GEO DataSets

(Submitter supplied) Here, we profile miRNA expression at high temporal resolution (1 hr interval) from 18h to 33h at 25°C, during C. briggsae postembryonic development, which identifies several miRNAs with highly dynamic concentration changes

Organism:

Caenorhabditis briggsae

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21214

16 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caenorhabditis briggsae; Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

4 related Platforms

226 Samples

Download data

(Submitter supplied) ChIP-seq for the SDC-2 and DPY-27 subunits of the dosage compensation complex in C. briggsae

Organism:

Caenorhabditis briggsae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27110

10 Samples

Download data: BW

(Submitter supplied) Piwi proteins and Piwi-interacting RNAs (piRNAs) are best known for their roles in suppressing transposons and promoting fertility. Yet piRNA biogenesis and its mechanisms of action differ widely between distantly related species. To better understand the evolution of piRNAs, we characterized the piRNA pathway in C. briggsae, a sibling species of the model organism C. elegans. Our analyses define 25,883 piRNA producing-loci in C. more...

Organism:

Caenorhabditis briggsae; Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL18245 GPL21214 GPL29990

12 Samples

Download data: FA

(Submitter supplied) Geographically distinct populations can adapt to the temperature conditions of their local environment, leading to temperature-dependent fitness differences between populations. Consistent with local adaptation, phylogeographically distinct Caenorhabditis briggsae nematodes show distinct fitness responses to temperature. The genetic mechanisms underlying local adaptation, however, remain unresolved. more...

Organism:

Caenorhabditis briggsae

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21214

18 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caenorhabditis briggsae; Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other

Platforms:

GPL31139 GPL18730

14 Samples

Download data: BW

(Submitter supplied) The movement of repetitive elements in the germline creates widespread genomic alterations and pressure for resolution. Here we show that the Caenorhabditis clade took advantage of two transposon expansions by integrating hundreds of elements into its germline transcriptional network. We find that about one-third of C. elegans germline-specific promoters have been co-opted from CERP2 and CELE2 MITE elements and are regulated by HIM-17, a THAP domain-containing transcription factor related to a transposase. more...

Organism:

Caenorhabditis briggsae

Type:

Other

Platform:

GPL31139

4 Samples

Download data: BW

(Submitter supplied) The movement of repetitive elements in the germline creates widespread genomic alterations and pressure for resolution. Here we show that the Caenorhabditis clade took advantage of two transposon expansions by integrating hundreds of elements into its germline transcriptional network. We find that about one-third of C. elegans germline-specific promoters have been co-opted from CERP2 and CELE2 MITE elements and are regulated by HIM-17, a THAP domain-containing transcription factor related to a transposase. more...

Organism:

Caenorhabditis briggsae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL31139

4 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caenorhabditis briggsae; Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing

Platforms:

GPL19757 GPL30947 GPL26672

147 Samples

Download data: BW, HIC, TAB

(Submitter supplied) Condensin complexes are evolutionarily conserved molecular motors from the structural maintenance of chromosomes (SMC) family, that use ATPase activity to translocate along DNA and form loops. Condensin and topoisomerase II (TOP-2) are essential for the structure and function of mitotic chromosomes. While condensin-mediated DNA looping is thought to direct TOP-2 chain-passing activity to separate sister chromatids, it is not known if TOP-2 in turn regulates loop formation. more...

Organism:

Caenorhabditis briggsae; Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30947 GPL19757

87 Samples

Download data: BW

(Submitter supplied) 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. more...

Organism:

Caenorhabditis briggsae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29990

10 Samples

Download data: TXT

(Submitter supplied) These data demonstrate that parental exposure to bacterial infection and osmotic stress intergenerational changes in offspring gene expression in C. elegans, C. kamaaina, C. briggsae and C. tropicalis. Many of these intergenerational changes in gene expression are observed in multiple species and this data identified >250 genes that exhibit intergenerational changes in expression in all species tested.

Organism:

Caenorhabditis tropicalis; Caenorhabditis briggsae; Caenorhabditis elegans; Caenorhabditis kamaaina

Type:

Expression profiling by high throughput sequencing

4 related Platforms

105 Samples

Download data: TXT

(Submitter supplied) The goal of this study is to identify differentially expressed genes in Cbr-spr-4(gu163)/Cbr-ivp-1(gu163) and Cbr-htz-1(gu167)/Cbr-ivp-2(gu167) mutant compare to AF16 wild-type (WT). Our study represents the first analysis of Cbr-spr-4/Cbr-ivp-1 and Cbr-htz-1/Cbr-ivp-2 transcriptomes in C. briggsae and facilitates investigations of Cbr-spr-4/Cbr-ivp-1 and Cbr-htz-1/Cbr-ivp-2 mediated processes 

Organism:

Caenorhabditis briggsae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16160

9 Samples

Download data: CSV, TAB

(Submitter supplied) Transcriptional profiling of heat-shocked worms was compared to non-heat-shocked worms to determine genes that are induced upon heat shock in each species; heat-shock-induced genes in each species were compared

Organism:

Caenorhabditis briggsae; Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22765 GPL27110

12 Samples

Download data: TXT

(Submitter supplied) Two introgression strains (ZZY10307 and ZZY10330) of C. briggsae onto the X chromosome of C. nigoni results in male sterility. In order to determine the cause, we sequenced the mRNAs from young adult males from these two strains, and compared to fertile males of the two parent species (AF16 and JU1421). Two wild-type female samples were also included as platform QC.

Organism:

Caenorhabditis nigoni; Caenorhabditis briggsae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21276 GPL21277

14 Samples

Download data: FASTA, TXT

(Submitter supplied) 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.

Organism:

Caenorhabditis nigoni; Caenorhabditis briggsae

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL21214 GPL21215

3 Samples

Download data: FA

(Submitter supplied) In Caenorhabditis elegans, the dosage compensation complex (DCC) specifically binds to and represses transcription from both X chromosomes in hermaphrodites. The DCC is composed of an X-specific condensin complex that interacts with several proteins. During embryogenesis, DCC starts localizing to the X chromosomes around the 40-cell stage, and is followed by X-enrichment of H4K20me1 between 100-cell to comma stage. more...

Organism:

Caenorhabditis briggsae; Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13657 GPL13776 GPL20977

146 Samples

Download data: TXT

(Submitter supplied) The overall goal of this investigation was to investigate X-content of sex-biased genes in several nematode species. The following species of nematode were investigated: *C. elegans, *N2; *C. brenneri, *PB2801; *C. briggsae, *AF16; *C. remanei*, PB4641; *P. **pacificus, *PS312*.* Genomic DNA sequencing data was used to assign X and autosomal - linkage to unassembled sequencing contigs. Male and female RNA seq data was then generated and used to determine sex-biased expression. more...

Organism:

Caenorhabditis elegans; Pristionchus pacificus; Caenorhabditis briggsae; Caenorhabditis brenneri; Caenorhabditis remanei

Type:

Expression profiling by high throughput sequencing; Other

5 related Platforms

31 Samples

Download data: BEDGRAPH, FPKM_TRACKING

(Submitter supplied) Spatiotemporal control of gene expression is crucial for development and subject to evolutionary changes. Although proteins are the final product of most genes, the developmental proteome of an animal has not yet been comprehensively defined, and the correlation between RNA and protein abundance during development is largely unknown. Here, we globally measured and compared protein and mRNA expression changes during the life cycle of the nematodes C. more...

Organism:

Caenorhabditis elegans; Caenorhabditis briggsae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18072 GPL13776

26 Samples

Download data: TXT

(Submitter supplied) The goal of this study is to identify and characterize sites in the C. elegans genome bound by the transcription factor TRA-1.

Organism:

Caenorhabditis briggsae; Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9269 GPL13657 GPL16160

19 Samples

Download data: BW