Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA sequencing based analysis of the bacterial transcriptome

ABSTRACT: To investigate the architecture of the E. coli K-12 transcriptome, we used two RNA-Seq technologies to analyze strand-specific transcription at single-nucleotide resolution. We analyzed the data by using an organizational schema to annotate the promoters and terminators that define transcription units across the genome. We found substantial evidence for differential gene expression within complex operons, which we categorized based on operon architecture. E. coli K-12 strain MG1655 substrain BW38028 and isogenic rpoS mutant were cultured in minimal glucose media (carbon, nitrogen, or phosphate limited) and the total transcriptome of log and stationary phase samples was sequenced.

ORGANISM(S): Escherichia coli BW38028

SUBMITTER: James Creecy

PROVIDER: E-GEOD-58556 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Unexpected complexity of the Escherichia coli K-12 transcriptome architecture revealed by single nucleotide resolution RNA sequencing

Project description:To investigate the architecture of the E. coli K-12 transcriptome, we used two RNA-Seq technologies to analyze strand-specific transcription at single-nucleotide resolution. We analyzed the data by using an organizational schema to annotate the promoters and terminators that define transcription units across the genome. Our results showed that most (ca. two-thirds) operons have a single promoter and terminator, whereas one-third of operons contain multiple transcription units. We found substantial evidence for differential gene expression within complex operons, which we categorized based on operon architecture. E. coli K-12 strain MG1655 substrain BW38028 and isogenic rpoS mutant were cultured in minimal glucose media and the total transcriptome of log and stationary phase samples was sequenced.

2014-07-08 | E-GEOD-52059 | biostudies-arrayexpress

RNA sequencing based analysis of the bacterial transcriptome

2014-12-11 | GSE58556 | GEO

Unexpected complexity of the Escherichia coli K-12 transcriptome architecture revealed by single nucleotide resolution RNA sequencing

2014-07-08 | GSE52059 | GEO

Expression profiling of E. coli rpoS knock-out strain during stationary phase in M9 minimal media with 0.2% glucose

Project description:Investigation of whole genome gene expression level in E. coli rpoS knock-out strain grown up to stationary phase in M9 minimal media supplemented with 0.2% glucose E. coli rpoS deletion mutant grown up to OD600nm 1.5 (stationary phase) in M9 minimal media supplemented with 0.2% glucose. The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide. Data for wild type controls are GSM389302, GSM389303, and GSM389304.

2014-02-05 | E-GEOD-46543 | biostudies-arrayexpress

Inhibition of the LSD1 (KDM1A) demethylase reactivates the all-trans-retinoic acid differentiation pathway in acute myeloid leukemia [Illumina HumanHT-12 gene expression array]

Project description:All-trans-retinoic acid (ATRA) has been successfully used in therapy of acute promyelocytic leukemia (APL), a cytogenetically distinct subtype of acute myeloid leukemia (AML) but the response of non-APL AML cases to ATRA-based treatment has been poor. Here we show that, via epigenetic reprogramming, inhibitors of LSD1/KDM1 demethylase including tranylcypromine (TCP) unlocked the ATRA-driven therapeutic response in non-APL AML. LSD1 inhibition did not lead to an increase in genome-wide H3 lysine4 dimethylation (H3K4me2) but did increase H3K4me2 and expression of myeloid differentiation-associated genes. Importantly, treatment with ATRA plus TCP dramatically diminished engraftment of primary human AML cells in vivo in NOD.SCID mice, suggesting that ATRA in combination with TCP may target leukemia-initiating cells. Furthermore, initiation of ATRA plus TCP co-treatment 15 days post-engraftment of human AML cells in NOD.SCID gamma mice also revealed the ATRA plus TCP drug combination to have a potent anti-leukemic effect, which was superior to treatment with either drug alone. These data identify LSD1 as a therapeutic target and strongly suggest that it may contribute to AML pathogenesis by inhibiting the normal pro-differentiative function of ATRA, paving the way for novel combinatorial therapies of AML. Overall, 30 specimens derived from HL-60 or TEX cell line were treated with drugs and hybridized to Illumina HumanHT-12 gene expression arrays.

2012-03-14 | E-GEOD-34672 | biostudies-arrayexpress

Association between OLIG2 Gene SNP rs1059004 and Negative Self-Schema Constructing Trait Factors Underlying Susceptibility to Depression

Project description:SNP rs1059004 and Negative Self-Schema

| PRJEB42840 | ENA

Transfer of Non-coding DNA Drives Regulatory Rewiring in Bacteria

Project description:The rapid pace of evolution in bacteria is widely attributed to the promiscuous horizontal transfer and recombination of protein-coding genes. However, it is not known whether the same forces also drive the evolution of non-coding regulatory regions. Here we demonstrate that regulatory region can M-bM-^@M-^XswitchM-bM-^@M-^Y between non-homologous alternatives and that such switching is ubiquitous, occurring across the bacterial domain. We show that such regulatory switching strongly impacts promoter architecture and expression divergence. We further show that regulatory transfer facilitates rapid phenotypic diversification of a human pathogen. This regulatory mobility enables bacterial genes to access a vast pool of potential regulatory elements, facilitating efficient exploration of the regulatory landscape. Examination of 2 E. coli strains in 2 conditions

2014-11-04 | E-GEOD-59468 | biostudies-arrayexpress

Identifying genes of Escherichia coli involved in interactions with Stenotrophomonas maltophilia in planktonic cultures and biofilms using transcriptomic analysis

Project description:Biofilm formation by Escherichia coli was significantly inhibited when co-cultured with Stenotrophomonas maltophilia in static systems. Genes of E. coli involved in species interactions with S. maltophilia were identified in order to allow the study of the mechanisms of inhibited E. coli biofilm formation in co-culture. A total of 89 and 108 genes were identified as differentially expressed in mixed species cultures when growing as biofilm and as planktonic cultures, respectively, compared to the counterpart of pure cultured E. coli. Differential expression of certain identified genes was confirmed using E. coli reporter strains combined with single-cell based flow cytometry analysis. Co-culture with S. maltophilia affected genes involved in metabolism, signal transduction, cell wall composition, and biofilm formation of E. coli. Several selected genes were further confirmed as affecting E. coli biofilm formation in mixed species cultures with S. maltophilia. The data suggest that these genes were involved in species interactions between E. coli and S. maltophilia. This SuperSeries is composed of the SubSeries listed below. Refer to individual Series.

2013-12-30 | E-GEOD-24915 | biostudies-arrayexpress

Escherichia coli cells: sorted vs. non-sorted

Project description:Transcription profile of sorted Escherichia coli cells was compared to that of non-sorted cells to evaluate the effect of sorting process on transcriptome of E. coli. E. coli cells were harvest from planktonic cultures in annular reactor and stored in RNAlater. Sorting includes 2-min homogenization with OMNI TH homogenizer on ice for E. coli cells pre-stored in RNAlater and then resuspended in nuclease free phosphate buffered saline for sorting with one-step immuno-magnetic separation with anti-E. coli antibody and microbeads on a MACS separator (Miltenyi, Auburn, CA). Two condition experiments: sorted vs non-sorted. Two biological replicates with individually grown and harvested E. coli cells. Each biological replicate has two technical replicates of labeling and hybridization on microarray slides. Each slide has three built-in replicates for each probe.

2010-07-13 | E-GEOD-22885 | biostudies-arrayexpress

Transcriptome and translatome landscape of Streptomyces coelicolor M145

Project description:We have integrated nucleotide resolution genome-scale measurements of the transcriptome and translatome of the Streptomyces coelicolor A3(2), the model antibiotic-producing actinomycete. Our systematic study determined 3,473 transcription start sites, leading to discovery of a high proportion (~21%) of leaderless mRNAs and 230 non-coding RNAs; this enabled deduction of promoter architecture on a genome-scale. Ribosome profiling analysis revealed that the translation efficiency was negatively correlated for secondary metabolic genes. These results provide novel fundamental insights into translational regulation of secondary metabolism that enables rational synthetic biology approaches to awaken such âsilentâ secondary metabolic pathways. Profiles of primary transcripts, whole transcripts, and ribosome protected fragments (RPFs) of Streptomyces coelicolor were generated by deep sequencing using Illumina Miseq.

2016-05-28 | E-GEOD-69350 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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