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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).

ORGANISM(S): Glycine max

PROVIDER: GSE49097 | GEO | 2014/07/15

SECONDARY ACCESSION(S): PRJNA213009

REPOSITORIES: GEO

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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). 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

2014-07-15 | E-GEOD-49097 | biostudies-arrayexpress

Glycine max

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

| PRJNA213009 | ENA

Lung response to oil vapor exposure in rats

Project description:The lung response to inhalation exposure to oil vapor particles was investigated in a rat model. Adult male Sprague-Dawley rats were exposed by whole-body inhalation to air or an aerosol containing oil vapor particles at concentrations of 300 ppm, 6 hours/day for 1 day (shot-term) or 300 ppm, 6 hours/day, 4 days/week for 4 weeks (long-term). The control and oil vapor exposed rats were euthanized at post-exposure time intervals of 1 and 28 days and lung toxicity determined. Analysis of bronchoalveolar lavage parameters of toxicity such as lactate dehydrogenase activity, oxidant generation, and inflammation did not reveal any significant lung toxicity in the oil vapor exposed rats. Approximately 50 genes each were found significantly differentially expressed in both the short- and long-term exposure groups of the rats at the one-day post-exposure time interval. The data obtained from the present study demonstrated that oil vapor inhalation exposure, under the exposure conditions employed in the present study, did not result in any significant lung toxicity in the rats despite the gene expression changes detected.

2022-12-31 | GSE152187 | GEO

Cigarette smoke but not novel tobacco vapor product cause epigenetic disruption and cell apoptosis.

Project description:Novel tobacco vapor product, generating vapor without combusting tobacco leaves, has been developed expecting the number and quantity of chemicals in the vapor of these products to be reduced compared to conventional combustible cigarettes. However, if the lower chemical levels correlate with lower toxicity remained to be clarified. Here we examined the difference of conventional cigarette smoke (CS) and novel tobacco vapor product (NTV) using cultured cancer cell line A549 and normal bronchial epithelium cell line BEAS-2B. 0.5% of 3R4F which is conventional CS markedly decreased cell proliferation of both A549 and BEAS-2B, however Ploom TECH or Ploom TECH+ which are commercially available NTV did not affect cell growth. To clarify the cause of decreased cell proliferation, Tunnel assay was performed and clarified that apoptosis was observed in both A549 and BEAS-2B after 24hours after exposure to 3R4F. To further explore the effect of CS to epigenetics, we performed western blotting Histone H2A phosphorylation which is known to correlate transcriptional regulation. Only 3R4F decreased histone H2A phosphorylation of both A549 and BEAS-2B. Then we examined alterations of gene expression after 3R4F treatment of A549 cell. 339, 107, 103 genes which were upregulated more than 2fold were observed in 3R4F, Ploom TECH or Ploom TECH+ treated A549 cell, respectively. Among 339 genes which was upregulated 3R4F, we focused EGR1, FOS, and FOSB gene since they were upregulated more than100 fold. We confirmed this upregulation using RTqPCR. These data suggest that Cigarette smoke but not novel tobacco vapor product cause epigenetic disruption and cell apoptosis possibly by elevating genes such as EGR1.

2020-12-07 | GSE157165 | GEO

VAPOR

Project description:Influenza Classification from Short Reads with VAPOR Facilitates Robust Mapping Pipelines and Zoonotic Strain Detection for Routine Surveillance Applications

| PRJEB33950 | ENA

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

MicroRNA expression data from CIE-vapor treated mice

Project description:We examined microRNA expression profiles in amygdala (AMY), nucleus accumbens (NAC) and prefrontal cortex (PFC) of male C57BL/6J mice exposed to 4 cycles of chronic intermittent ethanol (CIE) vapor. Animals were sacrificed at 0, 8, and 120 hr following the last ethanol exposure.

2017-12-01 | GSE90608 | GEO

Fast and chronic ethanol tolerance - time course

Project description:To better understand the molecular mechanisms underlying ethanol action we have developed an assay system to study sensitivity and fast and chronic tolerance to the sedative effects of ethanol. Flies developed fast ethanol tolerance after single exposure to 50% of ethanol vapor for 40 min. Flies can also develope chronic ethanol tolerance after 5x 40 min exposure to 50% ethanol vapor interspersed with 4x 80 min exposure to 10% ethanol vapor. We used microarray analysis to identify genes involved in the development of fast and chronic ethanol tolerance in Drosophila. More than 600 hundred genes were found to have changed their expression level in response to different ethanol treatment. Among these genes, Homer was picked for further study and is demonstrated that its expression in ellipsoid body is critical for the normal sensitivity and fast toleance to ethanol. Keywords: time course Whole heads of 3 groups of Drosophila were separated for RNA extraction and hybridization on Affymetrix microarrays. These 3 groups of flies were treated with different ethanol treatment. Naive group of flies (GSM101531, GSM101532, GSM101533, GSM101534, GSM101535, GSM101536) received only 50 min of humidified air. Fast group of flies (GSM101537, GSM101538, GSM101539, GSM101540, GSM101541, GSM101542) received humidified air for 50 min followed by a single exposure of 50% ethanol vapor for 40 min. Chronic group of flies (GSM101543, GSM101544, GSM101545, GSM101546, GSM101547, GSM101548) ) received humidified air for 50 min followed by 5 exposures of 50% ethanol vapor for 40 min.

2006-03-24 | E-GEOD-4531 | biostudies-arrayexpress

Fast and chronic ethanol tolerance - time course

2006-03-24 | GSE4531 | GEO

Biological changes in C57BL/6 mice following 3 weeks of inhalation exposure to cigarette smoke or e-vapor aerosols

Project description:We compared early biological changes in mice after inhalation exposures to cigarette smoke or e-vapor aerosols (MarkTen® cartridge with Carrier, Test-1, or Test-2 formulations; 4% nicotine). Female C57BL/6 mice were exposed to 3R4F cigarette smoke or e-vapor aerosols by nose-only inhalation for up to 4 hours/day, 5 days/week, for 3 weeks. The 3R4F and e-vapor exposures were set to match the target nose port aerosol nicotine concentration (∼41 µg/L). Only the 3R4F group showed postexposure clinical signs such as tremors and lethargy. At necropsy, the 3R4F group had significant increases in lung weight and changes in bronchoalveolar lavage parameters, as well as microscopic findings in the respiratory tract. The e-vapor groups had minimal microscopic changes, including squamous metaplasia in laryngeal epiglottis, and histiocytic infiltrates in the lung (Test-2 group only). The 3R4F group had a higher incidence and severity of microscopic findings compared to any e-vapor group. Transcriptomic analysis also showed that the 3R4F group had the highest number of differentially expressed genes compared to Sham Control. Among e-vapor groups, Test-2 group had more differentially expressed genes but the magnitude of gene expression-based network perturbations in all e-vapor groups was ∼94% less than the 3R4F group. On proteome analysis in the lung, differentially regulated proteins were detected in the 3R4F group only. In conclusion, 3-weeks of 3R4F exposure induced molecular and microscopic changes associated with smoking-related diseases in the respiratory tract, while e-vapor exposures showed substantially reduced biological activities.

2021-02-28 | E-MTAB-10166 | biostudies-arrayexpress

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