txid1822464[Organism] - GEO DataSets

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Select item 2002551551.

RNA-seq analysis in simulated microgravity unveils down-regulation of the beta-rhizobial siderophore phymabactin

(Submitter supplied) Exploiting the symbiotic interaction between crops and nitrogen-fixing bacteria is a simple and ecological solution to promote plants growth in prospective extraterrestrial human outposts. In this study, we investigated the adaptation of the legume symbiont Paraburkholderia phymatum to simulated microgravity (s0-g) at the transcriptome level by performing an RNA-Seq analysis. The results revealed a drastic effect on gene expression, with roughly 23 % of P. more...

Organism:: Paraburkholderia phymatum STM815

Type:: Expression profiling by high throughput sequencing

Platform:: GPL22728
6 Samples

Download data: TXT

Series

Accession:: GSE255155

ID:: 200255155

PubMed Full text in PMC Similar studies

Select item 2002464872.

Black Carbon Impacts on Paraburkholderia xenovorans Strain LB400 Cell Enrichment and Activity: Implications toward Lower-Chlorinated Polychlorinated Biphenyls Biodegradation

(Submitter supplied) Volatilization of lower-chlorinated polychlorinated biphenyls (LC-PCBs) from sediment poses health threats to nearby communities and ecosystems. Biodegradation combined with black carbon (BC) materials is an emerging approach to remove PCBs from sediment, but development of aerobic biofilms on BC for long-term, sustained LC-PCBs remediation is poorly understood. This work aimed to characterize cell enrichment and activity of biphenyl- and benzoate-grown Paraburkholderia xenovorans strain LB400 on various BCs. more...

Organism:: Paraburkholderia xenovorans

Type:: Expression profiling by high throughput sequencing

Platform:: GPL33884
12 Samples

Download data: XLSX

Series

Accession:: GSE246487

ID:: 200246487

PubMed Full text in PMC Similar studies

Select item 2001762873.

Metabolomics and Dual RNA-Sequencing on Root Nodules Revealed New Cellular Functions Controlled by Paraburkholderia phymatum NifA

(Submitter supplied) Paraburkholderia phymatum STM815 is a nitrogen-fixing endosymbiont that forms root nodules on the agriculturally important Phaseolus vulgaris and other host plants. We previously showed that the nodules induced by a STM815 mutant of the gene encoding the master regulator of nitrogen fixation NifA showed no nitrogenase activity (Fix-) and increased in number compared to P. vul-garis plants infected with the wild-type strain. more...

Organism:: Paraburkholderia phymatum STM815; Phaseolus vulgaris

Type:: Expression profiling by high throughput sequencing

Platform:: GPL30237
4 Samples

Download data: TXT

Series

Accession:: GSE176287

ID:: 200176287

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001560484.

Paraburkholderia phymatum σ54 controls utilization of dicarboxylates, motility and interbacterial competition

(Submitter supplied) Paraburkholderia phymatum is a beta-proteobacterium, which lives in the soil and is able to enter nitrogen-fixing symbiosis with different legumes. The biological nitrogen fixation (BNF) process is of great ecological and agronomic importance. We previously showed that the expression of the key P. phymatum BNF enzyme – the nitrogenase –is regulated by the sigma factor σ54 (or RpoN) inside root nodules. more...

Organism:: Paraburkholderia phymatum STM815

Type:: Expression profiling by high throughput sequencing

Platform:: GPL22728
6 Samples

Download data: TXT

Series

Accession:: GSE156048

ID:: 200156048

SRA Run Selector

Select item 2001119935.

Metabolomics and transcriptomics identify multiple downstream targets of Paraburkholderia phymatum σ54 during symbiosis with Phaseolus vulgaris

(Submitter supplied) RpoN (σ54) is the key sigma factor for the regulation of transcription of nitrogen fixation genes in diazotrophic bacteria, which include alpha- and beta-rhizobia. Our previous studies showed that a rpoN mutant of the beta-rhizobial strain Paraburkholderia phymatum formed root nodules on Phaseolus vulgaris that were unable to reduce atmospheric nitrogen into ammonia. In an effort to further characterize the RpoN regulon of P. more...

Organism:: Paraburkholderia phymatum STM815

Type:: Expression profiling by high throughput sequencing

Platform:: GPL22728
4 Samples

Download data: TXT

Series

Accession:: GSE111993

ID:: 200111993

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001073816.

In-nodule transcriptome analysis of Paraburkholderia phymatum during symbiosis with Phaseolus vulgaris

(Submitter supplied) Paraburkholderia phymatum belongs to the β-subclass of proteobacteria. It has recently been shown to be able to nodulate and fix nitrogen in symbiosis with several mimosoid and papillionoid legumes. In contrast to symbiosis of legumes with α-proteobacteria, very little is known about the molecular determinants underlying the successful establishment of this mutualistic relationship with β-proteobacteria. more...

Organism:: Paraburkholderia phymatum STM815

Type:: Expression profiling by high throughput sequencing

Platform:: GPL22728
9 Samples

Download data: TXT

Series

Accession:: GSE107381

ID:: 200107381

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000720527.

RNA-seq analysis of the degradation of chloroacetate by Burkholderia caribensis MBA4

(Submitter supplied) Burkholderia caribensis MBA4 is able to metabolize monochloroacetate (MCA) as sole carbon and energy source for growth. A haloacid dehalogenase is mainly responsible for the cleavage of the carbon-halogen bond. The MCA will be hydrolyzed to glycolate which would be further transformed to glyoxylate by glycolate oxidase. In order to identify inducible genes involved in mineralization of MCA, transcriptomes of MBA4 cells grown on MCA, glycolate or pyruvate were determined using RNA-seq technology. more...

Organism:: Paraburkholderia caribensis

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL20804 GPL20803
5 Samples

Download data: TXT

Series

Accession:: GSE72052

ID:: 200072052

SRA Run Selector

Select item 2000652908.

General Approach for Tetramer Based Identification of Autoantigen Reactive B Cells: Characterization of La and snRNP Reactive B Cells in Autoimmune BXD2 Mice

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Klebsiella pneumoniae; Porphyromonas gingivalis; Mycobacterium avium subsp. paratuberculosis; Mycobacterium tuberculosis; Homo sapiens; Mus musculus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Human herpesvirus 4 strain B95-8; Human immunodeficiency virus 1; Human herpesvirus 4 type 1; Coxsackievirus B4 (strain E2); Escherichia coli; Shigella flexneri; Haemophilus influenzae; Staphylococcus aureus; Lactobacillus delbrueckii subsp. bulgaricus; Mycobacterium avium; Human betaherpesvirus 6; human gammaherpesvirus 4; Human T-cell leukemia virus type I; Coxsackievirus A9; Human herpesvirus 4 type 2; Chlamydia pneumoniae; Human poliovirus 3 strain Sabin; Betapolyomavirus macacae; Helicobacter pylori; Yersinia enterocolitica; Chlamydia trachomatis; Mycobacterium tuberculosis variant bovis; Human alphaherpesvirus 2; Hepatitis C virus isolate HC-J6; Coxsackievirus B4; Coxsackievirus A20; Porphyromonas gingivalis W83; Mycobacterium avium subsp. paratuberculosis K-10; Proteus mirabilis; Streptococcus pyogenes; Mycobacterium gordonae; Trypanosoma cruzi; Caprine arthritis encephalitis virus; Human T-cell lymphotrophic virus type 1 (isolate MT-2); Human adenovirus 12; Human endogenous retrovirus K; Human Endogenous Retrovirus IDDMK1,2-22; Torque teno virus; Prochlorococcus marinus str. MIT 9202; Human rotavirus MP409; Paraburkholderia fungorum; Staphylococcus aureus A9635; Hepacivirus hominis

Type:: Protein profiling by protein array

Platforms:: GPL19700 GPL19692 GPL19701
29 Samples

Download data: XLSX

Series

Accession:: GSE65290

ID:: 200065290

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000652789.

Autoimmune peptide antigen reactivity in BXD2 mice with spontaneous systemic autoimmune disease Pepperchip 2.0

(Submitter supplied) The aim of the array was to determine the BXD2 mouse sera IgG and IgM reactivity profile to linear peptide epitopes. Pooled sera from three 6-9 month old BXD2 mice was diluted at 1:200 for IgG specific analysis or 1:1000 for IgM specific analysis and incubated on a PEPperPRINT peptide microarray platform printed with peptide autoantigens

Organism:: Helicobacter pylori; Shigella flexneri; Yersinia enterocolitica; Human alphaherpesvirus 2; Hepatitis C virus isolate HC-J6; Human T-cell leukemia virus type I; Coxsackievirus A20; Torque teno virus; Prochlorococcus marinus str. MIT 9202; Paraburkholderia fungorum; Porphyromonas gingivalis W83; Mycobacterium avium subsp. paratuberculosis K-10; Staphylococcus aureus A9635; Chlamydia trachomatis; Streptococcus pyogenes; Mycobacterium tuberculosis variant bovis; Mycobacterium tuberculosis; Trypanosoma cruzi; Homo sapiens; Human herpesvirus 4 strain B95-8; Human T-cell lymphotrophic virus type 1 (isolate MT-2); Coxsackievirus B4; Human adenovirus 12; Human Endogenous Retrovirus IDDMK1,2-22; Human rotavirus MP409; Hepacivirus hominis; Escherichia coli; Klebsiella pneumoniae; Proteus mirabilis; Porphyromonas gingivalis; Staphylococcus aureus; Mycobacterium avium subsp. paratuberculosis; Mycobacterium gordonae; Mus musculus; Human betaherpesvirus 6; Human immunodeficiency virus 1; Human herpesvirus 4 type 2; Human herpesvirus 4 type 1; Human endogenous retrovirus K; Chlamydia pneumoniae; Human poliovirus 3 strain Sabin; Haemophilus influenzae; Lactobacillus delbrueckii subsp. bulgaricus; Mycobacterium avium; Human alphaherpesvirus 1; Human betaherpesvirus 5; human gammaherpesvirus 4; Coxsackievirus A9; Coxsackievirus B4 (strain E2); Betapolyomavirus macacae

Type:: Protein profiling by protein array

Platform:: GPL19701
2 Samples

Download data: XLSX

Series

Accession:: GSE65278

ID:: 200065278

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20006527710.

Autoimmune peptide antigen reactivity in normal B6 mice Pepperchip 2.0

(Submitter supplied) The aim of the array was to determine the B6 mouse sera IgG and IgM reactivity profile to linear peptide epitopes. Pooled sera from three 6-9 month old B6 mice was diluted at 1:200 for IgG specific analysis or 1:1000 for IgM specific analysis and incubated on a PEPperPRINT peptide microarray platform printed with peptide autoantigens

Organism:: Helicobacter pylori; Proteus mirabilis; Yersinia enterocolitica; Porphyromonas gingivalis; Mycobacterium gordonae; Human alphaherpesvirus 2; Hepatitis C virus isolate HC-J6; Human herpesvirus 4 type 1; Coxsackievirus A20; Torque teno virus; Paraburkholderia fungorum; Porphyromonas gingivalis W83; Mycobacterium avium subsp. paratuberculosis K-10; Chlamydia trachomatis; Streptococcus pyogenes; Mycobacterium tuberculosis variant bovis; Trypanosoma cruzi; Human betaherpesvirus 6; Human T-cell lymphotrophic virus type 1 (isolate MT-2); Coxsackievirus B4; Human adenovirus 12; Human endogenous retrovirus K; Human Endogenous Retrovirus IDDMK1,2-22; Human rotavirus MP409; Hepacivirus hominis; Haemophilus influenzae; Lactobacillus delbrueckii subsp. bulgaricus; Mycobacterium avium; Mycobacterium tuberculosis; Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; human gammaherpesvirus 4; Human herpesvirus 4 strain B95-8; Human T-cell leukemia virus type I; Coxsackievirus A9; Prochlorococcus marinus str. MIT 9202; Coxsackievirus B4 (strain E2); Staphylococcus aureus A9635; Betapolyomavirus macacae; Escherichia coli; Klebsiella pneumoniae; Shigella flexneri; Staphylococcus aureus; Mycobacterium avium subsp. paratuberculosis; Mus musculus; Human immunodeficiency virus 1; Human herpesvirus 4 type 2; Chlamydia pneumoniae; Human poliovirus 3 strain Sabin

Type:: Protein profiling by protein array

Platform:: GPL19701
2 Samples

Download data: XLSX

Series

Accession:: GSE65277

ID:: 200065277

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20003030311.

Reliable analysis of the catabolic gene landscape and transcriptome for pollutant degradation using a custom open source microarray with internal calibration

(Submitter supplied) Despite various efforts to develop tools to detect and compare the activity and catabolic potential and activity for pollutant degradation of microorganisms in environmental samples, an open-source, curated and reliable method is still required. Here we report on a customize normalization system that can be applied to any microarray design, allowing the assessment of reliability of signals and enabling cross-experiment comparisons. more...

Organism:: Paraburkholderia xenovorans LB400; unidentified microorganism; Pseudomonas putida F1; Cupriavidus pinatubonensis JMP134; Rhizorhabdus wittichii RW1

Type:: Expression profiling by array

Platform:: GPL13771
23 Samples

Download data: TXT

Series

Accession:: GSE30303

ID:: 200030303

Analyze with GEO2R

Select item 20002009612.

Strains of increasing genetic divergence to the reference strain

(Submitter supplied) comparative genomic hybridization between Burkholderia cepacia sequenced strains to determine what are the limits to strain relativity in order to still provide accurate estimations of gene content

Organism:: Burkholderia cenocepacia J2315; Paraburkholderia xenovorans LB400; Burkholderia ambifaria AMMD; Burkholderia cenocepacia; Burkholderia vietnamiensis G4; Burkholderia cenocepacia HI2424; Burkholderia orbicola

Type:: Genome variation profiling by array

Platform:: GPL9990
12 Samples

Download data: TXT

Series

Accession:: GSE20096

ID:: 200020096

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 10003388413.

Illumina NovaSeq 6000 (Paraburkholderia xenovorans)

Organism:: Paraburkholderia xenovorans

1 Series
12 Samples

Download data

Platform

Accession:: GPL33884

ID:: 100033884

Select item 10003023714.

Illumina HiSeq 2500 (Paraburkholderia phymatum STM815; Phaseolus vulgaris)

Organism:: Phaseolus vulgaris; Paraburkholderia phymatum STM815

1 Series
4 Samples

Download data

Platform

Accession:: GPL30237

ID:: 100030237

Select item 10002272815.

Illumina HiSeq 2500 (Paraburkholderia phymatum STM815)

Organism:: Paraburkholderia phymatum STM815

4 Series
25 Samples

Download data

Platform

Accession:: GPL22728

ID:: 100022728

Select item 10002080416.

Illumina HiSeq 2000 (Burkholderia caribensis)

Organism:: Paraburkholderia caribensis

1 Series
3 Samples

Download data

Platform

Accession:: GPL20804

ID:: 100020804

Select item 10002080317.

Illumina HiSeq 1500 (Burkholderia caribensis)

Organism:: Paraburkholderia caribensis

1 Series
2 Samples

Download data

Platform

Accession:: GPL20803

ID:: 100020803

Select item 10001970118.

PEPperCHIP Autoimmunity Microarray 2.0

(Submitter supplied) Laser printer spotted peptides Protocol: Amino acid microparticles are laser printed onto a glass slide with a custom 24-color laser printer. One layer of an amino acid particle pattern is printed on a coated glass slide. A heating step melts the particles. Embedded amino acids can couple to the chip surface. In accordance with solid phase Fmoc chemistry, a cycle of synthesis is completed after removal of excessive material by washing and cleavage of the N-terminal Fmoc protection group. more...

Organism:: Helicobacter pylori; Escherichia coli; Klebsiella pneumoniae; Proteus mirabilis; Shigella flexneri; Yersinia enterocolitica; Haemophilus influenzae; Chlamydia trachomatis; Porphyromonas gingivalis; Staphylococcus aureus; Streptococcus pyogenes; Lactobacillus delbrueckii subsp. bulgaricus; Mycobacterium avium; Mycobacterium tuberculosis variant bovis; Mycobacterium avium subsp. paratuberculosis; Mycobacterium tuberculosis; Mycobacterium gordonae; Trypanosoma cruzi; Homo sapiens; Mus musculus; Human alphaherpesvirus 1; Human alphaherpesvirus 2; Human betaherpesvirus 5; Human betaherpesvirus 6; human gammaherpesvirus 4; Human herpesvirus 4 strain B95-8; Hepatitis C virus isolate HC-J6; Human immunodeficiency virus 1; Human T-cell leukemia virus type I; Human T-cell lymphotrophic virus type 1 (isolate MT-2); Coxsackievirus A9; Coxsackievirus B4; Human herpesvirus 4 type 2; Human adenovirus 12; Human herpesvirus 4 type 1; Coxsackievirus A20; Human endogenous retrovirus K; Human Endogenous Retrovirus IDDMK1,2-22; Torque teno virus; Chlamydia pneumoniae; Prochlorococcus marinus str. MIT 9202; Human rotavirus MP409; Coxsackievirus B4 (strain E2); Paraburkholderia fungorum; Porphyromonas gingivalis W83; Mycobacterium avium subsp. paratuberculosis K-10; Human poliovirus 3 strain Sabin; Staphylococcus aureus A9635; Betapolyomavirus macacae; Hepacivirus hominis