C. briggsae developmental timecourse
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis briggsae
PROVIDER: GSE15233 | GEO | 2009/08/31
SECONDARY ACCESSION(S): PRJNA123135
REPOSITORIES: GEO
Similar Datasets
Project description:To identify differences in gene expression patterns between C. elegans and C. briggsae we designed whole-genome species-specific microarrays.
2009-08-31 | GSE15234 | GEO
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
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 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’.
2009-08-31 | E-GEOD-15234 | biostudies-arrayexpress
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
Project description:An introgression of C. briggsae onto the X chromosome of C briggsae results in male sterility. In order to determine the cause, we sequenced small RNAs from this strain and compared to fertile males of the two parent species.
2016-05-11 | GSE75763 | GEO
Project description:Different populations of the same species survive different environments through local adaptation. Temperature is one of the most important driving forces that could result in local adaptation. Here, we studied the influence of extreme low temperature on the survival of two genetically and geographically distinct populations of the free-living Caenorhabditis briggsae. We found that Caenorhabditis briggsae strains of temperate origin had a cold resistant phenotype, while those originating from a tropical climate had reduced survival after cold treatment. Using this phenotypic difference between geographically diverse populations as a model for how species adapt to their local environment, we then analyzed the transcriptional profiles of two Caenorhabditis briggsae strains of tropical and temperate origin to find genes that are involved in survival after extreme cold. In summary, the response to the extreme low temperature that clearly distinguishes the temperate and tropical Caenorhabditis briggsae strains could serve as an excellent example for studying local adaption of species that show genetic separation associated with their geographical distribution.
2021-09-09 | GSE171725 | GEO
Project description:The goal of this study is to identify and characterize sites in the C. elegans genome bound by the transcription factor TRA-1. TRA-1 ChIP-seq was performed in the following stages of animals in duplicate: 1) L2 stage of C. elegans wild-type N2 strain; 2) L3 stage of C. elegans wild-type N2 strain; 3) young adult stage of C. elegans glp-4(bn2) mutant; 4) young adult stage of C. elegans spe-11(hc77) mutant; 5) L3 stage of C. briggsae wild-type AF16 strain. As a negative control, TRA-1 ChIP-seq was also performed in C. elegans L3 stage with tra-1(e1834) homozygous and heterozygous mutation. Input DNA was also sequenced in each condition.
2013-11-04 | E-GEOD-48917 | biostudies-arrayexpress
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
