Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome profiling of various organs at different developmental stages in rice (single-end)

ABSTRACT: To identificate long noncoding RNAs in rice, we profiled transcriptome of various organs at different developmental stages using stranded single-end RNA-seq based on poly(A) selection. Transcriptom profiling in flower buds, flowers, flag leaves and roots sampled before flowering and after flowering, milk grains and mature seeds.

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: Huan Wang

PROVIDER: E-GEOD-56463 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits.

Wang Huan H Niu Qi-Wen QW Wu Hui-Wen HW Liu Jun J Ye Jian J Yu Niu N Chua Nam-Hai NH

The Plant journal : for cell and molecular biology 20151001 2

Long non-coding RNAs (lncRNAs) have recently been found to widely exist in eukaryotes and play important roles in key biological processes. To extend our knowledge of lncRNAs in crop plants we performed both non-directional and strand-specific RNA-sequencing experiments to profile non-coding transcriptomes of various rice and maize organs at different developmental stages. Analysis of more than 3 billion reads identified 22 334 long intergenic non-coding RNAs (lincRNAs) and 6673 pairs of sense a ...[more]

PMID: 26387578

Similar Datasets

Transcriptome profiling of various organs at different developmental stages in rice (paired-end)

Project description:To identificate long noncoding RNAs in rice, we profiled transcriptome of various organs at different developmental stages using nondirectional paired-end RNA-seq based on poly(A) selection. Transcriptom profiling in flower buds, flowers, flag leaves and roots sampled before flowering and after flowering, milk grains and mature seeds.

2015-11-25 | E-GEOD-56462 | biostudies-arrayexpress

Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes.

Project description:Expression in seven tissues from Oryza sativa L. ssp japonica Nipponbare was profiled using RNA-sequencing: callus, leaf, root, seed, shoot, panicle before flowering, and panicle after flowering. The original experiment examined gene expression in the seven tissues, and utilized the data both to compare gene expression patterns between retrogenes and their parents and to compare patterns of expression divergence between RNA-based duplicates and DNA-based duplicates Note: All samples in SRA were assigned the same sample accession (DRS000668). This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.

2011-12-21 | E-MTAB-2037 | biostudies-arrayexpress

wheat seed phosphoproteome under water deficit

Project description:Drought is one of the most serious abiotic stresses, under which the crop yield is significantly reduced. Elite winter wheat cultivar Henong 341 (Triticum aestivum L.) was grown in experimental fields of China Hebei province (116°37′23″E, 37°41′02″N) Two different treatment conditions were designed: rain-fed (no water irrigation) and well-watered (water irrigation) conditions at jointing and flowering stages. Each treatment included three biological replicates and each plot was 25m2. In this study, a comprehensive phosphoproteomic analysis of developing grains of 26th day after flowering (DAF) in Chinese bread wheat cultivar Henong 341 under well-watered and water-deficit conditions was performed by means of TiO2 enrichment, LC/MS/MS analysis, and Label-free peptide-intensity quantification. Under well-watered conditions, a total of 590 unique phosphopeptides corresponding to 603 nonredundant phosphorylation sites, representing 471 phosphoproteins, were identified. While under water deficit, 63 unique phosphopeptides, corresponding to 61 phosphoproteins, were found to be differently regulated in phosphorylation status compared to well-watered conditions (≥2 fold intensities).

2016-07-09 | PXD000806 | Pride

Medicago truncatula seed development at 21-19Â°C

Project description:Transcriptional profiling of seeds of Medicago truncatula during maturation. To identify genes that are regulated during seed maturation in the model legume Medicago truncatula, plants at flowering stage were grown at controlled temperature of 21-19Â°C, 16h light. Seeds were then collected at different stages of development. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed to follow the differential expression of genes during seed maturation. Seeds of Medicago truncatula grown at 21-19Â°C were collected at different developmental stages, 15 developmental stages were analysed. Two replicates from each developmental stage were used for dye switch, each time the control was considered as the earlier developmental stage vs the treatment, corresponding to the later developmental stage. For each repetition 8 hybridisation were made: 8DAP vs 11DAP, 14DAP vs 17DAP, 20DAP vs 23DAP, 26DAP vs 29DAP,32DAP vs 35DAP, 38DAP vs 41DAP, 44DAP vs Abs, DS (Rep1 and Rep2) vs 8DAP (Rep3 and Rep4). For each biological replicates, RNA was extracted from 50 seeds collected from 5 different plants, grown in the same conditions. One replicate per array.

2013-07-31 | E-GEOD-49350 | biostudies-arrayexpress

Transcription profiling of barley maturing and germinating grains

Project description:Plant seeds prepare for germination already during seed maturation. We performed a detailed transcriptome analysis of barley grain maturation, desiccation and germination in two tissue fractions (endosperm/aleurone = e/a and embryo = em) using the Affymetrix barley1 chip. Experiment Overall Design: Barley developing and germinating seeds were harvested at different time points after flowering (developing) and imbibition (germinating). To further disseect the influence of different tissues, seeds were dissecte and tissues were analyzed individually.

2008-06-16 | E-GEOD-9365 | biostudies-arrayexpress

RNA-seq of wheat lodicules in four varieties at pre-flowering and early flowering stages

Project description:RNA-seq of wheat lodicules in two higly-chasmogamous (HCH) (Piko and Poezja) and two low-chasmogamy (LCH) (Euforia and KWS Dacanto) varieties at two developmental stages - pre-flowering and early flowering.

2022-09-18 | E-MTAB-12136 | biostudies-arrayexpress

Medicago truncatula seed development under different growth conditions

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-12-19 | E-GEOD-53526 | biostudies-arrayexpress

Expression data from Arabidopsis flowers under drought stress

Project description:We also used microarray analysis to examine transcriptomic changes under drought, identifying thousands of genes that potentially mediate drought responses in the flower, including genes encoding transcription factors that likely play crucial regulatory roles. Arabidopsis were well-watered until after just bolting (after 24 days growth with the main stem about 1 cm high) when drought treatment was started by withholding water (defined as day 0 for drought treatment). The relative soil moisture content decreased sharply and, after about 80 hours (defined as day 3 for drought treatment), the relative soil moisture content was near 35% of the soil water-holding capacity. The soil water condition was maintained by daily watering until almost all the fruits were mature and ready to harvest (about 50 days). For well-watered (control) plants, 90% of the soil water-holding capacity was maintained until tissue harvest or after seed maturation (pots were weighed and watered twice per day). Unopened flower samples were collected, from both treated and control plants, at day 0, 3, 4, 5, 10.

2013-11-06 | E-GEOD-40998 | biostudies-arrayexpress

dreb1a expression data from Arabidopsis flowers under drought stress

Project description:We used microarray analysis to examine transcriptomic changes upon dreb1a under drought, identifying hundreds of genes that potentially function downstream of DREB1A and mediate drought responses in the flower, including genes encoding transcription factors that likely play crucial regulatory roles. DREB1a mutant (CS872453) were well-watered until after just bolting (after 24 days growth with the main stem about 1 cm high) when drought treatment was started by withholding water (defined as day 0 for drought treatment). The relative soil moisture content decreased sharply and, after about 80 hours (defined as day 3 for drought treatment), the relative soil moisture content was near 35% of the soil water-holding capacity. The soil water condition was maintained by daily watering until almost all the fruits were mature and ready to harvest. Unopened flower samples were collected from drought treated plants, at day 3, 4, 5.

2013-11-06 | E-GEOD-43724 | biostudies-arrayexpress

Expression data from Arabidopsis flowers under moderate drought stress

Project description:We also used microarray analysis to examine transcriptomic changes under moderate drought, identifying thousends of genes that potentially mediate moderate drought responses in the flower, including genes encoding transcription factors that likely play crucial regulatory roles. Arabidopsis were well-watered until after just bolting (after 24 days growth with the main stem about 1 cm high) when moderate drought treatment was started by withholding water (defined as day 0 for moderate drought treatment). The relative soil moisture content decreased rapidly and, after about 48 hours the relative soil moisture content was near 50% of the soil water-holding capacity (first moderate drough treated sample M3 were collected at day 3 (72 h after withholding water)). The soil water condition was maintained by daily watering until almost all the fruits were mature and ready to harvest (about 50 days). For well-watered (control) plants, 90% of the soil water-holding capacity was maintained until tissue harvest or after seed maturation (pots were weighed and watered twice per day). Unopened floral bud samples were collected at day 0, 3, 4, 5, 10.

2014-06-01 | E-GEOD-55431 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data