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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genes Differentially Expressed in Slow Wilting Phenotypes under a High Vapor Pressure Deficit

ABSTRACT: The purpose of this study is to compare transcriptome profiles of one fast wilting and two slow wilting genotypes under low- and high- vapor pressure deficit Experiments: Five differential expression analyses were performed. 1. Differences within the Hutchesen line for slow and fast wilting; 2. Differences within the PI471938 line for slow and fast wilting; 3. Differences within the PI416937 line for slow and fast wilting; Differences between Hutchesen, PI471938 and PI416937 (regardless of pheotype); 5. Comparison between all lines and all pheotypes Methods: RNASeq data was generated using the Illumina HiSeq. Data passing quality control was processed as follows: Alignment to reference genome Gmax_109 using Tophat2 followed by the Tuxedo pipeline (cufflinks, cuffmerge, cuffdiff). Three cultivars, (wild-type Hutchesen and two parentla lines - PI471938 and PI416937; two conditions (normal and slow-wilting); two reps each for a total of 12 samples

ORGANISM(S): Glycine max

SUBMITTER: Elizabeth Scholl

PROVIDER: E-GEOD-49097 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genes Differentially Expressed in Slow Wilting Phenotypes under a High Vapor Pressure Deficit

Project description:The purpose of this study is to compare transcriptome profiles of one fast wilting and two slow wilting genotypes under low- and high- vapor pressure deficit Experiments: Five differential expression analyses were performed. 1. Differences within the Hutchesen line for slow and fast wilting; 2. Differences within the PI471938 line for slow and fast wilting; 3. Differences within the PI416937 line for slow and fast wilting; Differences between Hutchesen, PI471938 and PI416937 (regardless of pheotype); 5. Comparison between all lines and all pheotypes Methods: RNASeq data was generated using the Illumina HiSeq. Data passing quality control was processed as follows: Alignment to reference genome Gmax_109 using Tophat2 followed by the Tuxedo pipeline (cufflinks, cuffmerge, cuffdiff).

2014-07-15 | GSE49097 | GEO

Gill transcriptomic analysis in fast- and slow-growing individuals of the mussel Mytilus galloprovincialis reared under a daily air exposure regime

Project description:Gill transcriptome of fast- and slow-growing mussels reared under continuous food supply was recently analysed in order to ascertain the differential gene expression underlying interindividual differences in growth rate. The present study aims to analyse the gene expression differences between fast- and slow-growing mussels submitted to an air exposure of 8 hours a day during the rearing period. Transcriptome will be also compared with their continuously submerged counterparts in order to analyse the effect of air exposure on the gene expression of fast- and slow-growing individuals.

2019-09-15 | GSE131910 | GEO

Comparative analysis of drought-responsive transcriptome in soybean lines contrasting for canopy wilting

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of abiotic stress molecular pathways. The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of contrasting slow wilting lines to quantify transcript abumdance under drought stress condition Methods: The three biological replicates of DS line, Pana (control and drought samples) and DT line, PI 567690 (control and drought samples) leaf sample RNA were multiplexed and sequenced on an Illumina Hi-Seq 2000 platform. The RNA concentration of each sample was approximately 200ng/µl with a quantity of 50 µl.isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays

2015-08-31 | E-GEOD-70310 | biostudies-arrayexpress

Phosphoproteomic in soleus and biceps femoris muscle

Project description:We used phosphoproteomic profiling of slow-twitch (soleus, SOL) and fast-twitch (biceps femoris, BF) muscle to identify differences between these muscle types.

2022-08-16 | PXD036066 | iProX

Rattus norvegicus

Project description:Differences in gene expression between fast and slow muscle or between normal and denervated slow muscles

| PRJNA262975 | ENA

Identification of differentially expressed genes and pathways for myofiber characteristics in soleus and extensor digitorum longus muscles between chicken breeds differing in meat quality

Project description:In the modern chicken industry, fast-growing broilers have undergone strong artificial selection for muscle growth, which has led to remarkable phenotypic variations compared with slow-growing chickens. However, the molecular mechanism underlying these phenotypes differences remains unknown. In this study, a systematic identification of candidate genes and new pathways related to myofiber development and composition in chicken Soleus muscle has been made using gene expression profiles of two distinct breeds: Qingyuan partridge (QY), a slow-growing Chinese breed possessing high meat quality and Cobb 500 (CB), a commercial fast-growing broiler line. Agilent cDNA microarray analyses were conducted to determine gene expression profiles of soleus and extensor digitorum longus muscle sampled at sexual maturity age of QY (112 d) and CB (42 d).

2017-06-16 | GSE69918 | GEO

Comparative analysis of drought-responsive transcriptome in soybean lines contrasting for canopy wilting

2015-08-31 | GSE70310 | GEO

Fast and slow muscle proteins in scallops

Project description:We performed the first quantitative proteomics analysis of differences between striated (fast) and catch (slow) adductor muscle in Yesso scallop (Patinopecten yessoensis), with the goal to uncover muscle specific genes and proteins, as well as enzymes of metabolic pathways in fast and slow adductor muscle of scallops. The present findings highlight the functional roles of muscle contractile proteins, calcium signaling pathways, membrane and extracellular matrix proteins, and glycogen metabolism involved in the different contractile and metabolic properties between fast and slow muscles. The present findings will help better understand the molecular basis underlying muscle contraction and its physiological regulation in invertebrates.

2018-10-26 | PXD005166 | Pride

Transcription factor fluctuations underlie cell-to-cell variability in the Hedgehog response [bulk-RNAseq]

Project description:Stochastic differences among clonal cells can initiate cell fate decisions in development or cause cell-to-cell differences in the responses to drugs or extracellular ligands. We hypothesize that some of this phenotypic variability is caused by stochastic fluctuations in the activities of transcription factors. We tested this hypothesis in NIH3T3-CG cells using the response to Hedgehog signaling as a model cellular response. Here we present evidence for the existence of distinct fast and slow responding substates of NIH3T3-CG cells. These two substates have distinct expression profiles, and fluctuations in the activity of the Prrx1 transcription factor (TF) underlie some of the differences in expression and responsiveness between fast and slow cells. We speculate that similar variability in other TFs may underlie other phenotypic differences among genetically identical cells.

2022-06-18 | GSE206154 | GEO

Transcription factor fluctuations underlie cell-to-cell variability in the Hedgehog response

2022-05-19 | GSE203134 | GEO

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