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1.

RNAseq analysis of the N. punctiforme transcriptome during hormogonium development

(Submitter supplied) Change in gene expression for wild-type Nostoc punctiforme ATCC 29133 over the time course of hormogonium development
Organism:
Nostoc punctiforme PCC 73102
Type:
Expression profiling by high throughput sequencing
Platform:
GPL22983
5 Samples
Download data: TXT
Series
Accession:
GSE94020
ID:
200094020
2.

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; Rhodopseudomonas palustris CGA009; Neisseria meningitidis FAM18; Thermoplasma acidophilum DSM 1728; Mycoplasma bovis PG45; 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; Treponema caldarium DSM 7334; Treponema succinifaciens DSM 2489; Caldithrix abyssi DSM 13497; Meiothermus 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; Desulfovibrio cf. magneticus IFRC170; Aminiphilus circumscriptus DSM 16581; Caldicoprobacter oshimai DSM 21659; Geovibrio sp. L21-Ace-BES; Microbacterium sp. KROCY2; Thermogemmatispora carboxidivorans; Acidobacterium ailaaui; Ruminococcus flavefaciens AE3010; Selenomonas ruminantium AB3002; Butyrivibrio sp. FCS014; Polycyclovorans algicola TG408; Clostridium sp. KNHs205; Lachnospiraceae bacterium AC2029; Enterococcus faecalis 68A; Butyrivibrio sp. AE3004; 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; Sedimentitalea nanhaiensis DSM 24252; Sediminispirochaeta smaragdinae DSM 11293; Hirschia baltica ATCC 49814; Coraliomargarita akajimensis DSM 45221; Hungateiclostridium thermocellum DSM 1313; Acidobacteria bacterium KBS 146; Syntrophothermus lipocalidus DSM 12680; Syntrophobotulus glycolicus DSM 8271; Bacillus subtilis subsp. spizizenii str. W23; Bacteroides salanitronis DSM 18170; 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; Cellvibrionaceae bacterium Bs12; Oceanicola sp. HL-35; Algoriphagus marincola HL-49; Desulfovibrio sp. L21-Syr-AB; Alicyclobacillus macrosporangiidus CPP55; Sediminibacter sp. Hel_I_10; Hydrogenovibrio sp. MA2-6; Pseudobutyrivibrio ruminis HUN009; Lachnoclostridium phytofermentans KNHs212; Robinsoniella sp. KNHs210; Lactococcus lactis subsp. lactis; Lachnobacterium bovis; Clostridium perfringens ATCC 13124; Hungateiclostridium thermocellum ATCC 27405; Methanocaldococcus jannaschii DSM 2661; Methylorubrum extorquens AM1; Thermoplasma volcanium GSS1; 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; 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; Pseudomonas stutzeri RCH2; Frankia sp. DC12; 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; bacterium JKG1; Thioalkalivibrio sp. ARh3; Thiomonas sp. FB-6; Oxalobacteraceae bacterium AB_14; Desulfotignum balticum DSM 7044; Enterococcus gallinarum; Lactobacillus plantarum; Clostridium algidicarnis; Pyrococcus horikoshii OT3; Methylocystis sp. LW5; Methylobacterium sp. EUR3 AL-11; Bryobacter aggregatus MPL3; Ruminococcus albus AD2013; Eubacterium sp. AB3007; Ruminococcaceae bacterium AE2021; Lachnospiraceae bacterium AC2031; Selenomonas ruminantium AC2024; Peptostreptococcaceae bacterium VA2; Ruminococcus sp. HUN007; Agrobacterium fabrum str. C58; Persephonella; Mastigocladopsis repens PCC 10914; Neisseria gonorrhoeae FA 1090; Clostridioides difficile 630; Acidobacteriaceae bacterium TAA166; 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; Joostella marina; Saccharomonospora viridis DSM 43017; Verrucomicrobia bacterium LP2A; Thermanaerovibrio acidaminovorans DSM 6589; Meiothermus silvanus DSM 9946; 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; Hungateiclostridium clariflavum 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; Polaromonas sp. EUR3 1.2.1; [Ruminococcus] gnavus AGR2154; Lactobacillus 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
Type:
Methylation profiling by high throughput sequencing
228 related Platforms
237 Samples
Download data: CSV, GFF
Series
Accession:
GSE69872
ID:
200069872
3.

Transcriptome analysis of a N. punctiforme sigG mutant

(Submitter supplied) Nostoc punctiforme is a filamentous cyanobacterium capable if differentiating normal vegetative cells into nitrogen fixing heterocysts and spore-like akinetes. Here the effects of a sigma factor (sigG) mutation on the transcriptome was analyzed under 1) normal vegetative growth, and 2) following akinete induction. A zwf strain grown with fructose differentiates into akinetes following transfer to darkness. more...
Organism:
Nostoc punctiforme
Type:
Expression profiling by array
Platform:
GPL19195
2 Samples
Download data: TXT
Series
Accession:
GSE61442
ID:
200061442
4.

Identification of the global transcriptional regulator All3953 (RbcR) in the cyanobacterium Anabaena sp. PCC 7120 by ChIP-Seq analysis

(Submitter supplied) The whole regulon of the LTTR All3953 was determined at 3 h after Ci deficiency in the cyanobacterium Anabaena sp. PCC 7120 by ChIP-Seq analysis. A TAP-tagged version of the protein was used for the chromatin immunoprecipitation. A total of 142 peaks were found, mainly located in the chromosome of Anabaena.
Organism:
Nostoc sp. PCC 7120
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL11645
4 Samples
Download data: BED, TXT
Series
Accession:
GSE58861
ID:
200058861
5.

ChIP analysis unravels an exceptionally wide distribution of binding sites for the NtcA transcription factor in a heterocyst-forming cyanobacterium.

(Submitter supplied) The CRP-family transcription factor NtcA, universally found in cyanobacteria, was initially discovered as a regulator operating N control. It responds to the N regime signaled by the internal 2-oxoglutarate levels, an indicator of the C to N balance of the cells. NtcA-activated canonical promoters bear an NtcA-consensus binding site (GTAN8TAC) centered at about 41.5 nucleotides upstream from the transcription start point. more...
Organism:
Anabaena
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17858
2 Samples
Download data: BED, TXT
Series
Accession:
GSE51865
ID:
200051865
6.

Cell-specific gene expression in Anabaena variabilis grown phototrophically, mixotrophically, and heterotrophically

(Submitter supplied) For the filamentous cyanobacterium Anabaena variabilis to grow without combined nitrogen, certain cells differentiate into heterocysts that fix N2, while vegetative cells perform photosynthesis. Much remains unknown on how heterocysts differ from vegetative cells in terms of carbon and energy metabolisms. Microarrays were used to investigate gene transcription patterns in vegetative cells, heterocysts, and filaments of N2-fixing phototrophic, mixotrophic, and heterotrophic cultures.
Organism:
Trichormus variabilis ATCC 29413
Type:
Expression profiling by array
Platform:
GPL15883
27 Samples
Download data: PAIR
Series
Accession:
GSE46076
ID:
200046076
7.

Deep sequencing of HetR-bound DNA reveals novel HetR targets in Anabaena sp. strain PCC 7120

(Submitter supplied) We employed chromatin pull-down and deep sequencing to globally identify HetR DNA targets in vivo at 6 hours after fixed-nitrogen deprivation. We identified novel DNA binding targets of tagged HetR-6xHis and defined a consensus HetR binding site from these HetR target sequences.
Organism:
Nostoc sp. PCC 7120
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17863
2 Samples
Download data: TXT
Series
Accession:
GSE51886
ID:
200051886
8.

Comparative transcriptomics of wild-type (Nostoc punctiforme ATCC 29133) and hmpD-deletion strains (UCD 543) of Nostoc punctiforme ATCC 29133

(Submitter supplied) Change in gene expression for a wild-type (Nostoc punctiforme ATCC 29133) and hmpD-deletion strain (UCD 543) of Nostoc punctiforme ATCC 29133 over the time course of hormogonium development This study is further descirbed in Risser, D.D. and Meeks, J.C. 2013. Comparative transcriptomics with a motility deficient mutant leads to identification of a novel polysaccharide secretion system in Nostoc punctiforme. more...
Organism:
Nostoc punctiforme PCC 73102
Type:
Expression profiling by array
Platform:
GPL15966
42 Samples
Download data: XYS
Series
Accession:
GSE42859
ID:
200042859
9.

Comparative transcriptomics of wild-type (UCD 153) and patN-deletion strains (UCD 524) of Nostoc punctiforme ATCC 29133

(Submitter supplied) Heterocysts, cells specialized for nitrogen fixation in certain filamentous cyanobacteria, appear singly in a nonrandom spacing pattern along the chain of vegetative cells. A two-stage, biased initiation and competitive resolution model has been proposed to explain the establishment of this spacing pattern. There is substantial evidence that competitive resolution of a subset of cells initiating differentiation occurs by interactions between a self enhancing activator, HetR, and a diffusible inhibitor PatS-5 (RGSGR). more...
Organism:
Nostoc punctiforme PCC 73102
Type:
Expression profiling by array
Platform:
GPL15966
48 Samples
Download data: XYS
Series
Accession:
GSE40250
ID:
200040250
10.

Transcriptional Regulation of Anabaena 7120 response to Nitrogen Deprivation

(Submitter supplied) Here, we report the transcriptome of Anabaena sp. strain 7120, a cyanobacterium that forms specialized nitrogen-fixing cells called heterocysts. Our data suggests that cyanobacteria frequently have more complex transcripts than thought, with large 5' UTRs, numerous antisense transcripts, and multiple transcriptional start sites or processing sites.
Organism:
Nostoc sp. PCC 7120
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11645
4 Samples
Download data: BAM
Series
Accession:
GSE26633
ID:
200026633
11.

Illumina HiSeq 2000 (Nostoc punctiforme PCC 73102)

Organism:
Nostoc punctiforme PCC 73102
1 Series
5 Samples
Download data
Platform
Accession:
GPL22983
ID:
100022983
12.

Nostoc punctiforme printed microarray

(Submitter supplied) see website
Organism:
Nostoc punctiforme
1 Series
2 Samples
Download data
Platform
Accession:
GPL19195
ID:
100019195
13.

PacBio RS II (Mastigocladopsis repens PCC 10914)

Organism:
Mastigocladopsis repens PCC 10914
1 Series
1 Sample
Download data
Platform
Accession:
GPL20440
ID:
100020440
14.

Illumina HiSeq 1000 (Nostoc sp. PCC 7120)

Organism:
Nostoc sp. PCC 7120
1 Series
2 Samples
Download data
Platform
Accession:
GPL17863
ID:
100017863
15.

Illumina Genome Analyzer II (Anabaena)

Platform
Accession:
GPL17858
ID:
100017858
16.

Nostoc punctiforme ATCC 29133 Nimblegen expression array [090619_Npun_JM_EXP]

(Submitter supplied) Nimblegen Design ID 10188. Expression design for 7,151 genes from the Nostoc punctiforme ATCC 29133 chromosome and plasmids with 9 60 mer probe pairs per gene. Protocol: See manufacturer's website at http://www.nimblegen.com/.
Organism:
Nostoc punctiforme PCC 73102
2 Series
90 Samples
Download data: NDF, NGD
Platform
Accession:
GPL15966
ID:
100015966
17.

NimbleGen Anabaena variabilis ATCC 29413 Gene Expression Array [2006-07-27_TI240292_60mer]

(Submitter supplied) Design name: 2006-07-27_TI240292_60mer DESIGN_ID: 4385 Protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.
Organism:
Trichormus variabilis ATCC 29413
1 Series
27 Samples
Download data: NCD, NDF, NGD
Platform
Accession:
GPL15883
ID:
100015883
18.

Illumina Genome Analyzer II (Nostoc sp. PCC 7120)

Organism:
Nostoc sp. PCC 7120
2 Series
8 Samples
Download data
Platform
Accession:
GPL11645
ID:
100011645
19.

18 h

Organism:
Nostoc punctiforme PCC 73102
Source name:
N. punctiforme
Platform:
GPL22983
Series:
GSE94020
Download data
Sample
Accession:
GSM2467196
ID:
302467196
20.

12 h

Organism:
Nostoc punctiforme PCC 73102
Source name:
N. punctiforme
Platform:
GPL22983
Series:
GSE94020
Download data
Sample
Accession:
GSM2467195
ID:
302467195
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