GEO DataSets

(Submitter supplied) A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here we present the culmination of the efforts of the modENCODE (Model Organism ENCyclopedia Of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms, Drosophila melanogaster (fly) and Caenorhabditis elegans (worm). more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL26672 GPL13657

54 Samples

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

Organism:

Caenorhabditis elegans; Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

4 related Platforms

71 Samples

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(Submitter supplied) MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to form a complex that directs mRNA repression. One way that miRNAs are regulated is at the level of their stability. Some animal miRNAs are destabilized through a pathway in which pairing to specialized RNA transcripts recruits the ZSWIM8 E3 ubiquitin ligase, which polyubiquitinates AGO, leading to its degradation and exposure of the miRNA to cellular nucleases. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18245

6 Samples

Download data: XLSX

(Submitter supplied) MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to form a complex that directs mRNA repression. One way that miRNAs are regulated is at the level of their stability. Some animal miRNAs are destabilized through a pathway in which pairing to specialized RNA transcripts recruits the ZSWIM8 E3 ubiquitin ligase, which polyubiquitinates AGO, leading to its degradation and exposure of the miRNA to cellular nucleases. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL26672 GPL18245

59 Samples

Download data: XLSX

(Submitter supplied) Cell size and biosynthetic capacity generally increase with increased DNA content. Somatic polyploidy has therefore been proposed to be an adaptive strategy to increase cell size in specialized tissues with high biosynthetic demands. However, if and how DNA concentration limits cellular biosynthesis in vivo is not well understood. Here, we show that polyploidy in the C. elegans intestine is critical for cell growth and yolk biosynthesis, a central role of this organ. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26672

7 Samples

Download data: BW, TSV

(Submitter supplied) Cell size and biosynthetic capacity generally increase with increased DNA content. Somatic polyploidy has therefore been proposed to be an adaptive strategy to increase cell size in specialized tissues with high biosynthetic demands. However, if and how DNA concentration limits cellular biosynthesis in vivo is not well understood. Here, we show that polyploidy in the C. elegans intestine is critical for cell growth and yolk biosynthesis, a central role of this organ. more...

Organism:

Caenorhabditis elegans; Pristionchus pacificus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL35070

6 Samples

Download data: TSV

(Submitter supplied) Nuclear RNAi in C. elegans induces a set of transgenerationally heritable marks of H3K9me3, H3K23me3, and H3K27me3 at the target genes. The function of H3K23me3 in the nuclear RNAi pathway is largely unknown due to the limited knowledge of H3K23 histone methyltransferase (HMT). In this study we identified SET-21 as a novel H3K23 HMT. By taking combined genetic, biochemical, and genomic approaches we found that SET-21 functions synergistically with a previously reported H3K23 HMT SET-32 to deposit H3K23me3 at the native targets of germline nuclear RNAi. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25147

78 Samples

Download data: BW, CSV

(Submitter supplied) Nuclear RNAi in C. elegans induces a set of transgenerationally heritable marks of H3K9me3, H3K23me3, and H3K27me3 at the target genes. The function of H3K23me3 in the nuclear RNAi pathway is largely unknown due to the limited knowledge of H3K23 histone methyltransferase (HMT). In this study we identified SET-21 as a novel H3K23 HMT. By taking combined genetic, biochemical, and genomic approaches we found that SET-21 functions synergistically with a previously reported H3K23 HMT SET-32 to deposit H3K23me3 at the native targets of germline nuclear RNAi. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25147

16 Samples

Download data: BW

(Submitter supplied) Nuclear RNAi in C. elegans induces a set of transgenerationally heritable marks of H3K9me3, H3K23me3, and H3K27me3 at the target genes. The function of H3K23me3 in the nuclear RNAi pathway is largely unknown due to the limited knowledge of H3K23 histone methyltransferase (HMT). In this study we identified SET-21 as a novel H3K23 HMT. By taking combined genetic, biochemical, and genomic approaches we found that SET-21 functions synergistically with a previously reported H3K23 HMT SET-32 to deposit H3K23me3 at the native targets of germline nuclear RNAi. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25147

13 Samples

Download data: BW

(Submitter supplied) The interplay between ribosomal protein composition and mitochondrial function is essential for sustaining energy homeostasis. Precise stoichiometric production of ribosomal proteins is crucial to maximize protein synthesis efficiency while reducing the energy costs to the cell. However, the impact of this balance on mitochondrial ATP generation, morphology and function remains unclear. Particularly, the loss of a single copy ribosomal protein gene is observed in Mendelian disorders like Diamond Blackfan Anemia and is common in somatic tumors, yet the implications of this imbalance on mitochondrial function and energy dynamics are still unclear. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL26672

40 Samples

Download data: CSV

(Submitter supplied) XR-seq was performed to map the repair of UV-induced photoproducts.

Organism:

Caenorhabditis elegans

Type:

Other

Platform:

GPL32326

60 Samples

Download data: BEDGRAPH

(Submitter supplied) RNA-seq analysis was conducted to quantify the gene expression levels in each strain.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34620

6 Samples

Download data: TXT

(Submitter supplied) Damage-seq was performed to generate the damage map.

Organism:

Caenorhabditis elegans

Type:

Other

Platform:

GPL32326

16 Samples

Download data: BEDGRAPH

(Submitter supplied) The nematode Caenorhabditis elegans was treated with extracts of the Traditional Chinese Medicine plants Cuscuta chinensis and Eucommia ulmoides from the L4 stage. In aged worms (on the 7th and 12th day of adulthood) different health parameters were determined. Besides the prolongation of lifespan, we found that C. chinensis improved the swimming behavior, pharyngeal pumping rate, stress resistance, mechanosensation and memory of aged C. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26672

15 Samples

Download data: XLSX

(Submitter supplied) We utilized a Caenorhabditis elegans (C. elegans) model of human tauopathy to investigate the role of DNA glycosylases (Ung-1 and Nth-1 knockout worms) in disease development and progression. We then performed gene expression profiling analysis using data obtained from RNA-seq of 12 different genotypes grown under normal conditions.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26672

12 Samples

Download data: TXT

(Submitter supplied) We present a survey of longevity effects for compounds suggested by a previously published computational prediction set using the comprehensive, multi-species approach utilized by the Caenorhabditis Intervention Testing Program (CITP). The compound all-trans retinoic acid extended lifespan in the nematode Caenorhabditis elegans. Given the dependency of lifespan extension under atRA treatment, we used RNA-seq to assess transcriptional changes under atRA treatment in wildtype N2 animals. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22765

24 Samples

Download data: TXT

(Submitter supplied) Purpose: After infection there was dendrite degeneration in the mutant animals . To decipher the mechanism responsible and the changes in the gene expression of mutant worms Methods: Control and mutant worms were exposed at young adult stage to P.aeruginosa PA14 infection for 24 hours. Total RNA was extracted and RNA sequencing was done following standard protocols Results: Detailed analysis of the transcriptomic data show that immune genes were significantly upregulated. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22765

6 Samples

Download data: TXT

(Submitter supplied) In cells, transcription is tightly regulated on multiple layers. The condensation of the transcription machinery into distinct phases is hypothesized to spatio-temporally fine tune RNA polymerase II behaviour during two key stages, transcription initiation and the elongation of the nascent RNA transcripts. However, it has remained unclear whether these phases would mix when present at the same time or remain distinct chemical environments; either as multi-phase condensates or by forming entirely separate condensates. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32326

12 Samples

Download data: TAB

(Submitter supplied) To examine the ways in which gene expression varies in natural populations and its relationship to genetic divergence, we estimated allele-specific expression in the offspring of multiple wild C. elegans strains crossed with the laboratory reference strain N2. Allele-specific expression analyses are uniquely sensitively able to identify cis regulatory changes, and coupled with analyses of differential expression between parental strains and parents and offspring can determine the regulatory pattern and inheritance mode of gene expression across the genome. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34645

45 Samples

Download data: COUNTS, SF, TSV, TXT

(Submitter supplied) DNA topoisomerases are essential molecular machines that manage DNA topology in the cell and play important roles in DNA replication and transcription. We find that knocking down the enzyme Topoisomerase IIβ (Top2b) increases the lifespan of S. cerevisiae, C. elegans, and mice. TOP2B reduction also extends the health span of mice and alleviates the characteristics and pathologies of aging in multiple tissues. more...

Organism:

Caenorhabditis elegans; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23479 GPL25145

32 Samples

Download data: XLSX