Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data of Soybean (Glycine max) roots from different iron treatments.

ABSTRACT: Two Near Isogenic soybean (Glycine max) lines were grown in hydroponic conditions with either 50uM ferric nitrate or 100uM ferric nitrate. After 10 days, half the plants were harvested (total root tissue). At 12 days after planting, iron was added to plants grown in low iron conditions bringing them up to sufficient iron growth conditions. Root tissue was harvested for the remaining plants at 14 days after planting. Gene expression analysis from root tissue of two Near Isogenic Lines (NILs), Clark (PI548553) and IsoClark (PI547430), grown in iron stress or iron stress recovered conditions. A total of 24 samples from four growth conditions, three biological replicates per treatment

ORGANISM(S): Glycine max

SUBMITTER: Carroll Vance

PROVIDER: E-GEOD-22227 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

An integrative approach to genomic introgression mapping.

Severin Andrew J AJ Peiffer Gregory A GA Xu Wayne W WW Hyten David L DL Bucciarelli Bruna B O'Rourke Jamie A JA Bolon Yung-Tsi YT Grant David D Farmer Andrew D AD May Gregory D GD Vance Carroll P CP Shoemaker Randy C RC Stupar Robert M RM

Plant physiology 20100723 1

Near-isogenic lines (NILs) are valuable genetic resources for many crop species, including soybean (Glycine max). The development of new molecular platforms promises to accelerate the mapping of genetic introgressions in these materials. Here, we compare some existing and emerging methodologies for genetic introgression mapping: single-feature polymorphism analysis, Illumina GoldenGate single nucleotide polymorphism (SNP) genotyping, and de novo SNP discovery via RNA-Seq analysis of next-generat ...[more]

PMID: 20656899

Similar Datasets

Transcription profiling of Soybean iron deficiency in soybean leaf tissue

Project description:This study was designed to identify candidate genes associated with iron efficiency in soybeans. Two genotypes, Clark (PI548553) and IsoClark (PI547430), were grown in both iron sufficient (100uM Fe(NO3)3) and iron deficient (50uM Fe(NO3)3) hydroponics conditions. The second trifoliate was harvested for RNA extraction for the microarray experiment. Candidate genes were identified by comparing gene expression profiles within genotypes between the two iron growth conditions. Experiment Overall Design: This experiment was designed to compare expression profiles of Clark grown in iron sufficient and deficient iron conditions and of IsoClark grown in the same conditions. Plants grown in iron sufficient conditions were used as controls and plants grown in iron deficient conditions were considered experimental. For the Clark genotype, There were two biological replicates of iron deficient plants, and three biological replicates of iron sufficient plants. The IsoClark genotype had three biological replicates for both iron sufficient and deficient conditions.

2009-09-12 | E-GEOD-10730 | biostudies-arrayexpress

HCN regulates cellular processes through posttranslational modification of proteins by S-cyanylation

Project description:Hydrogen cyanide (HCN) is coproduced with ethylene in plant cells and primarily enzymatically detoxified by the mitochondrial ß-cyanoalanine synthase (CAS-C1). Permanent or transient depletion of CAS-C1 activity in Arabidopsis results in physiological alterations in the plant that suggest that the function of HCN is a gasotransmitter molecule. Label-free quantitative proteomic analysis of enriched mitochondrial samples isolated from the wild type and cas-c1 mutant revealed significant changes in protein content, identifying 451 proteins that are absent or less abundant in cas-c1 and 353 proteins that are only present or more abundant in the mutant background. Gene ontology classification of these proteins highlights proteomic changes that explains the root hairless phenotype and the altered immune response observed in the cas-c1 mutant. The mechanism of action of cyanide as a signaling molecule has been addressed using two proteomic approaches focused on identifying the S-cyanylation of cysteine as a posttranslational modification of proteins. Both the 2-imino-thiazolidine chemical method and the direct untargeted analysis of proteins using LC-MS/MS identified a set of 163 proteins susceptible to S-cyanylation that included sedoheptulose 1, 7-bisphosphatase (SBPase), the peptidyl-prolyl cis-trans isomerase (CYP20-3) and enolase 2 (ENO2). In vitro analysis of these proteins identified that this modification in the SBPase Cys74, CYP20-3 Cys259 and ENO2 Cys346 residues affected the enzymatic activity of the enzymes. GO classification and protein-protein interaction cluster analysis revealed the function of S-cyanylation in the regulation of primary metabolic pathways, such as glycolysis, and the Calvin and S-adenosylmethionine cycles.

2019-01-09 | PXD009929 | Pride

Effect of OsHRZ knockdown in rice roots under iron sufficiency and deficiency

Project description:Transcriptional profiling of rice genes analyzing the effect of knockdown of OsHRZ1 and OsHRZ2 in HRZ2i lines. NT and HRZ2i lines 1, 2 and 3 (2i-1, 2i-2 and 2i-3, respectively) were treated under iron sufficiency for 7 days (+Fe 7d) or under iron deficiency for 1 day (-Fe 1d) or 7 days (-Fe 7d) in hydroponic culture. Comparison between NT and HRZ2i lines at +Fe 7d, -Fe 1d and -Fe 7d. Biological replicates: 2-3 NT replicates, 3 HRZ2i replicates (one each for 2i-1, 2i-2 and 2i-3) for each treatment.

2013-10-17 | E-GEOD-39906 | biostudies-arrayexpress

Proteomic analysis in Arabidopsis tissues reveals hydrogen cyanide regulation of intracellular processes through posttranslational modification of proteins by S-cyanylation

Project description:Hydrogen cyanide (HCN) is co-produced with ethylene in plant cell and enzymatically detoxified mainly by the mitochondrial ß-cyanoalanine synthase (CAS-C1). Permanent or transient depletion of CAS-C1 activity in Arabidopsis results in physiological alteration in the plant that point to the function of HCN as a gasotransmitter molecule. Label-free quantitative proteomic analysis of enriched mitochondrial samples isolated from wild type and cas-c1 mutant reveled significant changes in protein content, identifying 451 proteins that are absent or less abundant in cas-c1 and 353 proteins only present or more abundant in the mutant background. Gene onthology classification of these proteins highlights proteomic changes that explains the root hairless phenotype and the altered inmune response observed in cas-c1 mutant. The mechanism of action of cyanide as signaling molecule has been addressed by two proteomic approaches focused on identifying S-cyanylation of cysteine as a posttranslational modification of proteins. Both the 2-imino-thiazolidine chemical method and direct untargeted analysis of proteins by LC-MS/MS identified a set of 163 proteins susceptibles to be S-cyanylated that include sedoheptulose 1, 7 biphosphatase (SBPase), the peptidyl-prolyl cis-trans isomerase (CYP20-3) and enolase 2 (ENO2). In vitro analysis of these proteins identified this modification in SBPase Cys74, CYP20-3 Cys259 and ENO2 Cys346 residues that affected the enzymatic activity of the enzymes. GO classification and protein-protein interaction cluster analysis revealed the function of S-cyanylation in the regulation of primary metabolic pathways as glycolysis, and the Calvin and S-adenosylmethionine cicles.

2019-01-09 | PXD009812 | Pride

Transcriptomic study of the impact of iron toxicity on rice plant

Project description:transcriptomic study of the impact of iron toxicity on rice plant (Oryza sativa L.; cv M-bM-^@M-^XI Kong PaoM-bM-^@M-^Y ) after short term (3 days) or long term (3 weeks) exposure to ferrous iron (125 ppm). Twenty five days old rice seedlings were exposed to 0 or 125 mg/L ferrous iron for 3 days and 3 weeks in hydroponic culture. Comparison between control and iron stressed plants were done at the shoot and the root levels. The assays were replicated twice on two independent plant cultures. 8 samples, Two-condition experiment, control (0 ppm ferrous iron) vs. iron treated (125 ppm ferrous iron). Biological replicates: 2 replicates for comparison shoot 3 days of stress, root 3 days of stress, shoot 3 weeks of stress and root 3 weeks of stress.

2012-05-14 | E-GEOD-36299 | biostudies-arrayexpress

Pinus massoniana Transcriptome Responses Involved in Phosphorus Deficiency

Project description:Masson pine (Pinus massoniana) has evolved some adaptations for growth in low P soils. To elucidate these mechanisms, we investigated global gene expression profiles of the masson pine responding to long-term phosphorus starvation and different Pi levels (P1, 0.01 mM P; P2, 0.06 mM P). Analysis used phosphorus-sufficient treatment RNA as control samples for comparison to the experimental samples (P1 and P2) taken at 12, 24, 48 and 60 day. Indirect comparisons were made across multiple arrays with raw data pulled from different channels for data analysis and comparison to the control data.

2013-11-30 | E-GEOD-52835 | biostudies-arrayexpress

Iron (Fe) deficiency in Citrus

Project description:Transcription profiling of citrus rootstock Poncirus trifoliata (L.) Raf. Keywords: Abiotic stress (Iron chlorosis) Total RNA from four replicates for each sample category (Poncirus trifoliata (L.) Raf watered for 60 days with 18 uM Fe-EDDHA or without Fe-EDDHA) were generated and compared.

2010-05-19 | E-GEOD-17255 | biostudies-arrayexpress

R. sphaeroides Δirr -Fe vs. R. sphaeroides Δirr +Fe under microaerobic conditions

Project description:Transcriptional profiling of R. sphaeroides Δirr under iron limitation (-Fe) compared to control R. sphaeroides Δirr under normal growth conditions (+Fe). Two strain experiment under normal iron (+Fe) and iron limitation (-Fe) conditions. 6 Biological replicates, independently grown and harvested at OD660=0,4; 1-3 pooled in replicate 1, 4-6 pooled in replicate 2

2011-11-09 | E-GEOD-33533 | biostudies-arrayexpress

bHLH39 overexpression

Project description:au13-06_fit - bhlh39 overexpression - Analyse the responses to bHLH39 overexpression. bHLH39 is one of the transcription factors regulating iron homeostasis responses. - Six day-old seedlings (wild type and bHLH39 overexpressor) were grown on Hoagland medium. Full seedlings were harvested for analysis. 21 dye-swap - normal vs transgenic comparaison

2015-02-14 | E-GEOD-65934 | biostudies-arrayexpress

Transcription profiling of rat duodenal samples at different developmental stages and the effects of iron-deficiency

Project description:The effect of iron-deficiency on duodenal gene expression was investigated in rats at different developmental stages.

2007-09-15 | E-GEOD-1892 | biostudies-arrayexpress