GEO DataSets

(Submitter supplied) microRNAs are frequently modified by addition of untemplated nucleotides to the 3' end, but the role of this tailing is often unclear. Here we characterize the prevalence and functional consequences of microRNA tailing in vivo, using Caenorhabditis elegans. MicroRNA tailing in C. elegans consists mostly of mono-uridylation of mature microRNA species, with rarer mono-adenylation which is likely added to microRNA precursors. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL24892 GPL19757

94 Samples

Download data: XLSX

(Submitter supplied) To maximize fitness, organisms must appropriately allocate energetic resources between essential cellular processes to maintain homeostasis. The nutritional regulators of energy homeostasis have been studied in detail; however, how developmental signals might impinge on these pathways to govern cellular metabolism is poorly understood. We identified a non-canonical role for Hedgehog (Hh), a classic regulator of development, in maintaining intestinal lipid homeostasis in C. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26672 GPL22765

36 Samples

Download data: TXT

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

Organism:

Caenorhabditis elegans

Type:

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

Platforms:

GPL13657 GPL26522

15 Samples

Download data

(Submitter supplied) Using ATAC-seq, we aimed to identify regions of open chromatin in the developing C. elegans nervous system. This dataset was used to determine regions of chromatin and compare it to ChIP-seq data of TFs of interest, to assist us in identifying ChIP-seq peaks which are solely expressed in neurons (vs. general, total worm binding). Specifically, since EGL-43 is expressed in many tissues, including both neuronal and the somatic gonad, ATAC-seq was particularly helpful in identifying neuronal-specific ChIP-seq peaks and NanoDam peaks of interest (GSE227552).

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13657

6 Samples

Download data: NARROWPEAK

(Submitter supplied) Activity-dependent mechanisms have been long known to play a critical role in synaptogenesis. Here, we utilize a recently adapted technology, NanoDam, to perform targeted DamID using endogenously tagged GFP transcription factors.

Organism:

Caenorhabditis elegans

Type:

Other

Platform:

GPL26522

9 Samples

Download data: BED, BEDGRAPH, GFF

(Submitter supplied) Gametogenesis involves active protein synthesis and heavily relies on proteostasis. How animals regulate germline proteostasis at the organismal level is poorly understood. Our recent work in C. elegans indicates that germline development requires coordinated activities between insulin/IGF-1 signaling and HSF-1, the transcriptional activator of many molecular chaperones in stress and physiological conditions. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26672

24 Samples

Download data: XLSX

(Submitter supplied) Examine the effect of lactic bacterium 2004 supplementation on expression profile in wld type animals.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13657

4 Samples

Download data: CSV

(Submitter supplied) The Integrator is an evolutionarily conserved protein complex that functions to process the 3’ maturation of small nuclear RNA molecules that are an essential part of the spliceosome. We performed a genome-wide RNAi screen in the C. elegans system and identified csr-1 as an essential gene required for this process. Knockdown of csr-1 activates an snRNA misprocessing reporter and causes aberrant 3’ cleavage of several endogenous snRNA transcripts. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13657

6 Samples

Download data: XLSX

(Submitter supplied) Our study elucidates the broad-spectrum effects of proteasome hyperactivation on the proteome, demonstrating its substantial influence on the proteostasis network. Through comprehensive analyses, we identified a significant reorganization of the transcriptome, enhanced mRNA processing, and increased translation activity. The study further reveals the hyperactivation's impact on intrinsically disordered proteins, lipid synthesis, and biogenesis, evidenced by major changes in lipid droplets and peroxisome proliferation. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26672

10 Samples

Download data: XLSX

(Submitter supplied) In embryos, DCC binding across the length of the ~17.7 Mb X chromosome initiates at a set of recruitment elements on the X (rex). Individual rex sites collectively contribute to recruitment and repression, thus deletion of one or few rex sites causes subtle changes, as measured by mRNA-seq in mixed-stage embryos. We previously constructed a strain deleting rex-1, located ~6 kb downstream of dpy-23 (https://0-doi-org.brum.beds.ac.uk/10.7554/eLife.23645). more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19757

6 Samples

Download data: TAB

(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