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TranscriptomicsIdentification and validation of antisense RNAs in Escherichia coli
In this study transcriptional start sites (TSS) of E. coli were determined for several growth conditions To detect the complement of transcripts expressed from E. coli, we collected two independent biological replicates (B1 and B2 samples) from MG1655 wild type strain grown to exponential (OD 600 ~0...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2014-10-18 | E-GEOD-55199 | biostudies-arrayexpress
TranscriptomicsPrimary transcriptome map of the hyperthermophilic archaeon ThermococcusM-BM- kodakarensis
Background: Prokaryotes have relatively small genomes, densely-packed and apparently dominated by protein-encoding sequences. However, data now generated by high throughput RNA sequencing (RNA-seq) reveal surprisingly more-complex transcriptomes with many previously unrecognized and unanticipated ...
ORGANISM(S): Thermococcus kodakarensis KOD1 
2014-08-18 | E-GEOD-56262 | biostudies-arrayexpress
TranscriptomicsDifferential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori
In this study transcriptional start sites (TSS) for H. pylori 26695 were determined To detect the complement of transcripts expressed from H. pylori, we collected three independent biological replicates (B1 – B3) from 26695 wild type strain grown to mid-exponential (OD 600 ~0.6) phase under microaer...
ORGANISM(S): Helicobacter pylori 26695 
2015-07-01 | E-GEOD-67564 | biostudies-arrayexpress
TranscriptomicsHigh-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates
Campylobacter jejuni is currently the leading cause of bacterial gastroenteritis in humans. Comparison of multiple Campylobacter strains revealed a high genetic and phenotypic diversity. However, little is known about differences in transcriptome organization, gene expression, and small RNA (sRNA) r...
ORGANISM(S): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 
2013-05-27 | E-GEOD-38883 | biostudies-arrayexpress
TranscriptomicsFunctional characterization of the RNA chaperone Hfq in opportunistic human pathogen Stenotrophomonas maltophilia
Stenotrophomonas maltophilia is an important opportunistic pathogen affecting primarily hospitalized and immuno-compromised hosts. We constructed an hfq deletion mutant (Delta-hfq) of S. maltophilia, and compared the behaviour of wild-type and Delta-hfq S. maltophilia cells in a variety of assays. D...
ORGANISM(S): Stenotrophomonas maltophilia 
2012-10-02 | E-GEOD-39705 | biostudies-arrayexpress
TranscriptomicsArgonaute proteins affect siRNA levels and accumulation of a novel extrachromosomal DNA from the Dictyostelium retrotransposon DIRS-1
We report on the function of the D. dictyostelium argonaute proteins AgnA and AgnB in the silencing mechanism of the retrotransposon DIRS-1. By deep sequencing analysis we found that AgnA is involved in the accumulation of DIRS-1 siRNAs since in respective knockout strains siRNAs are strongly reduce...
ORGANISM(S): Dictyostelium discoideum 
2014-12-04 | E-GEOD-56111 | biostudies-arrayexpress
TranscriptomicsThe primary transcriptome of barley (Hordeum vulgare L.) chloroplasts
Gene expression in plastids of higher plants is dependent on two different transcription machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. The division of labor between PEP and NEP du...
ORGANISM(S): Hordeum vulgare 
2011-11-23 | E-GEOD-33773 | biostudies-arrayexpress
TranscriptomicsIdentification of Hfq bound RNA by co-immunoprecipitation and RNA-sequencing
Co-immunoprecipitation with endogenous Hfq3xFlag in exponential, stationary, non-induced and virulence induced conditions, followed by RNA-sequencing, revealed 1697 mRNAs and 208 ncRNAs associated with Hfq. We identified 56 new ncRNAs and validated 3 Hfq-dependent trans sRNAs on by Northern blot ana...
ORGANISM(S): Agrobacterium tumefaciens 
2014-12-04 | E-GEOD-59123 | biostudies-arrayexpress
TranscriptomicsdRNA-Seq of Chlamydia pneumoniae
The obligate intracellular human pathogen Chlamydia pneumoniae was subjected to dRNA-Seq to gain insights into the transcriptome. The two distinct life cycle forms elementary bodies (EB) and reticulate bodies (RB) were isolated from human Hep2 cell line by differential gradient centrifugation. Total...
ORGANISM(S): Chlamydophila pneumoniae CWL029 
2011-08-18 | E-GEOD-24999 | biostudies-arrayexpress
TranscriptomicsIdentification of RNA molecules associated with the RNA-chaperone Hfq
We used high-throughput methods to discover the Salmonella RNAs that are targeted by the bacterial Sm-like protein, Hfq. Our generic approach, using chromosomal epitope tagging and coIP-on-chip will also be useful to identify the post-transcriptional regulons of many other RNA-binding proteins. Key...
ORGANISM(S): Salmonella enterica 
2010-06-20 | E-GEOD-10149 | biostudies-arrayexpress
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