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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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C. elegans developmental timecourse

ABSTRACT: To identify differences in gene expression patterns between C. elegans and C. briggsae we designed whole-genome species-specific microarrays. We designed two organism-specific microarrays which were then manufactured by Agilent as 44k arrays. Probes were designed to target the coding region, preferentially near the 3’ end, as well as in the presumptive 3’ UTR, up to 150bp downstream of the stop codon. 50-60mer probes were determined using OligoWiz (Wernersson and Nielsen 2005) which selects oligos based upon their cross-hybridization to other coding sequences, Tm, position along the transcript, folding potential, and low-complexity in the sequence. The probes were also restricted against spanning splice junctions to avoid missing transcripts due to errors in gene structure predictions. Each gene was assigned between one and five probes, where the probe with the best overall score was selected as the ‘A-probe’, and the remaining ranked ‘B’ through ‘E’.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Itai Yanai

PROVIDER: E-GEOD-15234 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved.

Yanai Itai I Hunter Craig P CP

Genome research 20090910 12

Genomic analyses have shown that adjacent genes are often coexpressed. However, it remains unclear whether the observed coexpression is a result of functional organization or a consequence of adjacent active chromatin or transcriptional read-through, which may be free of selective biases. Here, we compare temporal expression profiles of one-to-one orthologs in conserved or divergent genomic positions in two genetically distant nematode species-Caenorhabditis elegans and C. briggsae-that share a ...[more]

PMID: 19745112

Similar Datasets

C. briggsae developmental timecourse

Project description:To identify differences in gene expression patterns between C. elegans and C. briggsae we designed whole-genome species-specific microarrays. We designed two organism-specific microarrays which were then manufactured by Agilent as 44k arrays. Probes were designed to target the coding region, preferentially near the 3â end, as well as in the presumptive 3â UTR, up to 150bp downstream of the stop codon. 50-60mer probes were determined using OligoWiz (Wernersson and Nielsen 2005) which selects oligos based upon their cross-hybridization to other coding sequences, Tm, position along the transcript, folding potential, and low-complexity in the sequence. The probes were also restricted against spanning splice junctions to avoid missing transcripts due to errors in gene structure predictions. Each gene was assigned between one and five probes, where the probe with the best overall score was selected as the âA-probeâ, and the remaining ranked âBâ through âEâ.

2010-05-06 | E-GEOD-15233 | biostudies-arrayexpress

C. briggsae and C. elegans developmental timecourses

Project description:This SuperSeries is composed of the following subset Series: GSE15233: C. briggsae developmental timecourse GSE15234: C. elegans developmental timecourse Refer to individual Series

2009-08-31 | E-GEOD-15551 | biostudies-arrayexpress

Heat stress reveals heritable changes in mRNA profile in 4-cell stage embryos of the nematode Caenorhabditis elegans.

Project description:For centuries, scientists have wondered whether the responses of animals and plants to environmental change can be transmitted to subsequent generations. Lately, there been much interest in the inheritance of information that is not encoded by differences in DNA sequence. Here we show that transient, mild heat stress results in a heritable change in the messenger RNA profile of early-stage C. elegans embryos. After heat stress is removed for one generation, abundances of most, but not all, mRNAs have relaxed to the unstressed state. Our approach was to culture worms at 20°C, then split the culture into 20°C control and 25°C treatment, followed by return of the 25°C culture to 20°C. Specifically, we compared mRNA abundances in 4-cell stage embryos collected from mothers kept at 20°C, with embryos whose mothers were also reared at 20°C but whose grandparents had been reared at 25°C. Two strains and two generations under a treatment and under a control condition were analyzed by microarray with three separately collected 50-embryo replicates for each combination, for a total of 24 samples.

2011-12-31 | E-GEOD-30666 | biostudies-arrayexpress

A genomic signature of gene-environment interactions in C. elegans

Project description:The phenotype is an interplay between genetic and environmental components, however the relationship between these two is difficult to predict. For any particular environment only a handful of genes show gene environment interaction [refs]. This may imply that certain constrains prevent genes to participate in gene environment interaction that possibly could be used to predict potential targets for such interaction under different sets of environmental conditions. Our approach was to culture 6 C. elegans strains (5 geographical isolates + 1 mutant straint) at 20Â°C, then split the culture into 5 conditions. We measured mRNA abundances in 4-cell stage embryos using microarray with three separately collected 50-embryo replicates collected for each combination of strain and environment. 90 microarrays of C. elegans for 6 strains * 5 conditions in triplicates.

2012-06-29 | E-GEOD-34650 | biostudies-arrayexpress

Developmental milestones punctuate gene expression in the Caenorhabditis embryo

Project description:The complex process by which a metazoan develops from a single cell to a multi-cellular differentiated organism is typically organized by biologists into stages. For example, in the chordate embryo, the gastrula, the neurula and the tail-bud constitute characteristic processes. A debate runs through the history of embryology questioning whether such stages hint at the modularity of embryonic development1-3, or rather, that “stages exist in the mind of the biologist, and not in the larva”4 or embryo. It thus remains unclear which position accurately reflects the nature of development on a molecular, gene regulatory level. Here we demonstrate that development of five Caenorhabditis species proceeds through multiple distinct stages in which the transcriptome is resistant to differences in species-specific developmental timings. By comparing the complete protein-coding transcriptomes of individually staged embryos across ten morphological markers, we found that time-invariant stages occur throughout development, including a stage we identify as the nematode phylotypic stage. Between such stages, embryos follow transitory states characterized by an acceleration of transcriptional activity. Therefore, on a molecular level, development cannot be viewed as a single process continuously proceeding through time, but rather as a succession of discontinuous stages, or ‘milestones’. Comparing the nematode developmental transcriptome with that of the chordate we report on the macro evolution of a milestone by duplication and diversification. This modular view of development by milestones will allow for a more complete understanding of how the functional organization of the embryo has influenced the evolution of animal morphology and diversity. 150 microarrays, across 10 morphological markers of C. remanei, C. briggsae, C. brenneri, C. elegans and C. japonica wildtype embryos. For each of the two timecourse independent triplicates were generated.

2012-03-01 | E-GEOD-31422 | biostudies-arrayexpress

Expression Profiling of Caenorabditis elegans tdp-1 loss-of-function mutant

Project description:Transactive response DNA-binding protein of 43 kDa (TDP-43), a heterogeneous nuclear ribonucleoprotein (hnRNP) with diverse activities, is a common denominator in several neurodegenerative disorders including amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Orthologs of TDP-43 exist from mammals to invertebrates, but their functions in lower organisms remain poorly understood. Here we systematically studied mutant Caenorhabditis elegans lacking the nematode TDP-43 ortholog, TDP-1. To understand the global gene expression regulation induced by the loss of tdp-1, the C. elegans transcriptomes were compared between the N2 WT animals and the tdp-1(ok803lf) mutant. Transcriptional profiling demonstrated that the loss of TDP-1 altered expression of genes functioning in RNA processing and protein folding. These results suggest that the C. elegans TDP-1 as an RNA-processing protein may have a role in the regulation of protein homeostasis and aging. Global gene expression profiling was performed to compare the transcriptome of wild-type (N2) Caenorabditis elegans and that of tdp-1(ok803) loss-of-function mutant. We analyzed mixed stages of Caenorabditis elegans, wild-type N2 versus tdp-1(ok803), using the Affymetrix C. elegans genome array. Three biological replicates were performed.

2012-02-21 | E-GEOD-34113 | biostudies-arrayexpress

Mapping gene expression in two Xenopus: evolutionary constraints and developmental flexibility

Project description:Variation in gene expression is known to be important for morphological evolution, however little is known about its general propensity. Here we examine a pair of frogs M-bM-^@M-^S Xenopus laevis and Xenopus tropicalis M-bM-^@M-^S with highly similar embryology, and ask how their transcriptomes compare. Despite separation for over ~30-90 million years we found a strong conservation in gene expression in the vast majority of the expressed orthologs. There were a significant number of changes in the level of expression of genes. Changes in timing of expression, heterochrony, were much less common, and were often found in genes and pathways that reflect responses to selective features of the environment. Differences in gene expression levels were concentrated in the earliest embryonic stages. We propose that different evolutionary rates across developmental stages may be explained by the stabilization of cell fate determination pathways in later stages. 96 microarrays, across developmental stages in Xenopus laevis and Xenopus tropicalis in wildtype embryos. For each of the two timecourse indepenent triplicates (clutches) were generated.

2011-06-01 | E-GEOD-27227 | biostudies-arrayexpress

Predator induced gene expression in tadpoles

Project description:Tadpoles of the anuran species Rana pirica can undergo predator-specific morphological responses. Exposure to a predation threat by larvae of the salamander Hynobius retardatus results in formation of a bulgy body (bulgy morph) with a higher tail. The tadpoles revert to a normal phenotype upon removal of the larval salamander threat. The objective of the present study was to use our own fabricated tadpole Rana pirica cDNA microarray to profile gene expression patterns during the predation threat. Experimental design used to produce control, bulgy morph and reversion type tadpoles for the microarray analysis was as follows. One group of tadpoles was placed with a larval salamander for 4 days to induce formation of the bulgy morph phenotype; the predator was then removed and the tadpoles were allowed to revert to the normal phenotype for 4 days. This group is termed “8 day out tadpoles”. A second group of tadpoles was placed with the predator for the full 8 days. The control group was not exposed to a predator. Tadpoles from the predator induced groups were sampled at 6 hours, 4 days and 8 days, those from the control group at 0 hour, 4 days, and 8 days. The comparative design of the microarray analysis was performed as (Exp 6 hours VS Cont 0 hours), (Exp 4 days VS Cont 4 days), (Exp 8 days VS Cont 8 days), and (Exp 8 days-Out VS Exp 8 days), respectively. These analyses were performed in triplicate with a dye swap experiment. Samples 0hr~8days were as follows. Sample plate (1~3A):Channel 1-Cy5 Experiment,Channel 2-Cy3 Control. Sample plate (1~3B):Channel 1-Cy5 Control, Channel 2-Cy3 Experiment. In case of 8day-out samples were as follows. Sample plate (1~3A):Channel 1-Cy5 8day-out,Channel 2-Cy3 full 8day. Sample plate (1~3B):Channel 1-Cy5 full 8day,Channel 2-Cy3 8day-out.

2009-06-15 | E-GEOD-12005 | biostudies-arrayexpress

Transcription profiling of mouse lateral, medial and intermediolateral column motoneurons following spinal cord transection

Project description:To determine spinal cord injury (SCI) induced changes in gene expression, laser capture microscopy (LCM) and Affymetrix microarrays were used to profiles three distinct populations of motor neurons (MNs) in five sets of littermates. In each set, one littermate received a lamenectomy (sham operated), and the other received a complete spinal cord transection. Each MN population was caudal to the transection and not axotomized. Thus, MNs in transected animals were responding to two major insults: deafferentation and changing microenvironments due to spreading immune and inflammatory responses. A total of 30 expression profiles from sham operated control animals have been uploaded to GEO database with accession number GSE2595. The current series contains 32 motoneuron expression profiles from spinalized mice. All chips (30 sham + 32 transection) were generated together using RMA in 2004. Experiment Overall Design: In this study we determine SCI induced changes in gene expression in lateral motoneurons (LMN), medial motoneurons (MMN) and intermediolateral column motoneurons (IML). Five sets of male littermates were used in these experiments (sets a-e). In each set, one littermate received a lamenectomy (sham operated), and the other received a complete spinal cord transection. Four of the sets (a-d) consisted of one transect and one littermate sham operated control. The fifth set (e) had an additional transect. All surgeries were performed on postnatal day (P) 24. Three weeks later (P45), the animals were sacrificed and their spinal cords were removed and sectioned for LCM. Each of the three cell types was captured from every animal. The expression profiles of the three classes of MNs were obtained using Affymetrix microarrays.

2009-09-25 | E-GEOD-18179 | biostudies-arrayexpress

Proteomics of C. briggsae embryo and larvae

Project description:To gain mechanistic insights into the molecular changes of Caenorhabditis briggsae between the two developmental stages: embryo and larvae

2018-10-11 | PXD005549 | Pride

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