Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

NGM versus CeMM growth

ABSTRACT: These three arrays are replicate extractions and hybridizations. Each array hybridizes labeled RNA from NGM plate grown, mixed stage, animals (Channel 1) against labled RNA from liquid CeMM grown, mixed stage, animals (Channel 2). A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. Media: Channel 1 is NGM grown mixed stage animals, Channel 2 is CeMM grown mixed stage animals Keywords: replicate_design

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE6057 | GEO | 2006/10/18

SECONDARY ACCESSION(S): PRJNA97737

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of C. elegans NGM plate grown vs. liquid CeMM grown mixed stage cultures to explore development and lifespan extension of metabolic lifestyle alteration

Project description:These three arrays are replicate extractions and hybridizations. Each array hybridizes C. elegans labeled RNA from NGM plate grown, mixed stage, animals (Channel 1) against labled RNA from liquid CeMM grown, mixed stage, animals (Channel 2).

2006-11-06 | E-SMDB-3800 | biostudies-arrayexpress

mRNA expression profile of dop-1 mutants to wild- type animals during adulthood (L4+48 hours) using RNA-seq

Project description:Developmentally synchronized animals were obtained by hypochlorite treatment of gravid adults to release embryos. Synchronized embryos were hatched on NGM plates and grown at 20°C until 48 h after the L4 stage of development. Fluorodeoxyuridine was used to prevent the development of second-generation embryos once animals reached fertile adulthood. For each RNA-seq experiment, populations for odIs77[Pcol-19::UbG76V-GFP] and dop-1(vs100); [Pcol- 19::UbG76V-GFP] were grown simultaneously under the same conditions. Total RNA was isolated from animals using trizol (Invitrogen) combined with Bead Beater lysis in 3 biological replicates, and an mRNA library (single-end, 50-bp reads) was prepared for each sample/replicate using Illumina Truseq with PolyA selection.

2016-04-30 | GSE80807 | GEO

RNA sequencing to identify UNC-25-regulated genes in C. elegans defense against pathogen P. aeruginosa infection

Project description:Purpose: To gain molecular insights on how UNC-25 regulates C. elegans innate immunity, we used RNA sequencing to profile gene expression in unc-25(e156) animals relative to wild-type animals with or without P. aeruginosa (PA14) infection. Methods: Synchronized L1 worms were placed onto NGM plates seeded with E. coli OP50 and grown at 20 °C until the L4 stage. Worms were washed off the plates, collected with M9 solution and subsequently transferred to modified NGM plates containing E. coli OP50 or P. aeruginosa PA14 for 24 h at 25 °C. Then, the animals were washed off the plates with M9 solution and frozen in TRIzol (Transgen, ER501-01, China) with liquid nitrogen. Total RNA was isolated using a TransZol Up Plus RNA kit (Transgen, ER501-01, China). Results: RNA seq analyses shows enriched and signficant changed immune genes, neuropeptides, transcription factors and pathways that are dependent of GABA signaling. Conclusion: Our studies uncover that GABA signaling enhance the resistence to pathogen induced killing.

2023-06-26 | GSE195835 | GEO

Genome wide transcriptional analysis of P. aeruginosa PAO1, response to phosphate limitation

Project description:P. aeruginosa PAO1 grown as lawns on Nematode Growth Medium prepared without supplementation (NGM Pi<0.1 mM) has high killing ability against C. elegans, however, no mortality in worms has been observed during 48 hrs when feeding on PAO1 lawns grown on phosphate supplemented full NGM Pi 25 mM, pH 6.0 medium. We used a microarray to define the virulence-related genes in P. aeruginosa grown as lawns in NGM Pi<0.1 mM vs NGM Pi25 mM pH 6.0

2011-07-27 | GSE30967 | GEO

Expression data from C. elegans (wild type vs. tag-24)

Project description:To provide insights into the mechanism underlying the enhanced immunity of tag-24/octr-1 animals, we used genome microarrays to find clusters of genes commonly misregulated in tag-24 relative to wild-type animals grown on live P. aeruginosa. Gravid adult wild-type and tag-24/octr-1 animals were lysed using a solution of sodium hydroxide and bleach (ratio of 5:2), washed and the eggs were synchronized for 22 hours in S basal liquid medium at room temperature. Synchronized L1 larval animals were placed onto NGM plates seeded with E. coli OP50 and grown at 20°C until the animals had reached the L4 larval stage. Animals were collected and washed with M9 buffer before transferring to NGM plates containing P. aeruginosa PA14 for 4 hours at 25°C. After 4 hours, animals were collected and washed with M9 buffer, and RNA was extracted using TRIzol reagent (Invitrogen). Residual genomic DNA was removed by DNase treatment (Ambion Austin, TX).

2011-04-21 | E-GEOD-27867 | biostudies-arrayexpress

TJ1081)fer-15(b26)II; daf-16(m26)I) vs. BA713(fer-15(b26)II)

Project description:To identify changes in gene expression in daf-16 mutants, we compared expression in fer-15 young adults to expression in fer-15(b26); daf-16(m26) young adults grown at 25?C. At Stanford University, four samples of fer-15 and five samples of fer-15; daf-16 animals were prepared. At the University of Colorado, seven samples of fer-15 and six samples of fer-15; daf-16 was prepared. Set of arrays that are part of repeated experiments Place of growth: At Stanford vs Colorado Genotype: mutant strains vs wt (N2) mixed stage; some expts are reverse dye (wt in channel 2) Biological Replicate Computed

2008-07-29 | E-GEOD-12167 | biostudies-arrayexpress

Small RNA and total RNA sequencing of C. elegans with mutations in the hrde-1 and emb-4 genes

Project description:Synchronised animals were grown to young adult stage at 20C on HB101 seeded NGM plates. Animals were harvested and washed 3X in M9 buffer. Settled animals were mixed with Trisure reagent, bead beaten using zirconia beads, and the RNA is extracted using chloroform. For total RNA sequencing, Illumina Ribozero kit is used to remove ribosomal RNA from 1ug of total RNA prior to library preparation. RNA sequencing libraries are prepared using NEB Next Ultra library preparation kit. Small RNA sequencing is performed by treating 5ug of total RNA with Epicentre 5 polyphosphatase to remove the 5 triphosphate. After treatment, RNA is purified by phenol/chloroform extraction and 1ug of RNA is used to prepare small RNA libraries using Illumina TruSeq small RNA library preparation kit. Ribosomal depleted RNA and small RNA libraries are sequenced using Illumina HiSeq 1500 platform.

2017-07-01 | E-MTAB-4877 | biostudies-arrayexpress

Variation in cDNA microarray analysis of gene expression using unamplified poly(A)+ RNA

Project description:Zhao et al. Amplification BC2 uM This experiment was designed to assess the reproducibility of microarray hybridization using poly(A)+RNA. BC2 total RNA was isolated from which poly(A)+RNA was subsequently isolated. Three arrays were hybridized on the same day using arrays from the same batch. Two were done three months later using poly(A)+RNA freshly isolated from the same total RNA. A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. Keywords: replicate_design

2005-11-04 | GSE3559 | GEO

Response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source.

Project description:The global gene expression program that accompanies the adaptation of Saccharomyces cerevisiae to an abrupt transfer from a fermentable to a nonfermentable carbon source was characterized by using a cDNA microarray to monitor the relative abundances and polysomal distributions of mRNAs. Features of the program included a transient reduction in global translational activity and a severe decrease in polysome size of transcripts encoding ribosomal proteins. A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. Keywords: replicate_design

2005-08-25 | GSE3190 | GEO

TJ1081)fer-15(b26)II; daf-16(m26)I) vs. BA713(fer-15(b26)II)

2008-07-29 | GSE12167 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data