Expression data from Low Temperature Plasma-treated primary prostate cultures
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE119052 | GEO | 2018/08/27
REPOSITORIES: GEO
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Project description:Expression data from Low Temperature Plasma-treated primary prostate cultures
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Project description:To evaluate the effect of LTP-activated Ringer’s lactate solution (PAL) for malignant melanoma, the whole transcriptome sequencing of PAL treated A375 melanoma cells were performed.
2026-02-28 | GSE297697 | GEO
Project description:Aims: To investigate the inactivation kinetics of Bacillus cereus vegetative cells upon exposure to low-temperature nitrogen gas plasma and to reveal the mode of inactivation by transcriptome profiling. Methods and results: Exponentially growing B. cereus cells were filtered and put on agar plates. The plates, carrying the filters with the vegetative cells, were placed into nitrogen gas plasma at atmospheric pressure and cold temperature (~37°C). After different exposure times the cells were harvested for RNA extraction and enumeration. The RNA was used to perform whole transcriptome profiling using DNA microarrays. The transcriptome profile showed a large overlap with profiles obtained from conditions generating reactive oxygen species inside B. cereus. However, excess radicals such as peroxynitrite, hydroxyl and or superoxide were not found. Conclusions: Antibacterial activity of nitrogen gas plasmas is not based on UV radiation but on the formation of reactive oxygen or nitrogen species in the plasma jet rather than inside the targeted cells. Significance and impact of the study: This study represents the first investigation of differential gene expression on a genome-wide scale in B. cereus following nitrogen gas plasma exposure. This study may help to design cheap, safe, and effective plasma decontamination devices. Plasma treated sampes compared with nitrogen gas flow treated samples and plasma treated samples compared to untreated control samples. Nitrogen flow samples in duplicate, plasma treated samples 4 replicates. Replicates hybridized with dyes swapped.
2013-05-06 | E-GEOD-35060 | biostudies-arrayexpress
Project description:Purpose: Comparison of genes expression pattern in normal human epidermal keratinocytes (NHEKs) which were cultured at several specific temperatures or with rapamycin. Methods: Basically, NHEKs were cultured with irradiated 3T3J2 feeder cells in cFAD medium (Pr Green's method) for 1 week. NHEKs were cultured at 32, 35, 36, 37 and 38 degrees C from beginning to end of cell culture, respectively. Furthermore, 100 nM rapamycin-added cFAD medium and ed at 37 degrees C. 7days after cell cuture, NHEKs were harvested for RNAseq analysis. Results: The culture condition at 32 degrees C and 37 degrees C with rapamycin maintained human epidermal keratinocyte stem cells. Conclusions: mTORC1 inhibition via temperature changes favors ex vivo maintenance of human epidermal keratinocyte stem cells.
2023-05-29 | GSE199522 | GEO
Project description:Purpose: Comparison of genes expression pattern in normal human epidermal keratinocytes (NHEKs) which were cultured at several specific temperatures or with rapamycin. Methods: Basically, NHEKs were cultured with irradiated 3T3J2 feeder cells in cFAD medium (Pr Green's method) for 1 week. NHEKs were cultured at 32, 35, 36, 37 and 38 degrees C from beginning to end of cell culture, respectively. Furthermore, 100 nM rapamycin-added cFAD medium and ed at 37 degrees C. 7days after cell cuture, NHEKs were harvested for RNAseq analysis. Results: The culture condition at 32 degrees C and 37 degrees C with rapamycin maintained human epidermal keratinocyte stem cells. Conclusions: mTORC1 inhibition via temperature changes favors ex vivo maintenance of human epidermal keratinocyte stem cells.
2023-05-29 | GSE198696 | GEO
Project description:Aims: To investigate the inactivation kinetics of Bacillus cereus vegetative cells upon exposure to low-temperature nitrogen gas plasma and to reveal the mode of inactivation by transcriptome profiling. Methods and results: Exponentially growing B. cereus cells were filtered and put on agar plates. The plates, carrying the filters with the vegetative cells, were placed into nitrogen gas plasma at atmospheric pressure and cold temperature (~37°C). After different exposure times the cells were harvested for RNA extraction and enumeration. The RNA was used to perform whole transcriptome profiling using DNA microarrays. The transcriptome profile showed a large overlap with profiles obtained from conditions generating reactive oxygen species inside B. cereus. However, excess radicals such as peroxynitrite, hydroxyl and or superoxide were not found. Conclusions: Antibacterial activity of nitrogen gas plasmas is not based on UV radiation but on the formation of reactive oxygen or nitrogen species in the plasma jet rather than inside the targeted cells. Significance and impact of the study: This study represents the first investigation of differential gene expression on a genome-wide scale in B. cereus following nitrogen gas plasma exposure. This study may help to design cheap, safe, and effective plasma decontamination devices.
2013-05-06 | GSE35060 | GEO
Project description:Purpose: Study the differentially expressed genes in hippocampal rat CA1 regions 90 minutes after Long-Term Potentiation (LTP) was induced using field recordings Methods: hippocampal rat CA1 region mRNA profiles of control (unstimulated) and 90 minutes after LTPwas induced (LTP 90) were generated by deep sequencing. A pool of approximately 10 CA1 regions collected from at least 3 different animals were used. The seq library was prepared using TruSeq RNA Sample Prep Kit v2 protocol (Illumina, CA, USA). For the RNA-Seq data analysis Tophat 2.0.13, bowtie 2.1.0 , samtool 0.1.7 and cufflinks 1.3.0 were used. The rn5-bowtie2 index was generated with the command 'bowtie2-build rn5.fa rn5'. The 'rn5.fa'-file was downloaded from the UCSC genome browser. The mm10-bowtie2 index was downloaded from http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml. RefSeq geneTracks and GTF-files for the rn5 and mm10 genome assembly were downloaded from UCSC genome browser. Common gene ids in the GTF-files were matched to individual transcript_ids using the corresponding official symbols obtained from the geneTracks files. Conclusions: Our study illustrates the nature of the different transcripts in acute rat hippocampal slices after LTP 90 minutes was induced using field electrophysiology and compares them with control, unstimulated slices. Thius allowed us to identify wich genes are modulated in the hippocampus in order to promote and sustain LTP.
2018-10-02 | GSE120712 | GEO
Project description:Table grapes cv. Cardinal are highly perishable and their quality deteriorates during postharvest storage at low temperature mainly because of sensitivity to fungal decay and senescence of rachis. The application of a 3-day CO2 treatment with 20 kPa CO2 at 0C reduced total decay and retained fruit quality in early and late-harvested table grapes during postharvest storage. In order to study the transcriptional responsiveness of table grapes to low temperature and high CO2 levels in the first stage of storage and how the maturity stage affect these changes, we have performed a comparative large-scale transcriptional analysis. In the first stage of storage, low temperature led to a significantly intense change in grape skin transcriptome irrespective of fruit maturity, although there were different changes within each stage. In the case of CO2 treated samples, in comparison to fruit at time zero, only slight differences were observed. Functional enrichment analysis revealed that major modifications in the transcriptome profile of early- and late-harvested grapes stored at 0C are linked to biotic and abiotic stress-responsive terms. However, in both cases there is a specific reprogramming of the transcriptome during the first stage of storage at 0C in order to withstand the cold stress. Thus, genes involved in gluconeogenesis, photosynthesis, mRNA translation and lipid transport were up-regulated in the case of early-harvested grapes, and genes related to protein folding stability and intracellular membrane trafficking in late-harvested grapes. The beneficial effect of high CO2 treatment maintaining table grape quality seems to be an active process requiring the induction of several transcription factors and kinases in early-harvested grapes, and the activation of processes associated to the maintenance of energy in late-harvested grapes.
2016-09-04 | GSE83275 | GEO
Project description:This is a study to characterize gene expression profiles in stored Russet Burbank potato tubers. Tubers were harvested from commercial fields in the central sands region of Wisconsin in the fall of 2006. The tubers were put into storage at 55 degrees F for preconditioning and wound healing. Shortly after the temperature of the storage bin began to decrease, uniform, healthy tubers were selected for use in this microarray analysis. Tubers were at 53.6 degrees F at this time, and pieces of starch-storing tissue were collected for use as the reference sample. Other tubers were moved to temperature-controlled lockers and these were cooled gradually to either 48 or 40 degrees F following industry standard procedures. The expectation was that tubers held at 48 degrees would not have a significant accumulation of glucose and fructose, but that tubers cooled to 40 degrees would undergo low temperature sweetening and accumulate glucose and fructose to a degree that is unsuitable for processing. Three weeks later, when the locker temperatures were 48 degrees F and 41.5 degrees F, tissue samples were collected for RNA analysis. After another three weeks, samples were collected from tubers at 48 degrees F and 40 degrees F. At that time some tubers were moved from the 48 degree locker to the 40 degree locker in order to see if gene expression changes observed as a result of gradual cooling are similar to those that occur following a sudden decrease in temperature. Three weeks later, samples were collected from tubers held at 48 degrees F, tubers held at 40 degrees F, and from the tubers that were moved from 48 to 40 degrees F. At this time another set of tubers was transferred from 48 degrees to 40 degrees. Three weeks later the last samples were harvested from tubers held at 48 degrees F, from tubers held at 48 degrees F and from tubers that were transferred three weeks prior from 48 to 40 degrees. RNA was isolated from tissue extracted from three tubers. Keywords: Reference design
2008-02-13 | GSE10483 | GEO
Project description:Determine if cells in stationary-phase cultures respond to increased temperature. Yeast cells in stationary-phase cultures were exposed to temperature upshift (30C to 39C) with samples harvested every 30-minutes over 8 hours. All experimental samples are over an common reference. There are two replicates for each time point and six replicates of T0.
2010-06-30 | E-GEOD-3687 | biostudies-arrayexpress