SOLiD sequencing of C. elegans recombinant lines (RILs).
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR647997.fastq.gz | Fastqsanger.gz | |||
| ERR647998.fastq.gz | Fastqsanger.gz | |||
| ERR647999.fastq.gz | Fastqsanger.gz | |||
| ERR648000.fastq.gz | Fastqsanger.gz | |||
| ERR648001.fastq.gz | Fastqsanger.gz |
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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
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Project description:We analyzed the consequences of recombination in gene expression. For this, we measured expression patterns in two C. elegans wild types, N2 and CB4856 (CB). We compare these profiles with gene expression values from a Recombinant Inbred Population (RIL) derived from the same wild types. Expression values of the RILs (GSE17071) were obtained from Viñuela et al. (Genome Research, 2010). N2 and CB strain nematodes were cultured in identical conditions. Likewise, mRNA was extracted at three different ages (juveniles, reproductive and old worms) to investigate the transcriptional consequences of recombination in aging worms. Then, we explored gene expression heritability and transgression as genetic parameters for the analysis of gene expression divergence in natural isolates. Moreover, we investigated the progression of those parameters with age.
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Project description:Recombinant inbred lines were created by crossing the alpha-synuclein containing Caenorhabditis elegans strains NL5901 and SCH4856. These strains contain the human alpha-synuclein gene fused to YFP and under the control of an unc-54 promotor (unc-54p::alpha-synnuclein::YFP) in an N2 and CB4856 genetic background, respectively. These two strains were used to generate a total of 212 recombinant inbred lines, of which 88 were genotyped by whole-genome sequencing using a MiSeq. These recombinant inbred lines can be used for mapping genetic modifiers affecting protein accumulation.
2023-06-30 | E-MTAB-12575 | biostudies-arrayexpress
Project description:We analyzed the consequences of recombination in gene expression. For this, we measured expression patterns in two C. elegans wild types, N2 and CB4856 (CB). We compare these profiles with gene expression values from a Recombinant Inbred Population (RIL) derived from the same wild types. Expression values of the RILs (GSE17071) were obtained from Viñuela et al. (Genome Research, 2010). N2 and CB strain nematodes were cultured in identical conditions. Likewise, mRNA was extracted at three different ages (juveniles, reproductive and old worms) to investigate the transcriptional consequences of recombination in aging worms. Then, we explored gene expression heritability and transgression as genetic parameters for the analysis of gene expression divergence in natural isolates. Moreover, we investigated the progression of those parameters with age. In total, 14 dual-color microarrays were done on two wild type strains (N2 and CB4856) and three age groups (40, 96, and 214 hours). 5 replicates of t1 (juvenile) and t3 (senescent) samples, and 4 replicates of t2 (reproductive) samples, in a dye-swap design.
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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
Project description:Complex traits, including common disease-related traits, are affected by many different genes that function in multiple pathways and networks. The apoptosis, MAPK, Notch and Wnt signalling pathways play important roles in development and disease progression. At the moment we have a poor understanding of how allelic variation affects gene expression in these pathways at the level of translation. Here we report the effect of natural genetic variation on transcript and protein abundance involved in developmental signalling pathways in Caenorhabditis elegans. We used selected reaction monitoring to analyse proteins from the abovementioned four pathways in a set of recombinant inbred lines (RILs) generated from the wild-type strains Bristol N2 and Hawaii CB4856 to enable quantitative trait loci (QTL) mapping. Variation in gene expression was greater in the RILs than in the parental lines, at the proteome as well as at the transcriptome levels. We detected a trans-QTL on the left arm of chromosome II that affected protein abundance of the phosphatidylserine receptor protein PSR-1, and two separate QTLs that influenced embryonic and ionizing radiation-induced apoptosis on chromosome IV. Our results demonstrate that natural variation in C. elegans is sufficient to cause significant changes in signalling pathways both at the gene expression (transcript and protein abundance) and phenotypic levels.
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