Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

55 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microarray of five Caenorhabiditis elegans genotypes with or without a human alpha-synuclein transgene in the genetic background

ABSTRACT: Previous studies in Caenorhabditis elegans expressing the human alpha-synuclein protein, have shown that protein aggregation and some aetiologies of Parkinsons disease can be recapitulated in this model nematode. However, it is known that the genetic background is important in how the disease progresses in humans. This study sought to address this topic in the model nematode C. elegans. In this study we measured gene expression in C. elegans nematodes with different genetic backgrounds (JU511, JU1926, JU1931, and JU1941) with an introgression of and N2 region with the alpha-synuclein protein in chromosome IV. We measured expression in the wild-type strains and strains with the transgene. Each strain was measured in three biological replica's at an age of 48 hours post synchronization by bleaching.

INSTRUMENT(S): Maxwell 16 Instrument, Agilent High resolution C scanner

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Mark Sterken

PROVIDER: E-MTAB-6960 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

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

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

Microarray analysis of Caenorhabditis elegans recombinant inbred lines exposed to gld-1 or empty-vector RNAi

Project description:The glp-1/NOTCH pathway is a conserved pathway that plays an important role in developmental control. To study the effect of natural genetic variation on perturbations in this pathway, we used N2xCB4856 recombinant inbred lines of the nematode Caenorhabditis elegans. These were treated with empty vector or gld-1 RNAi, where gld-1 is a key developmental gene in the glp-1/NOTCH pathway. The recombinant inbred lines were exposed for two generation to the treatment and 47 hour old L4 juveniles were collected for RNA isolation. In total 39 RILs were exposed to the empty-vector treatment and 46 RILs were exposed to the gld-1 treatment. Gene expression was quantified using microarrays.

2022-12-20 | E-MTAB-9742 | biostudies-arrayexpress

Microarray on mock-treated or Orsay virus infected males and hermaphrodites of Caenorhabditis elegans

Project description:This experiment investigates changes in gene expression upon Orsay virus infection and between males and hermaphrodites in the nematode Ceanorhabditis elegans. The laboratory reference strain N2 was used. For this strain, males are less susceptible to Orsay virus infection than hermaphrodites. The goal of the experiment was to identify genes that show different expression patterns for both sexes upon Orsay virus infection. We mock-treated or infected 48h-old C. elegans populations with Orsay virus and took samples 30-hours after infection. For each treatment-sex combination 8 samples were collected. Thereafter RNA was isolated, labelled, and hybridized on microarray. The gene-expression dynamics of previously identified genes (e.g. from literature and from a highly replicated N2 versus CB4856 experiment) were analyzed.

2020-09-13 | E-MTAB-9561 | biostudies-arrayexpress

Microarray on an infection time-series of Orsay virus in three Caenorhabditis elegans genotypes

Project description:This experiment investigates the temporal dynamics in gene expression upon Orsay virus infection in the nematode Ceanorhabditis elegans. Three different strains were infected: JU1580, N2, and CB4856. Of these, JU1580 is highly susceptible, N2 moderately susceptible, and CB4856 the most resistant strain. The goal of the experiment was to identify genes that show different expression dynamics over the time-course of the infection. We (mock-)infected 40h-old C. elegans populations with Orsay virus and took samples over a 32-hour spanning time-course. For each treatment-strain combination 12 samples were collected. Thereafter RNA was isolated, labelled, and hybridized on microarray. The gene-expression dynamics of previously identified genes (e.g. from literature and from a highly replicated N2 versus CB4856 experiment) were analyzed.

2020-07-14 | E-MTAB-7573 | biostudies-arrayexpress

Transcriptional response to ethanol exposure in Caenorhabditis elegans measured by microarray

Project description:This study investigated the transcriptional response of C. elegans after 0, 30, 60, 120, and 480 minutes of ethanol or mock exposure (n=4 per timepoint and treatment). Age synchronized Bristol N2 animals were obtained by allowing fertile adults to lay eggs for 3 hours. After which adults were removed and the population was incubated for 3 days at 20 ˚C. After ethanol exposure, RNA was isolated, labeled and hybridized on Agilent C. elegans (V2) Gene Expression Microarray 4X44K slides.

2020-11-27 | E-MTAB-9663 | biostudies-arrayexpress

Microarray from roots of Arabidopsis Col-0 and knock-down UPL3, infected and non-infected with Heterodera schachtii

Project description:In this experiment we evaluate the transcriptional response to beet cyst nematode infection in wild-type (Col-0) and a upl3 knocked-down Arabidopsis thaliana. The data indicates that the upl3 knock-down alone does not induce a strong transcriptional regulation in the plant. However, the interaction of the mutation and infection by H. schachtii results in a strong transcriptional differential regulation, likely involving the plant’s immune responses. Samples were taken from whole root systems of 14 day-old seedlings (0 days post-infection) and mock or H. schahtii-infected 21 day-old seedlings (7 days post-infection). Each sample contained at least 18 plants and 4 biological replicates of each sample were collected.

2019-10-03 | E-MTAB-7968 | 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

Transcriptome profiling by microarray of Caenorhabditis elegans MT2124 x CB4856 RILs used for eQTL mapping

Project description:We crossed the MT2124 strain carrying the let-60 (n1046) gain of function mutation with the wild-type strain CB4856. From this cross a panel of mutation introgression recombinant inbred lines (miRILs) was generated. Using this population, the influence of genetic variation on the the let-60 (gf) mutation can be investigated. This analysis can pinpoint genetic loci A panel of 33 miRILs, the parental strains (4x), and transgenic lines amx-2(lf);Si[amx-2(Bristol)];let-60(gf) and amx-2(lf);Si[amx-2(Hawaii)];let-60(gf) containing the N2- or CB4856-allele of amx-2 in a amx-2(lf);let-60(gf) background were sampled. All the strains were grown on nematode growth medium dishes seeded with E. coli OP50. The temperature at which the strains were kept was 20 degrees Celsius and the strains were grown for 72 hours after synchronization by bleaching. Thereafter RNA was isolated, labelled, and hybridized on microarray. The gene expression profiles of the miRILs were used for eQTL mapping. The gene expression profiles of the transgenic strains were used for trans-band confirmation.

2017-07-21 | E-MTAB-5856 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data