNAs. Keywords: tissue

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

10 Samples

Download data: CEL

(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