GEO DataSets

(Submitter supplied) Cadmium is a naturally occurring heavy metal, and it is widely used in industry. Due to its persistent toxic effect, cadmium is classified as a category one human carcinogen. Its toxicity has been extensively studied in different organisms, including the nematode Caenorhabditis elegans. To investigate the transcriptomic responses following cadmium during early life exposure, C. elegans larval were exposed either from L1 to L3 stage or L1 to L4 stage to 20 µM cadmium chloride. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18245

12 Samples

Download data: TXT, XLSX

(Submitter supplied) Structural Maintenance of chromosomes (SMC) complexes, cohesin and condensins, have been named after their roles during meiosis and mitosis. Recent data in mammalian cells and Drosophila have described the additional role of cohesin for genome folding into loops and domains during interphase. However, determinants of genome folding in holocentric species remain unclear. Using high resolution chromosome conformation capture, we show that overlapping large-scale nuclear localization and small-scale epigenomic states compartmentalize the C. more...

Organism:

Caenorhabditis elegans

Type:

Other

Platforms:

GPL26672 GPL22765

16 Samples

Download data: COOL

(Submitter supplied) Structural Maintenance of chromosomes (SMC) complexes, cohesin and condensins, have been named after their roles during meiosis and mitosis. Recent data in mammalian cells and Drosophila have described the additional role of cohesin for genome folding into loops and domains during interphase. However, determinants of genome folding in holocentric species remain unclear. Using high resolution chromosome conformation capture, we show that overlapping large-scale nuclear localization and small-scale epigenomic states compartmentalize the C. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26672

4 Samples

Download data: BW

(Submitter supplied) Structural Maintenance of chromosomes (SMC) complexes, cohesin and condensins, have been named after their roles during meiosis and mitosis. Recent data in mammalian cells and Drosophila have described the additional role of cohesin for genome folding into loops and domains during interphase. However, determinants of genome folding in holocentric species remain unclear. Using high resolution chromosome conformation capture, we show that overlapping large-scale nuclear localization and small-scale epigenomic states compartmentalize the C. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26672

40 Samples

Download data: BW, SF

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

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL22765 GPL26672

60 Samples

Download data: BW, COOL, SF

(Submitter supplied) Primary microRNA (pri-miRNA) transcripts are processed by a protein complex called the Microprocessor comprised of the ribonuclease Drosha and its RNA binding partner DGCR8/Pasha. We sequenced small RNAs from animals containing a mutation in the WW domain of C. elegans pash-1. We found that these mutants have a modest but widespread reduction in miRNA levels when grown at 20˚C, which is further enhanced when grown at 25˚C. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25147

14 Samples

Download data: CSV

(Submitter supplied) We have established epidermal expression of chil-27p::GFP as the marker for activation of oomycete recognition response (ORR) in C. elegans. Through a forward genetic screen, we identified clec-27, clec-35, and ceh-37 to be the key players required for activating chil-27p::GFP upon exposure to the oomycete Myzocytiopsis humicola extract. To determine if activation of entire ORR is affected in these mutants, we analyzed their transcriptome in the presence and absence of extract and compared with that of wildtype C. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26672

30 Samples

Download data: H5

(Submitter supplied) NOT PROVIDED; REQUESTED

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13657

9 Samples

Download data: TXT

(Submitter supplied) We have adapted the eXcision Repair-sequencing (XR-seq) method to generate single-nucleotide resolution dynamic repair maps of UV-induced cyclobutane pyrimidine dimers (CPD) photoproducts in the Caenorhabditis elegans (C. elegans) genome.

Organism:

Caenorhabditis elegans

Type:

Other

Platform:

GPL32326

8 Samples

Download data: BED

(Submitter supplied) MicroRNAs (miRNAs) are essential regulators of several biological processes. To achieve their repressive function, they are loaded onto Argonaute (AGO) proteins, forming the microRNA Induced Silencing Complex (miRISC). Thus, regulating this loading step is essential for miRNA-dependent gene regulation. In this study, we identified the co-chaperone DNJ-12 as a new interactor of ALG-1, one of the two major miRNA-specific AGOs in Caenorhabditis elegans (C. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26672

24 Samples

Download data: TXT

(Submitter supplied) RNA-seq analysis was used to identify the gene expression changes of young adults after feeding 5mM tryptophan for 36 hours from the L4 period. Based on these sequencing data, the genes that were up-regulated or down-regulated by at least 2 times (|log2 (folding change) | ≥ 1 and padj ≤ 0.05) were analyzed. The analysis of these differentially expressed genes' pathway and gene ontology (GO) enrichment shows that the influence of different genders after feeding 5mM tryptophan is enriched to some signal pathways, including longevity、ribosome and protein degradation pathway in endoplasmic reticulum, etc.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13657

6 Samples

Download data: TXT

(Submitter supplied) Our research revealed that the transmembrane transcription factors MYRF-1 and MYRF-2 are crucial for activating the microRNA lin-4 at the end of the first larval stage in C. elegans. To determine whether MYRF regulates other microRNA genes during this period, we conducted a microRNA sequencing analysis to compare microRNA expression in late L1 larvae of wild type and myrf-1(ju1121) mutants. The myrf-1(ju1121) mutation causes a loss of function in both MYRF-1 and MYRF-2. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL26672

6 Samples

Download data: XLS

(Submitter supplied) Disruption of physiological homeostasis elicits cellular stress response and behavioral changes of the animal. We recently showed that mitochondrial stress induces aversive associative memory for food bacteria that C. elegans inherently prefers without stress. Depletion of atp-2 by RNA interference in the non-neural tissues causes mitochondrial disruption and induces bacterial avoidance in C. elegans. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26672

2 Samples

Download data: XLSX

(Submitter supplied) Alterations in the nuclear envelope are linked to a variety of rare diseases termed laminopathies. These include both tissue specific and systemic diseases. A single amino acid substitution in human barrier to autointegration factor (BAF) at position 12 (A12T) causes Néstor-Guillermo Progeria Syndrome (NGPS). This premature ageing condition affects a variety of tissues, leading to growth retardation and severe skeletal defects, including scoliosis. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19757

24 Samples

Download data: TXT

(Submitter supplied) Alterations in the nuclear envelope are linked to a variety of rare diseases termed laminopathies. These include both tissue specific and systemic diseases. A single amino acid substitution in human barrier to autointegration factor (BAF) at position 12 (A12T) causes Néstor-Guillermo Progeria Syndrome (NGPS). This premature ageing condition affects a variety of tissues, leading to growth retardation and severe skeletal defects, including scoliosis. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19757

16 Samples

Download data: CSV

(Submitter supplied) We presents a complete single-cell atlas of aging worms, encompassing both somatic and germ cell types. This atlas was built upon 241K nuclei across the worm lifespan at day 1, 6, 12, and 14 (100%, 99%, 61%, and 14% survival rates, respectively). The worms were aged under normal physiological conditions, without interfering with their reproductive processes.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26672 GPL32326 GPL27998

28 Samples

Download data: MTX, RDS, TSV

(Submitter supplied) Sex-specific traits and behaviors are facilitated by the acquisition of unique properties in the nervous system of each sex during development and continues in adulthood. However, the genetic events responsible for introducing these sex-specific features remain poorly understood. In this study, we created a comprehensive gene expression atlas for both sexes of the nematode Caenorhabditis elegans across development. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19757

40 Samples

Download data: XLSX

(Submitter supplied) Most DNA double-strand breaks (DSBs) are harmful to genome integrity. However, some forms of DSBs are essential to biological processes, such as meiotic recombination and V(D)J recombination. DSBs are also required for programmed DNA elimination (PDE) in ciliates and nematodes. In nematodes, the DSBs are healed with telomere addition. While telomere addition sites have been well-characterized, little is known regarding the DSBs that fragment nematode chromosomes. more...

Organism:

Ascaris suum; Parascaris univalens

Type:

Other

Platforms:

GPL31097 GPL34158 GPL31096

42 Samples

Download data: BW

(Submitter supplied) Cellular responses to co-morbid tau and TDP-43 preceding neurodegeneration have not been characterized. In this study, we evaluate transcriptomic changes at time-points preceding frank neuronal loss using a C. elegans model of tau and TDP-43 co-expression. We find significant differential expression and exon usage in genes enriched in multiple pathways including lipid metabolism and lysosomal degradation. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26672

32 Samples

Download data: SF

(Submitter supplied) microRNAs regulate gene expression through interaction with an Argonaute protein family member. While some members of this protein family retain an enzymatic activity capable of cleaving RNA molecules complementary to Argonaute-bound small RNAs, the role of the slicing activity in the canonical microRNA pathway is still unclear in animals. To address the importance of slicing Argonautes in animals, we created Caenorhabditis elegans mutant strains carrying catalytically dead endogenous ALG-1 and ALG-2, the only two slicing Argonautes essential for the miRNA pathway in this animal model. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL22765

31 Samples

Download data: TXT