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

Oryza sativa Transcriptome or Gene expression

ABSTRACT: Nitrogen (N), a critical macronutrient for plant growth and development, is a major limiting factor in most agricultural systems. Microarray analyses have been conducted to investigate genome-wide gene expression in response to changes in N concentrations. Although RNA-Seq analysis can provide a more precise determination of transcript levels, it has not previously been employed to investigate the expression of N-starvation-induced genes. We constructed cDNA libraries from leaf sheaths and roots of rice plants grown under N-deficient or -sufficient conditions for 12 h. Sequencing the libraries resulted in identification of 33,782 annotated genes. A comparison of abundances revealed 1,650 transcripts that were differentially expressed (fold-changeââ¥â2) due to an N-deficiency. Among them, 1,158 were differentially expressed in the leaf sheaths (548 up-regulated and 610 down-regulated) and 492 in the roots (276 up, 216 down).

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: Yang Wenzhu

PROVIDER: E-MTAB-4195 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Transcriptome analysis of nitrogen-starvation-responsive genes in rice.

Yang Wenzhu W Yoon Jinmi J Choi Heebak H Fan Yunliu Y Chen Rumei R An Gynheung G

BMC plant biology 20150203

<h4>Background</h4>Nitrogen (N), a critical macronutrient for plant growth and development, is a major limiting factor in most agricultural systems. Microarray analyses have been conducted to investigate genome-wide gene expression in response to changes in N concentrations. Although RNA-Seq analysis can provide a more precise determination of transcript levels, it has not previously been employed to investigate the expression of N-starvation-induced genes.<h4>Results</h4>We constructed cDNA lib ...[more]

PMID: 25644226

Similar Datasets

transcriptome sequencing of tomato

Project description:Gene expression of all tomato genes was determined by replicated (two biological replicates of each tissue) strand-specific Illumina RNA-Seq of root, leaf, flower (2 stages) and fruit (6 stages). Note: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.

2012-02-15 | E-MTAB-4812 | biostudies-arrayexpress

Selaginella moellenforfii, Arabidopsis thaliana, Equisetum arvense, Zea mays shoot meristems transcriptome

Project description:We used LM-RNAseq to compare the molecular fingerprints of cells enriched for subdomains within Selaginella, Equisetum, Arabidopsis and maize shoot apices. Three apical domains were isolated from the Selaginella and Equisetum SAMs: the AC domain, comprising the lone AC; the core domain, comprising the cells below the AC and above the initiating leaf primordium; and the initiating leaf primordium. LM-RNAseq analyses of these shoot apical subdomains generated hundreds of significantly DEGs for each cell type relative to whole-plant transcriptomes based on an FDR â¤ 0.05. These data were analyzed for the presence of homologous developmental genetic programs across these three species, and for the identification of unique developmental programs operating within each species.

2015-06-17 | E-MTAB-4374 | biostudies-arrayexpress

Populus tricho Raw sequence reads

Project description:We performed RNA-Seq of P. trichocarpa calluses that were firstly induced from roots. Then the total RNAs were isolated from the control and salt-stressed calluses (200 mM NaCl for 6, 12, 24, and 48 h) using a CTAB procedure. Note: All samples in SRA were assigned the same sample accession (SRS938530). This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.

2015-06-01 | E-MTAB-4364 | biostudies-arrayexpress

Transcriptome sequencing of leaves of resistant (RG-PtoR) and susceptible (RG-prf3 and RG-prf19) tomato plants treated with Pst DC3000

Project description:In order to study the transcriptome changes in tomato during Pto/Prf-mediated ETI, we infiltrated tomato Rio Grande (RG)-PtoR resistant plants (plants that have a functional Pto/Prf signaling pathway, Pto/Pto, Prf/Prf) and two different susceptible plants: RG-prf3 and RG-prf19 (Pto/Pto, prf/prf), with Pseudomonas syringae pv. tomato DC3000 (DC3000). The susceptible lines have a non-functional Prf gene due to a 1.1 kb deletion or a G-insertion at position 2,584 (which causes a frameshift), respectively. We collected leaf tissue at 4 and 6 h after inoculation (hai) to assess early changes in host gene expression after translocation of DC3000 effectors AvrPto and AvrPtoB, which occur at about 3 hai. The plants were then maintained in the same conditions to observe signs of disease. As expected, RG-PtoR plants did not develop speck disease whereas the RG-prf plants did. NOTE: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence Ã¢ÂÂSource NameÃ¢ÂÂ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.

2014-11-04 | E-MTAB-4796 | biostudies-arrayexpress

Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4 Kranz anatomy

Project description:Photosynthesis underpins the viability of most ecosystems, with C4 plants that exhibit âKranzâ anatomy being the most efficient primary producers. Kranz anatomy is characterized by closely spaced veins that are encircled by two morphologically distinct photosynthetic cell types. Although Kranz anatomy evolved multiple times, the underlying genetic mechanisms remain largely elusive, with only the maize scarecrow gene so far implicated in Kranz patterning. To provide a broader insight into the regulation of Kranz differentiation, we performed a genome-wide comparative analysis of developmental trajectories in Kranz (foliar leaf blade) and non-Kranz (husk leaf sheath) leaves of the C4 plant maize. Using profile classification of gene expression in early leaf primordia, we identified cohorts of genes associated with procambium initiation and vascular patterning. In addition, we used supervised classification criteria inferred from anatomical and developmental analyses of five developmental stages to identify candidate regulators of cell-type specification. Our analysis supports the suggestion that Kranz anatomy is patterned, at least in part, by a SCARECROW/SHORTROOT regulatory network, and suggests likely components of that network. Furthermore, the data imply a role for additional pathways in the development of Kranz leaves.

2013-07-29 | E-MTAB-4134 | biostudies-arrayexpress

Zea mays cultivar:W22 Transcriptome or Gene expression

Project description:Large scale transcriptomics study to establish gene expression in leaf tissue of W22 inbred line in Zea Mays. RNA was extracted from leaf tissue when the plants were at V6. Sequencing library was produced following the protocol mentioned in the following publication PMID:22039485

2015-04-29 | E-MTAB-4446 | biostudies-arrayexpress

Medicago truncatula Transcriptome or Gene expression

Project description:Transcriptome analysis of early transcriptional changes occuring in M. truncatula roots minutes to days after innoculation with Sinorhizobium medicae. With the goal of characterizing the hostâs earliest transcriptional responses to bacterial signals at high temporal resolution, 5-d-old roots of M. truncatula were inoculated with S. medicae ABS7M (pXLGD4) at densities of 150 cells ÂµLâ1 (optical density at 600 nm = 0.001). Tissue was sampled at nine points over a 48-h time course, with the first postinoculation time point at 30 min.

2015-01-31 | E-MTAB-5140 | biostudies-arrayexpress

Glycine max Transcriptome or Gene expression

Project description:Soybean (Glycine max, cv Williams82) leaf petiole explants exposed to 25 ul/l ethylene for 0 to 72 h. Explants were prepared from 21 day-old greenhouse grown plants. Leaf abscission zones (LAZ) consisted of 2 mm of tissue collected below the leaf blade. The petioles (NAZ) consisted of approximately 3 to 4 mm of petiole tissue with the AZ removed. Explants and tissue were collected in February, March and April of 2013. Tissue and RNA were collected at USDA, Beltsville, MD (Mark L Tucker, Joonyup Kim and Ronghui Yang). Library construction and sequencing was completed at Univ of Cornell, Itheca, NY using a Illumina HiSeq 2000 (James J Giovannoni and Zhangjun Fei).

2015-02-06 | E-MTAB-5066 | biostudies-arrayexpress

Oryza sativa Transcriptome or Gene expression

Project description:We analyzed the transcriptome profiles for rice grain from heat-tolerant and -sensitive lines in response to high night temperatures at the early milky stage using the Illumina Sequencing method. On the 8th day after the labeled florets flowered, plants with the same label were transferred to chambers and maintained at a temperature of 38.0âÂ±â0.5Â°C (treatment) or 25.0âÂ±â0.5Â°C (control) for the dark period (10 h), and 26.0âÂ±â0.5Â°C (both treatment and control) for the light period (14 h). Three biological replicates of the temperature treatments were grown under the same conditions. After 48 h of treatment, samples containing 45 grains with labels from the same region (middle to bottom part) of labelled ears were harvested, packed in aluminum foil, and flash-frozen in liquid nitrogen until further use. A total of 12 rice grain samples were harvested, i.e., controls (TC1, TC2 and TC3) and treatments (TT1, TT2 and TT3) of the three biological replicates of the heat-tolerant line, and controls (SC1, SC2 and SC3) and treatments (ST1, ST2 and ST3) of the three biological replicates of the heat-sensitive line.

2014-12-01 | E-MTAB-4348 | biostudies-arrayexpress

Arabidopsis thaliana response to cytokinin in roots and shoots

Project description:This study aims to identify genes which are differentially expressed in root and/or shoot material in response to exogenous cytokinin. Roots and shoots were collected separately.

2015-08-01 | E-MTAB-4298 | 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