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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Microarray analysis of Caenorhabditis elegans exposed to three hydrophilic genotoxicants in water in duplicate

ABSTRACT: In this study, we exposed Caenorhabditis elegans wild types N2 to two concentrations of the model genotoxicants formaldehyde (HCHO), N-ethyl-N-nitrosourea (ENU), and methyl methanesulfonate (MMS).We performed a concentration-response test to determine the non-toxic concentration range for studying the transcriptional effects of compounds. In microarray experiments, we studied two concentrations (1 mM and 5 mM) for each compound and a control of M9 medium. Age synchronized worms at developmental L4 larval stage were exposed to treatment for two hours. After flash freezing the samples, RNA was isolated, labeled and hybridized on oligo microarray (Agilent) slides.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Inez Dinkla

PROVIDER: E-MTAB-10264 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Development of a transcription-based bioanalytical tool to quantify the toxic potencies of hydrophilic compounds in water using the nematode Caenorhabditis elegans.

Karengera Antoine A Bao Cong C Riksen Joost A G JAG van Veelen H Pieter J HPJ Sterken Mark G MG Kammenga Jan E JE Murk Albertinka J AJ Dinkla Inez J T IJT

Ecotoxicology and environmental safety 20211023

Low concentrations of environmental contaminants can be difficult to detect with current analytical tools, yet they may pose a risk to human and environmental health. The development of bioanalytical tools can help to quantify toxic potencies of biologically active compounds even of hydrophilic contaminants that are hard to extract from water samples. In this study, we exposed the model organism Caenorhabditis elegans synchronized in larval stage L4 to hydrophilic compounds via the water phase a ...[more]

PMID: 34700171

Similar Datasets

Microarray analysis of Caenorhabditis elegans exposed to three hydrophilic genotoxicants in water

Project description:In this study, we exposed Caenorhabditis elegans wild types N2 to two concentrations of the model genotoxicants formaldehyde (HCHO), N-ethyl-N-nitrosourea (ENU), and methyl methanesulfonate (MMS).We performed a concentration-response test to determine the non-toxic concentration range for studying the transcriptional effects of compounds. In microarray experiments, we studied two concentrations (1 mM and 5 mM) for each compound and a control of M9 medium. Age synchronized worms at developmental L4 larval stage were exposed to treatment for four hours. After flash freezing the samples, RNA was isolated, labeled and hybridized on oligo microarray (Agilent) slides.

2021-04-23 | E-MTAB-10265 | biostudies-arrayexpress

Microarray analysis of Caenorhabditis elegans exposed to four indirect-acting toxicants

Project description:In this study, we exposed Caenorhabditis elegans wild types N2 to the model indirect-acting toxicants aflatoxin B1 (AFB1), benzo(a)pyrene (B(a)P), the PCB mixture Aroclor 1254 (PCB1254), and 2,3,7,8-tetrachlorodibenzodioxin (TCDD). In microarray experiments, we studied one concentration of AFB1 (30 μM), one concentration of B(a)P (30 μM), two concentrations of PCB1254 (1 μM and 30 μM), and two concentrations of TCDD (1 μM and 10 μM). As a control M9 medium with 0.5% DMSO was used. Age synchronized worms at developmental L4 larval stage were exposed to treatment for 24 hours. After flash freezing the samples, RNA was isolated, labeled and hybridized on oligo microarray (Agilent) slides.

2022-04-25 | E-MTAB-11143 | biostudies-arrayexpress

Microarray analysis of Caenorhabditis elegans exposed to six distinct water samples

Project description:In this study, we exposed Caenorhabditis elegans wild types N2 to water collected from six sources in the Dutch village Sneek. The sources were: wastewater from a hospital, a community (80 households), a nursing home, influent into the local municipal wastewater treatment plant, effluent of the wastewater treatment plant, and surface water samples. The goal of the experiment was to determine if C. elegans can be used to identify pollutants in the water by transcriptional profiling. Age synchronized worms at developmental L4 larval stage were exposed to treatment for 24 hours. After flash freezing the samples, RNA was isolated, labeled and hybridized on oligo microarray (Agilent) slides.

2022-12-03 | E-MTAB-11260 | biostudies-arrayexpress

Gene expression by microarray of a Caenorhabditis elegans recombinant inbred line panel carrying human alpha-synuclein

Project description:We conducted a timeseries experiment on a recombinant inbred line (RIL) panel of Caenorhabditis elegans derived from a NL5901 x SCH4856 cross. These RILs carry a human alpha-synuclein gene in an N2 and a CB4856 genetic background respectively. We grew synchronized populations of the nematodes (70 RILs, N2, CB4856, NL5901, and SCH4856) under normal conditions (20 degrees Celcius, feeding on Escherichia coli OP50) for 120 hours. The goal of the experiment was to identify loci affecting gene expression in the presence of human alpha-synuclein

2023-07-30 | E-MTAB-11658 | biostudies-arrayexpress

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

Project description:This explorative study investigated the transcriptional response of C. elegans wild types N2 and CB4856 after Orsay virus infection and Heat shock (n=1). Each strain had a sample that was heat-shocked and infected, one that was heat-shocked and mock-infected, one that was only infected and one that only underwent a mock infection. Age synchronized worms were treated separately according to different treatments mentioned before. After flash freezing, RNA was isolated, labeled and hybridized on oligo microarray (Agilent) slides.

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

Gene expression by microarray of two genotypes of Caenorhabditis elegans carrying human alpha-synuclein

Project description:We conducted a timeseries experiment on Caenorhabditis elegans genotypes NL5901 and SCH4856, which carry a human alpha-synuclein gene in an N2 and a CB4856 genetic background respectively. We grew synchronized populations of the nematodes under normal conditions (20 degrees Celcius, feeding on Escherichia coli OP50) for 24 to 216 hours. Each 24 hours plates were sampled. The goal of the experiment was to identify a timepoint where the differential development speed of the two genotypes had little influence on gene expression profiles.

2023-05-30 | E-MTAB-11657 | biostudies-arrayexpress

Gene expression by microarray of Caenorhabditis elegans introgression lines carrying human alpha-synuclein

Project description:We conducted an experiment on introgression lines of Caenorhabditis elegans derived from a NL5901 cross with three previously constructed CB4856>N2 ILs (WN268, WN269, and WN270). The tested ILs carry a combination of chromosome V introgressions and the alpha-synuclein trans-gene: CB4856>N2 / aS, CB4856>N2 / -, - / aS, and - / -. We grew synchronized populations of the nematodes (12 ILs, N2, CB4856, NL5901, and SCH4856) under normal conditions (20 degrees Celcius, feeding on Escherichia coli OP50) for 120 hours. This experiment was repeated three times. The goal of the experiment was to identify loci affecting gene expression in the presence of human alpha-synuclein

2023-07-30 | E-MTAB-11661 | biostudies-arrayexpress

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

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

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

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