txid1183400[Organism] - GEO DataSets

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Select item 2002531751.

RNA-seq gene expression profiling comparing WT and DccrM Ptac-ccrM Agrobacterium tumefaciens C58 cells cultivated in ATGN+/-IPTG.

(Submitter supplied) The cell cycle-regulated DNA methyltransferase CcrM is conserved in most Alphaproteobacteria, but its role in bacteria with complex or multicentric genomes remains unexplored. Here, we compare the methylome, the transcriptome and the phenotypes of wild-type and CcrM-depleted Agrobacterium tumefaciens cells with a dicentric genome with two essential replication origins. We find that DNA methylation has a pleiotropic impact on motility, biofilm formation and viability. more...

Organism:: Agrobacterium tumefaciens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL34084
9 Samples

Download data: TXT

Series

Accession:: GSE253175

ID:: 200253175

Select item 2002402432.

The LysR‐type transcription factor LsrB regulates beta‐lactam resistance in Agrobacterium tumefaciens

(Submitter supplied) We investigated the role of the LysR-type transcriptional regulator LsrB (Atu2186) from Agrobacterium tumefaciens C58 (alias A. fabrum C58), which regulates the expression of small-regulatory-RNA (sRNA) and several protein-coding genes, such as ampD (atu2113). In our current study we invesigated the role of LsrB in beta-lactam resistance. For this purpose, we constructed a vtlR/lsrB deletion mutant. more...

Organism:: Agrobacterium fabrum; Agrobacterium fabrum str. C58

Type:: Expression profiling by high throughput sequencing

Platform:: GPL33656
3 Samples

Download data: CSV

Series

Accession:: GSE240243

ID:: 200240243

PubMed Similar studies

Select item 2001963193.

Centromere interactions promote the maintenance of the multipartite genome in Agrobacterium tumefaciens

(Submitter supplied) Many pathogens and symbionts contain multipartite genomes, but how they are stably maintained is poorly understood. The plant pathogen, Agrobacterium tumefaciens, contains four replicons. Recent work indicates that their replication origins cluster at cell poles in a manner that depends on their ParB-family centromeric proteins. Here, we provide evidence that centromeric clustering is mediated by interactions between these centromeric proteins. more...

Organism:: Bacillus subtilis PY79; Agrobacterium tumefaciens

Type:: Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:: GPL30555 GPL28115
29 Samples

Download data: CSV, TXT, ZIP

Series

Accession:: GSE196319

ID:: 200196319

PubMed Full text in PMC Similar studies

Select item 2001738274.

Transposon sequencing for pathway-specific unipolar polysaccharide biosynthesis screen in Agrobacterium tumefaciens C58

(Submitter supplied) Performed en masse sequencing of transposon insertions among A. tumefaciens mutants deficient in unipolar polysaccharide (UPP) production in two different genetic backgrounds, each one specific for one of the two chemical species of UPP (UPPGlcN and UPPGalN)

Organism:: Agrobacterium fabrum str. C58

Type:: Other

Platform:: GPL30075
5 Samples

Download data: TSV

Series

Accession:: GSE173827

ID:: 200173827

SRA Run Selector

Select item 2001828815.

Conformation and dynamic interactions of the multipartite genome in Agrobacterium tumefaciens

(Submitter supplied) Bacterial species from diverse phyla contain multiple replicons, yet how these multipartite genomes are organized and segregated during the cell cycle remains poorly understood. Agrobacterium tumefaciens has a 2.8 Mb circular chromosome (Ch1), a 2.1 Mb linear chromosome (Ch2), and two large plasmids (pAt and pTi). We used this alpha proteobacterium as a model to investigate the global organization and temporal segregation of a multipartite genome. more...

Organism:: Agrobacterium tumefaciens

Type:: Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:: GPL25733 GPL30555
42 Samples

Download data: CSV, TXT

Series

Accession:: GSE182881

ID:: 200182881

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001744676.

RNASeq Analysis of MirA Regulator in Agrobacterium tumefaciens C58

(Submitter supplied) Performed RNASeq analysis comparing A. tumefaciens C58 (fabrum) harboring a plasmid driving ectopic expression of mirA regulator gene (ATU_RS08050) from Plac promoter with the isogenic strain haboring the same plasmid with no mirA (Vector control)

Organism:: Agrobacterium fabrum str. C58

Type:: Expression profiling by high throughput sequencing

Platform:: GPL30075
6 Samples

Download data: TXT

Series

Accession:: GSE174467

ID:: 200174467

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001739217.

Decreased Peptidoglycan Synthesis Induces the RSI Invasion Switch in Agrobacterium tumefaciens

(Submitter supplied) We report that depletion of PBP1a in Agrobacterium tumefaciens induces transcriptional changes remarkably similar to the RSI invasion switch. Using RNA-seq with NextSeq 500 sequencing, we identified genes that are differentially expressed during depletion of PBP1a after 6 hours and after 16 hours. Depletion of PBP1a after 6 hours results in upregulation in genes associated with Type VI Secretion and succinoglycan production and downregulation of genes associated with flagellar motility and chemotaxis. more...

Organism:: Agrobacterium fabrum str. C58

Type:: Expression profiling by high throughput sequencing

Platform:: GPL30075
20 Samples

Download data: XLSX

Series

Accession:: GSE173921

ID:: 200173921

SRA Run Selector

Select item 2001599618.

The LysR-type transcriptional regulator VtlR/LsrB controls expression of multiple small RNA and small protein genes in Agrobacterium tumefaciens

(Submitter supplied) We investigated the role of the LysR-type transcriptional regulator VtlR/LsrB (Atu2186) from Agrobacterium tumefaciens C58 (alias A. fabrum C58), which regulates the expression of small-regulatory-RNA (sRNA) genes such as AbcR1 and the expression of genes encoding small proteins with a domain of unknown function DUF1127. For this purpose, we constructed a vtlR/lsrB deletion mutant. Total RNA was isolated from this mutant as well as from an AbcR1 deletion mutant (Wilms et al., 2011) at optical densities (OD) of 0.5 or 0.5 and 1.5, respectively. more...

Organism:: Agrobacterium fabrum str. C58

Type:: Expression profiling by high throughput sequencing

Platform:: GPL28562
9 Samples

Download data: CSV

Series

Accession:: GSE159961

ID:: 200159961

PubMed Similar studies SRA Run Selector

Select item 2001509419.

Arginine-rich small proteins with a domain of unknown function DUF1127 play a role in phosphate and carbon metabolism of Agrobacterium tumefaciens

(Submitter supplied) The genome of Agrobacterium tumefaciens C58 harbors three genes encoding small proteins (<50 aa) with a domain of unknown function DUF1127 (ATU_RS08170, ATU_RS08175, ATU_RS21905). To investigate their function we created a triple-deletion mutant lacking those genes. Total RNA was isolated from A. tumefaciens wild type and from the triple mutant (∆∆∆) at optical densities (OD) of 0.5 and 1.5, and after 24 h of growth (30 °C in YEB medium at 180 rpm) and sequenced on an Illumina platform. more...

Organism:: Agrobacterium fabrum str. C58

Type:: Expression profiling by high throughput sequencing

Platform:: GPL28562
18 Samples

Download data: TXT

Series

Accession:: GSE150941

ID:: 200150941

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20012188910.

The biotroph Agrobacterium tumefaciens thrives in tumors by exploiting a wide spectrum of plant host metabolites

(Submitter supplied) Purpose: The goals of this study is to compare the reponse of Agrobacterium tumefaciens C58 in the presence of GHB and GABA to delineated the key-genes associated to the response of these metabolites in A. tumefaciens C58.

Organism:: Agrobacterium tumefaciens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL25733
12 Samples

Download data: TXT

Series

Accession:: GSE121889

ID:: 200121889

PubMed Similar studies SRA Run Selector

Select item 20010625711.

Trancriptome analysis of Agrobacterium tumefaciens C58 cells in the presence of abundant opines

(Submitter supplied) Purpose: The goals of this study is to compare the reponse of Agrobacterium tumefaciens C58 in the presence and absence of the two opines nopaline and agrocinopine (more precisely agrocinopine A) to delineated the key-genes associated to opines-response in A. tumefaciens C58.

Organism:: Agrobacterium tumefaciens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24197
6 Samples

Download data: TXT

Series

Accession:: GSE106257

ID:: 200106257

PubMed Similar studies SRA Run Selector

Select item 20010884512.

The LsrB protein is required for Agrobacterium tumefaciens interaction with host plants

(Submitter supplied) We found 465 genes were significantly differentially expressed (upregulation of 162 genes and downregulation of 303 genes) in the mutant compared to the wild-type strain by RNA-sequencing.

Organism:: Agrobacterium fabrum str. C58

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24478
2 Samples

Download data: XLS

Series

Accession:: GSE108845

ID:: 200108845

SRA Run Selector

Select item 20006987213.

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:: 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; 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; 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; [Clostridium] methoxybenzovorans SR3; [Clostridium] 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

Select item 20007126714.

Comparison of expression profiles for Agrobacterium tumefaciens wild-type strain C58 and isogenic pdhS2 (Atu1888) deletion strain

(Submitter supplied) A conserved regulatory pathway directs developmental transitions and asymmetries in Agrobacterium tumefaciens. Core components of this coordination of division and development (CDD) pathway include two integrated phosphorelays. One of these phosphorelays includes at least four histidine sensor kinase homologues, DivJ, PleC, PdhS1, and PdhS2, and at least two response regulators, DivK and PleD. Previously we demonstrated that PdhS2 reciprocally regulates biofilm formation and swimming motility. more...

Organism:: Agrobacterium tumefaciens

Type:: Expression profiling by array

Platform:: GPL18993
3 Samples

Download data: GPR, PDF, XLSX

Series

Accession:: GSE71267

ID:: 200071267

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20007126615.

Comparison of expression profiles for Agrobacterium tumefaciens wild-type strain C58 grown with or without manganese

(Submitter supplied) The plant pathogen Agrobacterium tumefaciens attaches to and forms biofilms on both biotic and abiotic surfaces. The transition between free-living, planktonic A. tumefaciens and multicellular biofilms is regulated by several well-defined environmental and nutritional inputs, including pH, oxygen tension, and phosphate concentration. In many bacterial species limiting iron levels inhibit attachment and biofilm formation. more...

Organism:: Agrobacterium tumefaciens

Type:: Expression profiling by array

Platform:: GPL18993
4 Samples

Download data: GPR, PDF, XLSX

Series

Accession:: GSE71266

ID:: 200071266

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20007113816.

Comparison of expression profiles for Agrobacterium tumefaciens wild-type strain C58 grown with or without iron.

Organism:: Agrobacterium tumefaciens

Type:: Expression profiling by array

Platform:: GPL18993
4 Samples

Download data: GPR, XLS

Series

Accession:: GSE71138

ID:: 200071138

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20005912317.

Identification of Hfq bound RNA by co-immunoprecipitation and RNA-sequencing

(Submitter supplied) 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 analysis. Interestingly, 55% of the ncRNAs were encoded antisense to a protein coding sequence. Abundance of 4 asRNAs and their corresponding target mRNAs was altered upon hfq, indicating a substantial influence of Hfq on asRNA-target interactions.

Organism:: Agrobacterium tumefaciens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18897
8 Samples

Download data: WIG

Series

Accession:: GSE59123

ID:: 200059123

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20006173818.

Prokaryote whole-genome tiling microarray design and validation

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

Organism:: Agrobacterium fabrum str. C58; Escherichia coli str. K-12 substr. MG1655

Type:: Expression profiling by genome tiling array

Platforms:: GPL19222 GPL19219
38 Samples

Download data: PAIR

Series

Accession:: GSE61738

ID:: 200061738

Analyze with GEO2R

Select item 20006173719.

Agrobacterium tumefaciens C58 whole-genome tiling microarray design and validation

(Submitter supplied) This research focuses on the design, manufacturing and validation of a new Agrobacterium tumefaciens C58 whole-genome tiling microarray platform for novel RNA transcript discovery. A whole-genome tiling microarray allows both annotated genes as well as previously unknown RNA transcripts to be detected and quantified at once. The Agrobacterium tumefaciens C58 genome is re-acquired with next-generation sequencing and then used to design the tilinlg microarray with the thermodynamic analysis program Picky. more...

Organism:: Agrobacterium fabrum str. C58

Type:: Expression profiling by genome tiling array

Platform:: GPL19222
20 Samples

Download data: PAIR, TXT

Series

Accession:: GSE61737

ID:: 200061737

Analyze with GEO2R

Select item 20006056520.

Comparison of Expression Profiles for Agrobacterium tumefaciens visR mutant to wild-type strain.

(Submitter supplied) Many bacteria colonize surfaces and transition to a sessile mode of growth. The plant pathogen Agrobacterium tumefaciens produces a unipolar polysaccharide (UPP) adhesin at single cell poles that contact surfaces. Here we report that elevated levels of the intracellular signal cyclic diguanosine monophosphate (c-di-GMP) lead to surface-contact-independent UPP production and a red colony phenotype due to production of UPP and the exopolysaccharide cellulose, when A. more...

Organism:: Agrobacterium tumefaciens

Type:: Expression profiling by array

Platform:: GPL18993
3 Samples

Download data: GPR, TXT

Series

Accession:: GSE60565

ID:: 200060565

PubMed Full text in PMC Similar studies Analyze with GEO2R

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