Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

37 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cold stress in sugarcane exp2

ABSTRACT: Tropical and subtropical plants are generally sensitive to cold and can show appreciable variation in their response to cold stress when exposed to low positive temperatures. Using nylon filter arrays, we analyzed the expression profile of 1536 expressed sequence tags (ESTs) of sugarcane (Saccharum sp.) exposed to cold for 3-48 h. Thirty-four cold-induced ESTs were identified, of which 23 were novel cold-responsive genes that had not previously been reported as being cold-inducible. This series has the samples from replicate experiment number 2. Keywords = sugarcane Keywords = cold Keywords = nylon arrays

ORGANISM(S): Saccharum sp.

SUBMITTER: Paulo Arruda

PROVIDER: E-GEOD-84 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

RNA expression profiles and data mining of sugarcane response to low temperature.

Nogueira Fábio T S FT De Rosa Vicente E VE Menossi Marcelo M Ulian Eugênio C EC Arruda Paulo P

Plant physiology 20030801 4

Tropical and subtropical plants are generally sensitive to cold and can show appreciable variation in their response to cold stress when exposed to low positive temperatures. Using nylon filter arrays, we analyzed the expression profile of 1,536 expressed sequence tags (ESTs) of sugarcane (Saccharum sp. cv SP80-3280) exposed to cold for 3 to 48 h. Thirty-four cold-inducible ESTs were identified, of which 20 were novel cold-responsive genes that had not previously been reported as being cold indu ...[more]

PMID: 12913139

Similar Datasets

Cold stress in sugarcane exp1

Project description:Tropical and subtropical plants are generally sensitive to cold and can show appreciable variation in their response to cold stress when exposed to low positive temperatures. Using nylon filter arrays, we analyzed the expression profile of 1536 expressed sequence tags (ESTs) of sugarcane (Saccharum sp.) exposed to cold for 3-48 h. Thirty-four cold-induced ESTs were identified, of which 23 were novel cold-responsive genes that had not previously been reported as being cold-inducible. This series has the samples from replicate experiment number 1. Keywords = sugarcane, cold, nylon arrays

2010-06-05 | E-GEOD-83 | biostudies-arrayexpress

MeJA treatment in sugarcane

Project description:Using nylon filter arrays, we analyzed the expression profile of 1536 expressed sequence tags (ESTs) of sugarcane (Saccharum sp.) exposed to the phytormone methyl jasmonate (MeJA) for 0-12 h. 26 ESTs were differentially expressed, including novel genes and also genes that had not previously been reported as being MeJA-inducible. Data are for two independent experiments. Keywords = sugarcane Keywords = methyl jasmonate Keywords = nylon arrays

2010-10-08 | E-GEOD-1546 | biostudies-arrayexpress

Cold stress in sugarcane exp1

2003-01-03 | GSE83 | GEO

Cold stress in sugarcane exp2

2003-01-03 | GSE84 | GEO

MeJA treatment in sugarcane

2004-07-23 | GSE1546 | GEO

Distinctive gene expression patterns in gastrointestinal stromal tumors identified with cDNA arrays

Project description:Gastrointestinal stromal tumors (GIST) are phenotypically and clinically heterogeneous mesenchymal tumors. Using the cDNA array technique, we analyzed the gene expression profiles of 22 GIST and 7 non-neoplastic gastrointestinal smooth muscle specimens, in order to detect molecular differences between GIST and non-neoplastic tissue, and to detect differences between GIST of various phenotypic and clinical subgroups. As a result, we found 796 differentially expressed genes and ESTs between GIST and smooth muscle tissue, including promising new candidate genes for the pathogenesis of GIST. Furthermore, we identified differences in gene expression between GIST of different site, size, and immunohistochemical expression of CD34 and SMA. Our data show that alterations in gene expression are associated with morphologically and clinically detectable features of GIST and provide new aspects for the understanding of these tumors. Keywords = Gastrointestinal Stromal Tumor (GIST)

2003-04-10 | E-GEOD-112 | biostudies-arrayexpress

Analysis of transcription in the Drosophila melanogaster testis

Project description:Identification and annotation of all the genes in the sequenced Drosophila genome is a work in progress. Wild-type testis function requires many genes and is thus of potentially high value for the identification of transcription units. We therefore undertook a survey of the repertoire of genes expressed in the Drosophila testis by computational and microarray analysis. We generated 3141 high-quality testis expressed sequence tags (ESTs). Testis ESTs computationally collapsed into 1560 cDNA set used for further analysis. Of those, 11% correspond to named genes, and 33% provide biological evidence for a predicted gene. A surprising 47% fail to align with existing ESTs and 16% with predicted genes in the current genome release. EST frequency and microarray expression profiles indicate that the testis mRNA population is highly complex and shows an extended range of transcript abundance. Furthermore, >80% of the genes expressed in the testis showed onefold overexpression relative to ovaries, or gonadectomized flies. Additionally, >3% showed more than threefold overexpression at p <0.05. Surprisingly, 22% of the genes most highly overexpressed in testis match Drosophila genomic sequence, but not predicted genes. These data strongly support the idea that sequencing additional cDNA libraries from defined tissues, such as testis, will be important tools for refined annotation of the Drosophila genome. Additionally, these data suggest that the number of genes in Drosophila will significantly exceed the conservative estimate of 13,601.

2010-06-05 | E-GEOD-462 | biostudies-arrayexpress

Expression profile in internodes 1, 5 and 9 from high and low brix plants for sucrose content

Project description:Summary The expression profile of internodes from high brix plant was compared to internodes from low brix plants. Mature (In9), intermediate (In5) and immature internodes (In1) were collected from two different Progenies and immediately frozen in liquid nitrogen. Total RNA was extracted using Trizol. Progeny 1 was derived from two intra-specific polycrosses, one among Saccharum officinarum genotypes and the other combining Saccharum spontaneum genotypes. For each generation, 500 individuals were sampled for brix content and gene expression. The extreme segregants were selected for further analysis. The F3 hybrid individuals selected for molecular studies were planted in a field in single rows of 5 m using standard sugarcane cultivation practices. Brix readings and tissue samples were collected very early in the season, and in March of the following year, when plants were 10 months old. The soluble solids (brix) content of mature internodes of each sugarcane stalk was measured with a portable refractometer (N1 model, ATAGO, Japan). Individuals or pools of eight individuals had their tissues collected and RNA extracted. Progeny 2 was derived from a cross between two commercial varieties (SP80-180 x SP80-4966). Five hundred sugarcane F1 plants were field-grown. The stem sugar content from the different plants showed a normal distribution, and seven plants with extreme brix values were collected. Keywords: Expression profiling by array Total RNA from internodes pool from high brix plants and low brix plants was hybridized to dual channel arrays. Internodes from the same stage of development and from the same progeny were compared. The quantification of each hybridization was submitted in two files, one for each slide side (technical replicates).

2009-02-11 | E-GEOD-14730 | biostudies-arrayexpress

Evaluation of cold tolerant Saccharum spontaneum and identification of proteins related to cold tolerance by proteomic analysis

Project description:Saccharum spontaneum L., the main source of tolerance gene in sugarcane variety, is one of the most valuable germplasms for sugarcane breeding. In this study, 22 clones of S.spontaneum L. were selected from more than 690 collections in our preliminary experiment, and the cold tolerance of these clones were evaluated by physiological and biochemical indicators. Then 2 clones which were designated as lines 1027 and 3217,with contrasting cold tolerance ability were selected for further proteome analysis using DIA and PRM technology.

2023-03-11 | PXD038181 | Pride

Lactococcus lactis stringent response

Project description:The stringent response was defined in Lactococcus lactis through transcript profiling after the addition of a chemical inductor, the norvaline. Gene expression was measured in the exponential growth phase (reference sample) and at 1.6 h after norvaline addition. Four hundred and sixty one differentially expressed genes were identified and constituted the stringent response regulon. Keywords: stress response, time course Stringent response was imposed through norvaline addition during the growth of Lactococcus lactis IL1403 under controlled conditions (30 Â°C, pH 6.6, nitrogen atmosphere). Cell samples were harvested in exponential phase and 1.6 h after norvaline addition. Total RNA was extracted from these samples and radiolabelled cDNA were prepared and hybridized on nylon arrays. 2053 amplicons specific of Lactococcus lactis IL1403 genes were spotted twice on the array. The 2 time-points were analyzed simultaneously and 3 independent repetitions were performed.

2010-06-25 | E-GEOD-10254 | 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