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Items: 1 to 20 of 562

1.

Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [RNA-Seq]

(Submitter supplied) Genomic mutations allow bacteria to adapt rapidly to adverse stress environments. The three-dimensional conformation of the genome also may plays an important role in transcriptional regulation and environmental adaptation. Here, using chromosome conformation capture, we investigate the high-order architecture of the Zymomonas mobilis chromosome in response to genomic mutant and ambient stimuli (acetic acid and furfural, derived from lignocellulosic hydrolysate). more...
Organism:
Zymomonas mobilis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32966
15 Samples
Download data: TXT
Series
Accession:
GSE221498
ID:
200221498

PubMed Full text in PMC Similar studies

2.

Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [Hi-C]

(Submitter supplied) Genomic mutations allow bacteria to adapt rapidly to adverse stress environments. The three-dimensional conformation of the genome also may plays an important role in transcriptional regulation and environmental adaptation. Here, using chromosome conformation capture, we investigate the high-order architecture of the Zymomonas mobilis chromosome in response to genomic mutant and ambient stimuli (acetic acid and furfural, derived from lignocellulosic hydrolysate). more...
Organism:
Zymomonas mobilis
Type:
Other
Platform:
GPL32966
10 Samples
Download data: MCOOL, TXT
Series
Accession:
GSE221497
ID:
200221497

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3.

Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [ChIP-Seq]

(Submitter supplied) Genomic mutations allow bacteria to adapt rapidly to adverse stress environments. The three-dimensional conformation of the genome also may play an important role in transcriptional regulation and environmental adaptation. Here, using chromosome conformation capture, we investigate the high-order architecture of the Zymomonas mobilis chromosome in response to genomic mutant and ambient stimuli (acetic acid and furfural, derived from lignocellulosic hydrolysate). more...
Organism:
Zymomonas mobilis
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL32966
10 Samples
Download data: BW, NARROWPEAK
Series
Accession:
GSE221496
ID:
200221496

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4.

Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Zymomonas mobilis
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing
Platform:
GPL32966
35 Samples
Download data: BW, NARROWPEAK, TXT
Series
Accession:
GSE221499
ID:
200221499

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5.

Gene expression analysis of Zymomonas mobilis ZM4 for promoter strengths prediction

(Submitter supplied) Looking at the expression levels of all the genes of Zymomonas mobilis ZM4; and in particular we would like to predict the strengths of the genes located on the native plasmids.
Organism:
Zymomonas mobilis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL33295
3 Samples
Download data: TXT
Series
Accession:
GSE242573
ID:
200242573

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6.

Investigated the responses of ZM532 and wild-type ZM4 to acetic acid and furfural by using RNA-seq

(Submitter supplied) In our previous study, we successfully constructed an engineered Zymomonas mobilis ZM532 strain tolerant these double inhibitors by genome shuffling, but the molecular mechanisms of tolerance to these inhibitors are still unknown. The goal of this study investigated the responses of ZM532 and wild-type ZM4 to acetic acid and furfural using Transcriptome
Organism:
Zymomonas mobilis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29852
12 Samples
Download data: TXT
Series
Accession:
GSE168900
ID:
200168900

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7.

Cold plasma pretreatment reinforces the lignocellulose-derived aldehyde inhibitors tolerance and bioethanol fermentability for Zymomonas mobilis

(Submitter supplied) To investigate the molecular mechanism of the increased bioethanol fermentability, we carried out RNA-Seq sequencing assays for the wild and mutant strain Z. mobilis after pretreated with cold plasma. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at one time points.
Organism:
Zymomonas mobilis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL33295
6 Samples
Download data: TXT
Series
Accession:
GSE228538
ID:
200228538

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8.

Multistage  Transcriptomics Data Set of Zymomonas mobilis 2032 During Fermentation in 6% and 9% Glucan-Loading AFEX-Pretreated Corn Stover Hydrolysates and 7% Glucan-Loading AFEX-Pretreated Switchgrass Hydrolysate

(Submitter supplied) The fermentation of Zymomonas mobilis 2032 was conducted in 6% and 9% glucan-loading AFEX-pretreated corn stover hydrolysates, as well as in 7% glucan-loading AFEX-pretreated switchgrass hydrolysate, and RNA samples were collected at both glucose and xylose growth stages. Here we present a comprehensive RNA-Seq data set at both growth stages.
Organism:
Zymomonas mobilis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29852
25 Samples
Download data: TXT
Series
Accession:
GSE201229
ID:
200201229

PubMed Full text in PMC Similar studies

9.

ZMO1162 Overexpression Boosts Phenolic Aldehyde Conversion and Ethanol Production of Zymomonas mobilis ZM4

(Submitter supplied) we aimed to screen candidate kinase genes under the stress of phenolic aldehydes during ethanol fermentation for Zymomonas mobilis ZM4
Organism:
Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32076
18 Samples
Download data: XLSX
Series
Accession:
GSE199182
ID:
200199182

10.

Genome-scale transcription–translation mapping reveals novel features of Zymomonas mobilis promoters and transcription units 

(Submitter supplied) We collected sample-matched multiomics data including RNA-seq, transcription start site sequencing (TSS-seq), termination sequencing (term-seq), ribosome profiling, and label-free shotgun proteomic mass spectrometry across different growth conditions to improve annotation and assign functional sites in the Zymomonas mobilis subsp. mobilils ZM4 genome. Proteomics and ribosome profiling informed revisions of protein-coding genes, which included 44 start codon changes and 42 added proteins. more...
Organism:
Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL27722 GPL26046
94 Samples
Download data: BEDGRAPH, TXT
Series
Accession:
GSE139939
ID:
200139939

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11.

Mapping regulatory networks of Zymomonas mobilis small RNAs Zms4 and Zms6

(Submitter supplied) sRNAs represent a powerful class of regulators that influence multiple mRNA targets but remain largely uncharacterized outside of model organisms. Zymomonas mobilis is a natural ethanol-producing bacterium in which multiple small RNAs (sRNAs) have recently been identified, some of which show differential expression in ethanol stress. In this study, we show that sRNAs Zms4 and Zms6 have significant impacts on ethanol tolerance in Z. more...
Organism:
Zymomonas mobilis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24294
21 Samples
Download data: GFF
Series
Accession:
GSE107219
ID:
200107219

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12.

Impacts of Z. mobilis sRNAs Zms4 and Zms6 overexpression on gene networks

(Submitter supplied) The induction of Z. mobilis sRNAs Zms4 and Zms6 reveals their regulatory impacts on gene networks.
Organism:
Zymomonas mobilis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24294
12 Samples
Download data: GFF
Series
Accession:
GSE107193
ID:
200107193

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13.

MS2-affinity purification coupled to RNA-sequencing (MAPS) reveals targetomes of Z. mobilis sRNAs Zms4 and Zms6

(Submitter supplied) The MS2-affinity purification coupled to RNA-sequencing (MAPS) approach was used to identify RNA targets that physically associate in vivo with Zymomonas mobilis small RNAs Zms4 and Zms6.
Organism:
Zymomonas mobilis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24294
9 Samples
Download data: GFF
Series
Accession:
GSE107192
ID:
200107192

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14.

Multiomic Fermentation Using Chemically Defined Synthetic Hydrolysates Revealed Multiple Effects Of Lignocellulose-Derived Inhibitors On Cell Physiology and Xylose Utilization In Zymomonas mobilis

(Submitter supplied) The conversion of sugars in lignocellulosic hydrolysates to bioethanol represents an industrially relevant system for understanding microbial physiology associated with production of bio-based fuels and chemicals. To this end we have developed a new version of synthetic hydrolysate (SynH) modeled on highly concentrated 9% AFEX-pretreated cornstove hydrolysate (ACSH) with and without lignocellulose-derived inhibitors (LDIs) added, termed SynH3 and SynH3- respectively. more...
Organism:
Zymomonas mobilis subsp. mobilis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27043
24 Samples
Download data: TXT
Series
Accession:
GSE135718
ID:
200135718

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15.

Systems-level Analysis of Oxygen Exposure in Zymomonas mobilis: Implications for Isoprenoid Production

(Submitter supplied) Zymomonas mobilis is an aerotolerant anaerobe and prolific ethanologen with attractive characteristics for industrial bioproduct generation. However, there is currently insufficient knowledge of the impact that environmental factors have on flux through industrially relevant biosynthetic pathways. Here, we examine the effect of oxygen exposure on metabolism and gene expression in Z. mobilis by combining targeted metabolomics, mRNA sequencing, and shotgun proteomics. more...
Organism:
Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26046
38 Samples
Download data: TXT
Series
Accession:
GSE125123
ID:
200125123

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16.

Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

(Submitter supplied) In this study, we reported the updated chromosome and plasmid sequence of ZM4, and its two engineered xylose-utilizing strains derivatives (strains 2032 and 8b). The majority of plasmid genes have either homologs from other organisms or some conserved domains. Our bioinformatics analysis suggested that several plasmid genes may be essential genes of ZM4. To further validate the function of these plasmid genes, an RNA-Seq pipeline was developed for Z. more...
Organism:
Zymomonas mobilis subsp. mobilis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24485
17 Samples
Download data: TXT
Series
Accession:
GSE108890
ID:
200108890

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17.

Phenotypic, genomic and transcriptional analysis of Zymomonas mobilis ZM4 mutants with enhanced ethanol tolerance

(Submitter supplied) Background: Growth in the global population and industrial activities has increased world energy consumption. Bioethanol is considered as an alternative renewable energy source. Among various ethanol-producing microbes, Zymomonas mobilis ZM4 has received special attention due to its higher ethanol yield and tolerance. Advances in genetic engineering are particularly important for developing microorganisms with improved ethanol production. more...
Organism:
Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
Type:
Expression profiling by array
Platform:
GPL22693
6 Samples
Download data: XLS
Series
Accession:
GSE90043
ID:
200090043

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18.

Transcriptomic Profiles of Xylose-utilizing Zymomonas mobilis 8b to Pretreatment Inhibitor Furfural

(Submitter supplied) Background: Lignocellulosic biomass is a promising renewable feedstock for the microbial production of fuels. To release the major fermentable sugars such as glucose and xylose, pretreatment, hydrolysis, and subsequent conditioning of biomass feedstock are needed. During this process, many toxic compounds are produced or introduced which subsequently inhibit microbial growth and in many cases the production titer and rate. more...
Organism:
Zymomonas mobilis
Type:
Expression profiling by genome tiling array
Platform:
GPL18675
30 Samples
Download data: TXT
Series
Accession:
GSE63540
ID:
200063540

PubMed Full text in PMC Similar studies Analyze with GEO2R

19.

The Epigenomic Landscape of Prokaryotes

(Submitter supplied) DNA methylation is an important regulator of genome function in the eukaryotes, but it is currently unclear if the same is true in prokaryotes. While regulatory functions have been demonstrated for a small number of bacteria, there have been no large-scale studies of prokaryotic methylomes and the full repertoire of targets and biological functions of DNA methylation remains unclear. Here we applied single-molecule, real-time sequencing to directly study the methylomes of 232 phylogenetically diverse prokaryotes. more...
Organism:
Enterococcus gallinarum; Clostridium algidicarnis; Pyrococcus horikoshii OT3; Methylocystis sp. LW5; Agrobacterium fabrum str. C58; Persephonella; Mastigocladopsis repens PCC 10914; Neisseria gonorrhoeae FA 1090; Clostridioides difficile 630; Thiobacillus denitrificans ATCC 25259; Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150; Sulfurimonas denitrificans DSM 1251; Sulfolobus acidocaldarius DSM 639; Flavobacterium psychrophilum JIP02/86; Methanocorpusculum labreanum Z; Cronobacter; Pseudarthrobacter chlorophenolicus A6; Saccharomonospora viridis DSM 43017; Verrucomicrobia bacterium LP2A; Thermanaerovibrio acidaminovorans DSM 6589; Corynebacterium aurimucosum ATCC 700975; Zymomonas mobilis subsp. pomaceae ATCC 29192; Klebsiella aerogenes FGI35; Cellulophaga algicola DSM 14237; Flexistipes sinusarabici DSM 4947; Sulfurospirillum barnesii SES-3; Gillisia limnaea DSM 15749; Spirochaeta thermophila DSM 6578; Ruminococcus sp. NK3A76; Spirochaeta africana DSM 8902; Holophaga foetida DSM 6591; Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7; Acetivibrio clariflavus 4-2a; Thermacetogenium phaeum DSM 12270; Methylophilus sp. 5; Arthrobacter sp. 31Y; Methylophilus sp. 42; Methylotenera versatilis 79; Psychrilyobacter atlanticus DSM 19335; Prevotella sp. 10(H); Methylotenera sp. 73s; Acidovorax sp. JHL-3; Gillisia sp. JM1; Cellulomonas sp. KRMCY2; Clostridium sp. ASBs410; Limisalsivibrio acetivorans; Polaromonas sp. EUR3 1.2.1; Levilactobacillus brevis AG48; Pediococcus acidilactici AGR20; Exiguobacterium chiriqhucha; Prevotella sp. HUN102; Flavimarina sp. Hel_I_48; Lachnospiraceae bacterium AC2012; Clostridioides mangenotii LM2; Exiguobacterium aurantiacum DSM 6208; Exiguobacterium acetylicum DSM 20416; Exiguobacterium oxidotolerans JCM 12280; Exiguobacterium antarcticum DSM 14480; Methylobacter tundripaludum 21/22; Lachnoclostridium phytofermentans KNHs2132; Staphylococcus epidermidis AG42; Butyrivibrio sp. AE3003; Streptococcus equinus; Salmonella enterica subsp. arizonae serovar 62:z4,z23:-; Xylella fastidiosa Temecula1; Acetivibrio thermocellus ATCC 27405; Rhodopseudomonas palustris CGA009; Neisseria meningitidis FAM18; Thermoplasma acidophilum DSM 1728; Hydrogenovibrio crunogenus XCL-2; Chloroflexus aggregans DSM 9485; Thermosipho melanesiensis BI429; Shewanella woodyi ATCC 51908; Bradyrhizobium elkanii USDA 76; Dinoroseobacter shibae DFL 12 = DSM 16493; Parabacteroides distasonis ATCC 8503; Anoxybacillus flavithermus WK1; Escherichia coli str. K-12 substr. MG1655; Capnocytophaga ochracea DSM 7271; Haloterrigena turkmenica DSM 5511; Palaeococcus ferrophilus DSM 13482; Acetivibrio thermocellus DSM 1313; Gracilinema caldarium DSM 7334; Treponema succinifaciens DSM 2489; Caldithrix abyssi DSM 13497; Calidithermus chliarophilus DSM 9957; Cohnella panacarvi Gsoil 349; Methylobacterium sp. 10; Xanthobacter sp. 91; Geopsychrobacter electrodiphilus DSM 16401; Hydrogenovibrio marinus DSM 11271; Nocardia sp. BMG111209; Klebsiella oxytoca BRL6-2; Polaribacter sp. Hel_I_88; Methylohalobius crimeensis 10Ki; Streptomyces sp. WMMB 714; Ruminiclostridium josui JCM 17888; Alteromonas sp. ALT199; Aminiphilus circumscriptus DSM 16581; Caldicoprobacter oshimai DSM 21659; Microbacterium sp. KROCY2; Thermogemmatispora carboxidivorans; Ruminococcus flavefaciens AE3010; Butyrivibrio sp. FCS014; Polycyclovorans algicola TG408; Clostridium sp. KNHs205; Lachnospiraceae bacterium AC2029; Enterococcus faecalis 68A; Butyrivibrio sp. AE3004; Teredinibacter purpureus; Lactococcus lactis subsp. lactis; Lactiplantibacillus plantarum; Lachnobacterium bovis; Clostridium perfringens ATCC 13124; Methanocaldococcus jannaschii DSM 2661; Methylorubrum extorquens AM1; Thermoplasma volcanium GSS1; Acidobacteriaceae bacterium TAA 166; Mycoplasmopsis bovis PG45; Methanospirillum hungatei JF-1; Actinobacillus succinogenes 130Z; Fervidobacterium nodosum Rt17-B1; Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088; Staphylothermus marinus F1; Thermoanaerobacter sp. X514; Xenorhabdus nematophila ATCC 19061; Galbibacter orientalis; Dyadobacter fermentans DSM 18053; Streptosporangium roseum DSM 43021; Pedobacter heparinus DSM 2366; Rhizobium etli CIAT 652; Meiothermus ruber DSM 1279; Planctopirus limnophila DSM 3776; Methanothermus fervidus DSM 2088; Sebaldella termitidis ATCC 33386; Methanohalophilus mahii DSM 5219; Aminobacterium colombiense DSM 12261; Acidobacteriaceae bacterium KBS 146; Pontibacter actiniarum DSM 19842; Thermobacillus composti KWC4; Marinithermus hydrothermalis DSM 14884; Bernardetia litoralis DSM 6794; Desulfobacca acetoxidans DSM 11109; Rikenella microfusus DSM 15922; Echinicola vietnamensis DSM 17526; Orenia marismortui DSM 5156; Sporocytophaga myxococcoides DSM 11118; Niabella soli DSM 19437; Sinorhizobium medicae WSM1115; Hippea alviniae EP5-r; Hippea sp. KM1; Sphingomonas melonis C3; Methylophilaceae bacterium 11; Thioalkalivibrio sp. ARh3; Thiomonas sp. FB-6; Oxalobacteraceae bacterium AB_14; Solidesulfovibrio cf. magneticus IFRC170; Desulfotignum balticum DSM 7044; Methylobacterium sp. EUR3 AL-11; Kallotenue papyrolyticum; Bryobacter aggregatus MPL3; Ruminococcus albus AD2013; Eubacterium sp. AB3007; Ruminococcaceae bacterium AE2021; Lachnospiraceae bacterium AC2031; Selenomonas ruminantium AC2024; Selenomonas sp. AB3002; Peptostreptococcaceae bacterium VA2; Ruminococcus sp. HUN007; Teredinibacter turnerae; Escherichia coli CFT073; Salmonella bongori NCTC 12419; Treponema denticola ATCC 35405; Akkermansia muciniphila ATCC BAA-835; Phaeobacter inhibens DSM 17395; Actinosynnema mirum DSM 43827; Staphylococcus aureus subsp. aureus USA300_TCH1516; Sphaerobacter thermophilus DSM 20745; Veillonella parvula DSM 2008; Streptobacillus moniliformis DSM 12112; Allomeiothermus silvanus DSM 9946; Sedimentitalea nanhaiensis DSM 24252; Sediminispirochaeta smaragdinae DSM 11293; Hirschia baltica ATCC 49814; Coraliomargarita akajimensis DSM 45221; Syntrophothermus lipocalidus DSM 12680; Stutzerimonas stutzeri RCH2; Syntrophobotulus glycolicus DSM 8271; Bacillus spizizenii str. W23; Phocaeicola salanitronis DSM 18170; Pseudofrankia sp. DC12; Nitratifractor salsuginis DSM 16511; Cellulophaga lytica DSM 7489; Asinibacterium sp. OR53; Solitalea canadensis DSM 3403; Patulibacter minatonensis DSM 18081; Acetobacterium woodii DSM 1030; Nocardia sp. BMG51109; Halomicrobium katesii DSM 19301; Nitriliruptor alkaliphilus DSM 45188; Methylophilus sp. 1; Pseudomonas aeruginosa NCAIM B.001380; Kangiella aquimarina DSM 16071; Pelobacter seleniigenes DSM 18267; Thiomicrospira pelophila DSM 1534; Desulfurobacterium sp. TC5-1; Bacteroides sp. 14(A); Clostridium sp. 12(A); Hydrogenovibrio kuenenii DSM 12350; Leptolyngbya sp. PCC 6406; Maribacter sp. Hel_I_7; Desulfospira joergensenii DSM 10085; Tolumonas lignilytica; Cellvibrionaceae bacterium 1162T.S.0a.05; Lacrimispora indolis SR3; Lacrimispora indolis DSM 755; Desulforegula conservatrix Mb1Pa; Oceanicola sp. HL-35; Algoriphagus marincola HL-49; Desulfohalovibrio reitneri; Alicyclobacillus macrosporangiidus CPP55; Pseudacidobacterium ailaaui; Mediterraneibacter gnavus AGR2154; Sediminibacter sp. Hel_I_10; Hydrogenovibrio sp. MA2-6; Pseudobutyrivibrio ruminis HUN009; Lachnoclostridium phytofermentans KNHs212; Robinsoniella sp. KNHs210
Type:
Methylation profiling by high throughput sequencing
228 related Platforms
237 Samples
Download data: CSV, GFF
Series
Accession:
GSE69872
ID:
200069872

PubMed Full text in PMC Similar studies SRA Run Selector

20.

Transcriptional analysis of adaptation to high glucose concentration in Zymomonas mobilis

(Submitter supplied) High glucose concentrations were desirable for ethanol fermentation of Zymomonas mobilis, but it can lead to decrease in ethanol production and productivity. Sorbitol as a compatible solute can be absorbed or synthesized to counteract the detrimental osmotic stress caused from external high glucose concentrations by Z. mobilis. Currently, molecular mechanisms of tolerance to high glucose concentrations and sorbitol promoting ethanol fermentation are still unclear for Z. more...
Organism:
Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
Type:
Expression profiling by array
Platform:
GPL17542
12 Samples
Download data: PAIR
Series
Accession:
GSE49620
ID:
200049620

PubMed Similar studies Analyze with GEO2R

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