GEO DataSets

Analysis of L4 larvae mutant for RRF-3 or ERI-1. RRF-3 and ERI-1 encode proteins required for the accumulation of endogenous secondary siRNAs. Results provide insight into the transcriptional effects caused by the loss of the RRF-3 and ERI-1 proteins and provide further insight into their functions.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array, count, 3 genotype/variation sets

Platform:

GPL200

Series:

GSE8659

9 Samples

Download data: CEL, CHP

(Submitter supplied) RRF-3 and ERI-1 are first identified proteins required for accumulation of at least some endogenous secondary siRNAs in C.elegans. Genome wide gene expression analysis was performed on L4 stage rrf-3 and eri-1 mutant C. elegans to study effects caused by loss of these proteins. Mutant rrf-3 and eri-1 strains exhibited similar expression patterns when compared to N2 wild type, while 72 transcripts were found to be co-overexpressed and 4 transcripts co-underexpressed (> 2-fold, p< 0.05). more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Dataset:

GDS3038

Platform:

GPL200

9 Samples

Download data: CEL, CHP

(Submitter supplied) Using a C. elegans whole genome DNA microarray in this study, the effects of five different xenobiotics on the gene expression of the nematode were investigated. The exposure time for the following five applied compounds beta-NF (5 mg/l), Fla (0.5 mg/l), atrazine (25 mg/l), clofibrate (10 mg/l) and DES (0.5 mg/l) was 48+/-5 h. The analysis of the data showed a clear induction of 203 genes belonging to different families like the cytochromes P450, UDP-glucoronosyltransferases (UDPGT), glutathione S-transferases (GST), carboxylesterases, collagenes, C-type lectins and others. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

5 related Platforms

16 Samples

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(Submitter supplied) We present a global overview of muscle gene expression in C. elegans using a novel technique called mRNA-tagging, and have identified genes involved in contraction, muscle structure, and energy utilization. Furthermore, we found that muscle-expressed genes are clustered in groups of 2-5 along the chromosomes, suggesting that expression from a chromatin domain can extend over several genes. These observations reveal a higher-order organization of the structure of the genome in which the order of genes along the chromosome is correlated with their expression in specific tissues. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL2653

6 Samples

Download data

(Submitter supplied) To characterize the role of the ERI-6/7 helicase in endogenous small RNA pathways in C. elegans, small RNA populations from null alleles of eri-6 and eri-7, and from mutants of known endogenous RNAi pathway factors, eri-1 and ergo-1, were determined by deep sequencing, and compared to wild type.

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9269

7 Samples

Download data

(Submitter supplied) Expession data from L1-L2 stage nematodes (C. elegans), wild type and four mutants (alg-1, zfp-1, rde-4, lin-35). In C. elegans, a vast number of endogenous short RNAs corresponding to thousands of genes have been discovered recently. This finding suggests that these short interfering RNAs may contribute to regulation of many developmental and other signaling pathways in addition to silencing viruses and transposons. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL200

15 Samples

Download data: CEL

(Submitter supplied) Although non-coplanar PCBs are ubiquitous organic chemicals known to induce numerous biological responses and thus are toxic to man and wildlife, little is known about the toxic mode of action. Using PCB52, an ortho-substituted, 2,2’,5,5’-tetrachlorobiphenyl, it was possible to pinpoint the relationship between induced gene expression and observed toxicity in the model nematode Caenorhabditis elegans. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL4469

8 Samples

Download data

(Submitter supplied) d-serine is naturally present throughout the human body. It is also used as add-on therapy for treatment-refractory schizophrenia. d-Serine interacts with the strychnine-insensitive glycine binding site of NMDA receptor, and this interaction could lead to potentially toxic activity (i.e., excitotoxicity) in brain tissue. The transcriptomic changes that occur in the brain after d-serine exposure have not been fully explored. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Dataset:

GDS3643

Platform:

GPL1355

24 Samples

Download data: CEL

Analysis of forebrains of animals treated with up to 500 mg/kg D-serine for 96 hours. D-serine is involved in many physiological processes through its interaction with the glycine binding site of the NMDA receptor. Results provide insight into the impact of D-serine exposure on neuronal functions.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, count, 2 agent, 6 dose sets

Platform:

GPL1355

Series:

GSE10748

24 Samples

Download data: CEL

(Submitter supplied) By culturing and isolating wild-type and mec-3 mutant cells from embryos and applying their amplified RNA to DNA microarrays, here we have identified genes that are known to be expressed in touch receptors, a previously uncloned gene (mec-17) that is needed for maintaining touch receptor differentiation, and more than 50 previously unknown mec-3-dependent genes. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platforms:

GPL2754 GPL2646

6 Samples

Download data

(Submitter supplied) Analysis of small RNAs with 5'p, 3'OH Raw data files are available on our FTP site: ftp://ftp.ncbi.nlm.nih.gov/pub/geosup/Series/GSE20341

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9309 GPL9085

11 Samples

Download data: TXT

(Submitter supplied) Short interfering RNAs (siRNAs) are a class of regulatory effectors that enforce gene silencing though formation of RNA duplexes. While progress has been made in identifying the capabilities of siRNAs in silencing of foreign RNA and transposable elements, siRNA functions in endogenous gene regulation have remained mysterious. In certain organisms, siRNA biosynthesis involves novel enzymes that act as RNA-directed RNA polymerases (RdRPs). more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9269

5 Samples

Download data: FA, PSL

(Submitter supplied) Activity-dependent changes in synapses rely on functional changes in resident proteins and on gene expression. We addressed the relationship between synapse activity and the expression of synaptic genes by comparing RNA levels in the neocortex of normal mice versus synaptically silent munc18-1 null mutants, using microarray expression analysis, quantitative PCR and Northern blotting. We hypothesized that genes under control of synaptic activity are differentially expressed between mutants and controls and found that few synaptic signaling genes were differentially expressed. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL3106

11 Samples

Download data

(Submitter supplied) Activity-dependent changes in synapses rely on functional changes in resident proteins and on gene expression. We addressed the relationship between synapse activity and the expression of synaptic genes by comparing RNA levels in the neocortex of normal mice versus synaptically silent munc18-1 null mutants, using microarray expression analysis, quantitative PCR and Northern blotting. We hypothesized that genes under control of synaptic activity are differentially expressed between mutants and controls and found that few synaptic signaling genes were differentially expressed. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL3106

4 Samples

Download data

(Submitter supplied) Activity-dependent changes in synapses rely on functional changes in resident proteins and on gene expression. We addressed the relationship between synapse activity and the expression of synaptic genes by comparing RNA levels in the neocortex of normal mice versus synaptically silent munc18-1 null mutants, using microarray expression analysis, quantitative PCR and Northern blotting. We hypothesized that genes under control of synaptic activity are differentially expressed between mutants and controls and found that few synaptic signaling genes were differentially expressed. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL3106

6 Samples

Download data

(Submitter supplied) The aryl hydrocarbon receptor (AHR) functions in higher organisims in development, metabolism and toxic responses. Its Caenorhabditis elegans (C. elegans) ortholog, AHR-1, facilitates neuronal development, growth and movement. We investigated the effect of AHR mutation on the transcriptional profile of L4 stage C. elegans using RNA-seq and quantitative real-time PCR in order to understand better AHR-1 function at the genomic level. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13657

3 Samples

Download data: XLS

(Submitter supplied) The number of annotated protein coding genes in the genome of Caenorhabditis elegans is similar to that of other animals, but the extent of its non-protein coding transcriptome remains unknown. Expression profiling on whole genome tiling microarrays applied to a mixed stage C. elegans population verified the expression of 71% of all annotated exons. Only a small fraction (11 %) of the polyadenylated transcription is non-annotated, and appears to consist of approximately 3200 missed or alternative exons and 7800 small transcripts of unknown function (TUFs). more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by genome tiling array

Platform:

GPL5634

3 Samples

Download data: BAR, CEL, TXT

(Submitter supplied) In every domain of life, Argonaute proteins and their associated small RNAs regulate gene expression. Despite great conservation of Argonaute proteins throughout evolution, there are not many other conserved proteins involved in small RNA pathways. Gametocyte-specific factor 1 (Gtsf1) proteins, characterized by two tandem CHHC zinc fingers and an unstructured, acidic C-terminal tail, represent one such conserved small RNA pathway component. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13657

18 Samples

Download data: BAM, BW

(Submitter supplied) Endogenous RNA-directed RNA polymerases (RdRPs) are cellular components capable of synthesizing new complementary RNAs from existing RNA templates. We present evidence for successive engagement of two different RdRPs in an endogenous siRNA-based mechanism targeting specific mRNAs in C. elegans soma. In the initiation stage of this process, a group of mRNA species are chosen as targets for downregulation, leading to accumulation of rare 26-nt 5'-phosphorylated antisense RNAs that depend on the RdRP homolog RRF-3, the argonaute ERGO-1, DICER, and a series of associated (ERI) factors. more...

Organism:

Caenorhabditis elegans

Type:

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

Platform:

GPL9269

26 Samples

Download data: FA

(Submitter supplied) We used Au nanoparticles (Au-NPs) as a model for studying particle specific effects of manufactured nanomaterials (MNMs) by examining the toxicogenomic responses in a model soil organism, free living nematode Caenorhabditis elegans. Global genome expression for nematodes exposed to 4-nm citrate-coated Au-NPs at the LC10 (5.9 mg L-1) revealed significant differential expression of 797 genes. The levels of expression for five genes (apl-1, dyn-1, act-5, abu-11, and hsp-4) were confirmed independently with qRT-PCR. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Dataset:

GDS4571

Platform:

GPL200

6 Samples

Download data: CEL