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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Time series of gene expression profiles describing the temporal response to prolonged heat stress in C. elegans.

ABSTRACT: This experiment broadens our understanding of the temporal dynamics underlying the transcriptional response to heat stress. Using C. elegans hermaphrodite N2 populations, we have created a high-resolution time series of gene expression profiles taken at different time points during prolonged heat stress (35 C) conditions. Samples ware taken after 0h, 0.5h, 1h, 2h, 3h, 4h, 6h, 8h, and 12h of heat exposure with 3-5 biological replicas per time point.

INSTRUMENT(S): Promega MaxwellÂ® 16 AS2000

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Katharina Jovic

PROVIDER: E-MTAB-5753 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Recovery time-series after increasing heat-stress exposures in Caenorhabditis elegans measured by microarray

Project description:Increased exposure to heat-stress leads to an increasingly altered transcriptome in Caenorhabditis elegans. It is however unclear how the recovery from heat-stress progresses after increased heat-stress exposures. Hence, we exposed populations of the N2 strain to a 2, 3, 4, or 6 hour heat-shock of 35 degrees Celsius and took samples from 1 - 4 hours after termination of stress. This experiment was conduced in three biological replicates.

2019-11-12 | E-MTAB-7948 | biostudies-arrayexpress

Time series of gene expression profiles from C. elegans exposed to heat-stress and during subsequent recovery

Project description:This data set provides insight into the temporal dynamics of gene expression changes during heat-stress (at 35C) and during subsequent recovery (at 20C) in Caenorhabditis elegans. Age synchronized C. elegans CB4856 hermaphrodite populations were exposed to heat stress (35C) for 0h, 0.5h, 1h, 2h, 4h, and 6h. A recovery time-series was created by using age-synchronized N2 populations exposed to heat stress (35C) for 2 hours with a subsequent recovery period of 0.5h, 1h, 1.5h, 2h, 4h, and 6h at 20C. The samples were collected at the indicated time-points during heat stress or recovery. Gene expression profiles were created using microarray technology. This data set is an extension of the data provided under accession number E-MTAB-5753 (i.e. time series describing the gene expression dynamics during heat stress of N2).

2019-09-30 | E-MTAB-7007 | biostudies-arrayexpress

Recovery from heat-stress time series in Caenorhabditis elegans measured by microarray

Project description:After measuring the transcriptional response to increasing exposure of Caenorhabditis elegans N2 to 35 degrees Celsius, we wondered how recovery from heat-stress would progress. Hence, we exposed populations of the N2 strain to a 2 hour heat-shock of 35 degrees Celsius and took samples from 0 - 7 hours after termination of stress. This experiment was conduced in three biological replicates.

2023-05-30 | E-MTAB-7947 | biostudies-arrayexpress

Gene expression profiling in control, heat-shock, and recovery treatment in a RIL population of Caenorhabditis elegans L4 larvae

Project description:This experiment investigates the genetic architecture of gene expression (eQTL) in three different treatments in a N2xCB4856 RIL population of Caenorhabditis elegans. The goal is to identify genetic variation linked to differences in gene expression. We exposed 48 RILs per treatment to a control, heat-stress, and recovery treatment. More specifically these three conditions can be characterized as: (i) the control treatment was grown for 48 hours at 20C, (ii) the heat-stress treatment was grown for 46 hours at 20C followed by 2 hours at 35C, and (iii) the recovery treatment was grown for 46 hours at 20C, followed by 2 hours at 35C and thereafter 2 hours at 20C. Thereafter RNA was isolated, labelled and hybridized on microarray. The gene expression profiles were used for eQTL mapping.

2017-05-30 | E-MTAB-5779 | biostudies-arrayexpress

Gene expression profiling in control, heat-shock, and recovery treatment in an introgression line population of Caenorhabditis elegans L4 larvae

Project description:This experiment investigates the genetic architecture of gene expression (eQTL) in three different treatments in an N2xCB4856 introgression line population of Caenorhabditis elegans. The goal is to compare the effect of small CB4856 introgressions in an N2 genetic background versus a previously conducted experiment using recombinant inbred lines (RILs) derived from the same parental strains. We exposed ILs to a control (56 ILs), heat-stress (56 ILs), and recovery treatment (55 ILs). Additionally, also both parental strains, N2 and CB4856 were exposed to these three treatments (in at least 3 replicas per treatment). More specifically, these three conditions can be characterized as: (i) the control treatment was grown for 48 hours at 20C, (ii) the heat-stress treatment was grown for 46 hours at 20C followed by 2 hours at 35C, and (iii) the recovery treatment was grown for 46 hours at 20C, followed by 2 hours at 35C and thereafter 2 hours at 20C. Thereafter RNA was isolated, labelled and hybridized on microarray. The gene expression profiles were used for comparison versus findings in the RIL population (E-MTAB-5779).

2019-05-29 | E-MTAB-7424 | biostudies-arrayexpress

A standardized and reproducible workflow for membrane glass slides in routine histology and spatial proteomics

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2023-10-24 | PXD040281 | Pride

Operation of a TCA cycle subnetwork in the mammalian nucleus

Project description:Nucleic acid and histone modifications critically depend on central metabolism for substrates and co-factors. Although a few enzymes related to the formation of these metabolites have been reported in the nucleus, the corresponding metabolic pathways are considered to function elsewhere in the cell. Here we show that a substantial part of the mitochondrial tricarboxylic acid (TCA) cycle, the biosynthetic hub of epigenetic modification factors, is operational also in the nucleus. Using 13C-tracer analysis, we identified activity of glutamine-to-fumarate, citrate-to-succinate, and glutamine-to-aspartate routes in the nuclei of HeLa cells. Proximity labeling mass-spectrometry revealed a spatial vicinity of the involved enzymes with core nuclear proteins, supporting their nuclear location. We further show nuclear localization of aconitase 2 and 2-oxoglutarate dehydrogenase in mouse embryonic stem cells. Together, our results demonstrate operation of an extended metabolic pathway in the nucleus warranting a revision of the canonical view on metabolic compartmentalization and gene expression regulation.

2022-10-13 | PXD022608 | Pride

Gene expression effects in Caenorhabditis elegans strains of feeding on Erwinia rhapontici or Escherichia coli

Project description:Diet can have a strong impact on development, to test this effect the strains N2, CB4856, three strains from Orsay (JU1581, JU1944, and JU1949), and three strains from Santeuil (JU1921, JU1930, and JU1932) were grown on two different food-sources. These sources were the standard lab food, Escherichia coli OP50, and the Gram-negative plant pathogen Erwinia rhapontici. The effect of these bacteria on development could also be measured by the start of reproduction, which was delayed while feeding on E. coli. To measure the transcriptional effects, age-synchronized strains were grown for 48 hours at 20 degrees Celsius. The impact of food-source on gene expression was determined by a transcriptional ruler based on the strain N2 (E-MTAB-7019).

2019-07-12 | E-MTAB-8129 | biostudies-arrayexpress

Preparation of tirapazamine-resistant hepatoma cell line

Project description:The aim of the project was to obtain murine hepatoma MH22a [1] cell subline, resistant to anticancer agent 3-amino-1,2,4-benzotriazine-1,4-dioxide (tirapazamine, TPZ), and examine the changes of the protein expression as compared with parental cells, with the main emphasis on the changes of redox proteins. MH22a cells obtained from the Institute of Cytology of the Russian Academy of Sciences (St. Petersburg, Russia), were grown at 37Â°C in DMEM medium, supplemented with 10% fetal bovine serum and antibiotics in T25 flasks until reaching 70-80% confluence. The medium is then changed to an analogous medium with 5.0 Î¼M TPZ, and, depending on cell viability, 50% of the medium with TPZ is changed 1-2 times a week, repeating that procedure for 3.5 months to form a stable monolayer. The resulting monolayer is inoculated 1:2 and further grown by changing 50% of the culture medium twice a week until re-inoculation. 20 passages were made over 2.5 months in total. We were unable to obtain a cell subline in a stepwise fashion by growing the cells in increasing concentrations of TPZ, because its concentration increase up to 10 Î¼M caused cell death after 1 month. For analysis, one flask per each sample, 3 samples of parental cell line and 3 samples of TPZ-resistant cell line (between 15th and 20th passages), were selected. Cells were rinsed three times with PBS, detached with TrypLE Express (ThermoFisher Scientific, Waltham, MA, USA) and cell concentration and viability was determined with Trypan blue and Countess 2 (ThermoFisher Scientific, Waltham, MA, USA) automated cell counter. Cells were rinsed by centrifuging 500xg for 5 min and suspending in PBS three times. Finally, cells were flash frozen in liquid nitrogen and transferred to -86Â°C freezer for storage. [1] European Collection of Authenticated Cell Cultures (ECACC), Catalogue No. 96121721.

2023-05-10 | PXD039876 | Pride

Microarray of C. elegans wild types N2 and CB4856 after Orsay virus infection and heat-shock treatment.

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2021-03-08 | E-MTAB-10214 | biostudies-arrayexpress

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