Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

An optimized RNA amplification method for prokaryotic expression profiling analysis

ABSTRACT: Conventional prokaryotic RNA labeling method usually requires large amounts of starting materials and tends to generate high background signals. Recently, two novel methods based on amplification systems were introduced. Here, we compared three alternative strategies: direct labeling method, ployadenylation-involved oligo-dT priming amplification method and random priming amplification method (hereafter referred to as DL, PAOD and RPA method in this article) for prokaryotic RNA labeling employing the expression profiling investigation in Escherichia coli (E. coli) heat shock model.

ORGANISM(S): Escherichia coli

PROVIDER: GSE17074 | GEO | 2009/07/25

SECONDARY ACCESSION(S): PRJNA119813

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

An optimized RNA amplification method for prokaryotic expression profiling analysis

Project description:Conventional prokaryotic RNA labeling method usually requires large amounts of starting materials and tends to generate high background signals. Recently, two novel methods based on amplification systems were introduced. Here, we compared three alternative strategies: direct labeling method, ployadenylation-involved oligo-dT priming amplification method and random priming amplification method (hereafter referred to as DL, PAOD and RPA method in this article) for prokaryotic RNA labeling employing the expression profiling investigation in Escherichia coli (E. coli) heat shock model. To identify an optimal RNA labeling method for prokaryotic microarray analysis, experiments were performed with starting RNA obtained from E.coli growing at control (37Â°C) or heat shock (43Â°C) condition. We employed 0.5 Î¼g of total RNA for a single round of amplification using PAOD and RPA methods coupling to IVT to generate cDNA targets. In addition, an approach using DL method was also performed. Three types of cDNA mixtures containing Cy5-labeled (or Cy3-labeled) control DNA and Cy3-labeled (or Cy5-labeled) DNA targets were hybridized with E.coli microarrays in a dye-swap strategy. Replicate experiments were conducted from the same batch of total RNA to assess technique reproducibility of each approach.

2010-05-15 | E-GEOD-17074 | biostudies-arrayexpress

Prokaryotic Single-Cell RNA Sequencing by In Situ Combinatorial Indexing

Project description:We present Prokaryotic Expression-profiling by Tagging RNA In Situ and sequencing (PETRI-seq), a high-throughput prokaryotic scRNA-seq pipeline. We demonstrated that PETRI-seq effectively barcoded single bacterial cells in a species-mixing experiment with E. coli (MG1655) and S. aureus (USA300). Within the S. aureus population, we found rare prophage induction in 0.04% of cells. We further demonstrated that PETRI-seq was able to distinguish between E. coli growth phases based on mRNA expression patterns by combining stationary E. coli with exponential E. coli in multiple experiments.

2020-05-25 | GSE141018 | GEO

Sensing prokaryotic mRNA signifies microbial viability and promotes immunity

Project description:MyD88-independent signal transduction associated with Toll-like receptors (TLRs) 3 and TLR4 is mediated through the adapter protein TRIF (TIR-domain-containing adapter-inducing interferon-beta). It has been proposed that TLR signalling is important for the transcription of crucial inflammasome components like NLRP3, a process that has been termed "priming". In order to test whether TRIF signalling was required for the priming of inflammasome components, we performed a genome wide transcriptional analysis on wild-type and Trif-knockout bone marrow derived macrophages (BMMs) before and 1, 3 and 6 hours after phagocytosis of E. coli. These results indicated that TRIF was involved in the activation and not transcriptional priming of the NLRP3 inflammasome.

2011-05-22 | GSE27960 | GEO

Sensing prokaryotic mRNA signifies microbial viability and promotes immunity

2011-05-22 | E-GEOD-27960 | biostudies-arrayexpress

Mycobacteria excises DNA damage in 12- or 13-nucleotide-long oligomers by prokaryotic-type dual incisions and performs transcription-coupled repair

Project description:In nucleotide excision repair, bulky DNA lesions such as UV-induced cyclobutane pyrimidine dimers (CPDs) are removed from the genome by concerted dual incisions bracketing the lesion, followed by gap filling and ligation. So far, two dual incision patterns have been discovered: prokaryotic type which removes the damage in 11-13 nucleotide-long oligomers and eukaryotic type which removes the damage in 24-32 nucleotide-long oligomers. However, a recent study reported that the UvrC protein of Mycobacterium tuberculosis removes damage in a manner analogous to yeast and humans in a 25-mer oligonucleotide arising from incisions at 15 nucleotides from the 3’ end and 9 nucleotides from the 5’ end flanking the damage. To test this model we used the in vivo excision assay and the XR-seq genome-wide repair mapping method developed in our lab to determine the repair pattern and genome-wide repair map of M. smegmatis. We find that M. smegmatis, which possesses homologues of the E. coli UvrA, B, and C genes, removes CPDs from the genome in a manner identical to the prokaryotic pattern by incising 7 nucleotides 5’ and 3 or 4 nucleotides 3’ to the photoproduct.

2020-10-06 | GSE159048 | GEO

Prokaryotic Proteogenomics

Project description:Prokaryotic Proteogenomics

| PRJNA66995 | ENA

prokaryotic metagenome

Project description:prokaryotic metagenome Metagenome

| PRJNA608846 | ENA

Prokaryotic expression profiling analysis for single or combined chaperones deletion

Project description:Chaperones have essential role in assist nascent peptides folding, prevent proteins aggregation and maintain cellular protein homeostasis. Considering spatial and temporal features of chaperones regulating in vivo, changes in single or combined chaperone-depleted E.coli strain is needed to be put into understand at transcriptional level. Here, we utilized expression microarrays to investigate global transcriptional response upon deletion of single or multiple chaperones in E. coli for understanding the transcriptional network affected by chaperones. To identify prokaryotic expression profiles in deletion of chaperones, several E.coli mutants were constructed in the following: Z116 (△tig 37℃), Z125(△dnaK37℃), Z625(△tig△dnaK 37℃ or 30℃), Z629(△tig△dnaK 30℃), NM (C-domain of tig was deleted 37℃), MC (N-domain of tig was deleted 37℃), NC (M-domain of tig was deleted 37℃). Two types of cDNA mixtures containing Cy3-labeled (or Cy5-labeled) control DNA (from BW25113) and Cy5-labeled (or Cy3-labeled) DNA targets (from mutant strain) were hybridized with E.coli microarrays in a dye-swap strategy.

2015-06-18 | GSE69912 | GEO

Escherichia coli

Project description:An optimized RNA amplification method for prokaryotic expression profiling analysis

| PRJNA119813 | ENA

Prokaryotic expression profiling analysis for single or combined chaperones deletion

2015-06-18 | E-GEOD-69912 | biostudies-arrayexpress