Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Acidianus filamentous virus 2

ABSTRACT: Cold stress greatly affects plant growth and crop yield. To identify novel genes and possible mechanisms involved in chilling tolerance responses in rice seedlings, RNA sequencing (RNA-seq) technology was used for genome-wide gene expression profiling analysis to compare three cold-tolerant genotypes and one cold-sensitive genotype under both normal temperature and cold stress treatments.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Oryza sativa

SUBMITTER: Mengliang Cao

PROVIDER: E-MTAB-4407 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Oryza sativa Raw sequence reads

Project description:Using the HiSeqTM 2000 sequencing platform, the anther transcriptome of photo thermo sensitive genic male sterile lines (PTGMS) rice Y58S and P64S (Peiâai 64S) were analyzed at the fertility sensitive stage under cold stress.These datas would be most beneficial for further studies investigating the molecular mechanisms of rice responses to cold stress.

2015-04-22 | E-MTAB-4312 | biostudies-arrayexpress

Zea mays Transcriptome or Gene expression

Project description:Transcriptome of Zea mays genotypes under control and stress conditions. Stress conditions include heat, cold, salt, and UV. We extracted and sequenced RNA from 14 day old seedlings of inbred lines B73, Mo17 and Oh43 grown using standard conditions as well as seedlings that had been subjected to cold (5Â°C for 16 hours), heat (50Â°C for 4 hours), high salt (watered with 300 mM NaCl 20 hours prior to collection) or UV stress (2 hours). For each stress the plants were sampled immediately following the stress treatment and there were no apparent morphological changes in these plants relative to control plants.

2015-01-31 | E-MTAB-4258 | biostudies-arrayexpress

TTV018 RORC IBD associated genotype effects on RORgT expression and function in ex vivo T cells

Project description:RNA sequencing of peripheral immune cells from patients +/- an IBD risk variant. Peripheral immune cells +/- in vitro test compound treatment.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2016-07-11 | E-ERAD-443 | biostudies-arrayexpress

Study of low dose gamma irradiation effects in esophageal epithelial cell fate

Project description:Effect of low-doses of ionizing radiation on the behaviour of epithelial cells. The aim of the study is to check whether a single exposure of 50 mGy of ioninzing radiation promotes changes in RNA transcription levels and/or mutations.

2016-02-23 | E-ERAD-429 | biostudies-arrayexpress

Genome-wide transcriptome analysis of explant regeneration in be1-3

Project description:The Arabidopsis Branching Enzyme 1 (BE1) gene encodes a putative glycoside hydrolase involved in carbohydrate metabolism. A partial loss-of-function mutation of the BE1 gene (be1-3 mutant) severely impaired adventitious shoot formation and somatic embryogenesis but not root formation in tissue culture. To gain a better understanding of the molecular mechanism underlying the in vitro plant regeneration defects caused by the BE1 gene mutation, we performed RNA sequencing analysis (RNA-seq) to examine the differential gene expression between WS and be1-3 mutant at dedifferentiation and redifferentiation stages.

2014-02-12 | E-MTAB-4394 | biostudies-arrayexpress

Epigenetic variation through the breeding processes of maize

Project description:The concurrent epigenetic changes during this period of remarkable improvement in maize grain yield remain unknown. Here, we performed MethylC-seq and RNA-seq on 4 related inbred lines with known pedigree information. Analysis of epigenetic changes over the course of historical maize breeding is a valuable new avenue in the exploration for crop improvement. These data lead us to suggest that novel epihaplotypes, in addition to DNA variation, are a substrate of selection during breeding, and that epigenetic variation between parents may also contribute to heterosis in hybrids. Xie, S; et al. 2013. Maize Genetics Conference Abstracts. 54:P326

2015-06-01 | E-MTAB-4238 | biostudies-arrayexpress

The Zeanome

Project description:Maize exhibits levels of structural variation (SV) of non-repeat sequences that are unprecedented among higher eukaryotes. This SV includes hundreds of copy number variants (CNVs) and thousands of presence/absence variants (PAVs). Many of the PAVs contain intact, expressed, single-copy genes that are present in one haplotype but absent from another. The goal of this project is to test the hypothesis that differences in gene copy number (both gains and losses) contribute to the extraordinary phenotypic diversity and plasticity of maize. Maize is a good model for these studies because it exhibits a rapid decay of linkage disequilibrium (LD) and because a draft genome sequence of the B73 inbred and mapping populations are available. As a first step, the Zeanome, a near-complete set of genes present in B73, other maize lines and the wild ancestor of maize (teosinte), is being defined using transcriptomic data. Note: All samples in SRA were assigned the same sample accession (SRS302561). 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.

2012-03-29 | E-MTAB-4386 | biostudies-arrayexpress

Arabidopsis thaliana transcriptome with FLOWERING LOCUS T over expression

Project description:Over expression study of FLOWERING LOCUS T, a transcriptome study

2015-07-12 | E-MTAB-4236 | biostudies-arrayexpress

Triticum urartu strain:PI 428198 Genome sequencing and Transcriptome or Gene expression

Project description:For this project, we have sequenced, assembled and annotated a transcriptome of a diploid wheat Triticum urartu accession PI 428198. The sequencing libraries were prepared from shoot and root tissues harvested from 2-3 week old seedlings. All sequencing was carried out on the Illumina HiSeq platform using the 100 bp pair-end protocol (248.5 million reads). The assembly was constructed using a multiple k-mer approach with a de novo assembly algorithm implemented in CLC Genomics Workbench 5.5 and additional redundancy reduction with CD-HIT and blast2cap3 programs. Open reading frames and proteins were predicted using BLASTX searches and a findorf algorithm.

2013-06-11 | E-MTAB-5037 | biostudies-arrayexpress

Arabidopsis thaliana CPL3 RNASeq

Project description:To determine transcriptome dynamics regulated by CPL3 during elicitation of immune responses, we performed RNA sequencing (RNA-seq) analysis of Col-0 WT and cpl3-3 mutant treated without or with flg22 for 30 min.

2014-12-05 | E-MTAB-4397 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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