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Items: 1 to 20 of 64

1.

Characterization of the transcriptome of Haloferax volcanii with mixed RNA-Seq

(Submitter supplied) Recently a dRNA-Seq study with Haloferax volcanii has been published that led to the discovery of nearly 2800 novel transcription start sites for non-coding RNAs. However, the dRNA-Seq results are confined to the 5'-end of transcripts and does not contain any length information. Therefore, a major aim of the present RNA-Seq study was the elucidation of the lengths of the novel non-coding RNAs. A second aim was to analyze the operon structure of protein-coding genes. more...
Organism:
Haloferax volcanii
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23691
1 Sample
Download data: WIG
Series
Accession:
GSE119686
ID:
200119686
2.

3D interaction maps in wild-type and histone variant deletion mutants generated by chromosome conformation capture [Hi-C II]

(Submitter supplied) Interaction matrices were generated by applying in situ Hi-C to wild-type and deletion mutant trypanosomes.
Organism:
Trypanosoma brucei brucei
Type:
Other
Platform:
GPL22141
12 Samples
Download data: TXT
Series
Accession:
GSE118764
ID:
200118764
3.

3D interaction maps in wild-type and histone variant deletion mutants generated by chromosome conformation capture [Hi-C I]

(Submitter supplied) Interaction matrices were generated by applying in situ Hi-C to wild-type and deletion mutant trypanosomes.
Organism:
Trypanosoma brucei brucei
Type:
Other
Platform:
GPL22141
4 Samples
Download data: TXT
Series
Accession:
GSE118763
ID:
200118763
4.

Maps of histone variant H3.V deposition in Trypanosoma brucei brucei

(Submitter supplied) Chromatin immunoprecipitation of genomic loci in Trypanosoma brucei where histone variant H3.V is deposited. This was achieved by deletion of one H3.V allele and N-terminal tagging of the second H3.V allele with a Ty1 tag. During the ChIP experiment, the DNA was digested with MNase to obtain mononucleosomes. Nucleosomes containing H3.V were pulled down by using a BB2 anti-Ty1 antibody. Cross links are reversed and mononucleosomal DNA is purified and prepared for Illumina sequencing.
Organism:
Trypanosoma brucei brucei
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL22141
4 Samples
Download data: WIG
Series
Accession:
GSE118917
ID:
200118917
5.

Maps of histone variant H4.V deposition in Trypanosoma brucei brucei

(Submitter supplied) Chromatin immunoprecipitation of genomic loci in Trypanosoma brucei where histone variant H4.V is deposited. A previously generated cell line (Siegel et al., 2009) in which both endogenous H4.V alleles are knockout out and ectopic overexpression of a Ty1-tagged version of H4.V can be induced was used. During the ChIP experiment, the DNA was digested with MNase to obtain mononucleosomes. Nucleosomes containing H4.V were pulled down by using a BB2 anti-Ty1 antibody. more...
Organism:
Trypanosoma brucei brucei
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL22141
4 Samples
Download data: WIG
Series
Accession:
GSE118938
ID:
200118938
6.

ATACseq in T. brucei wild-type and histone variant deletion cell lines.

(Submitter supplied) 3x107 cells were harvested and washed in 30 ml cold 1x TDB. The pellet was resuspended in 300 µl permeabilization buffer with protease inhibitors, 3 µl of 4 mM digitonin was added and incubated for 5 minutes at RT. The cells were pelleted, resuspended in 600 µl isotonic buffer with protease inhibitors and split in two samples, containing 1x107 and 2x107 cells, respectively. The transposition reaction was performed by adding 50 µl of transposition mix to the pellet (25 µl TD (2x reaction buffer from Nextera kit), 25 µl TDE1 (Tn5 transposase from Nextera kit), 22.5 µl nuclease-free water) and incubation for 30 minutes at 37 °C. more...
Organism:
Trypanosoma brucei brucei
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL22141
10 Samples
Download data: WIG
Series
Accession:
GSE118902
ID:
200118902
7.

H3.V and H4.V

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Trypanosoma brucei brucei
Type:
Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL22141
46 Samples
Download data: TXT, WIG
Series
Accession:
GSE100896
ID:
200100896
8.

RNAseq of wildtype and deletion mutants (H3.V KO, H4.V KO, H3.V/H4.V KO)

(Submitter supplied) RNA was extraced from wildtype and deletion mutants and a comparative analysis of gene expression was performed using DESeq2.
Organism:
Trypanosoma brucei brucei
Type:
Expression profiling by high throughput sequencing
Platform:
GPL22141
12 Samples
Download data: CSV, FASTA
Series
Accession:
GSE100895
ID:
200100895
9.

Identification of small RNAs expressed in Caulobacter crescentus in response to DNA damage

(Submitter supplied) RNA-based regulation of gene expression is substantially contributing to the ability of bacteria to rapidly adapt to changing environmental conditions. This study employs RNAseq to define the transcriptome of Caulobacter in response to treatment with the DNA-crosslinking agent mitomycin C. We identify a small, regulatory RNA ChvR synthesized under the control of the conserved ChvIG two-component system which represses production of a TonB-dependent receptor, ChvT, in Caulobacter crescentus. more...
Organism:
Caulobacter vibrioides NA1000
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21317
6 Samples
Download data: WIG
Series
Accession:
GSE104186
ID:
200104186
10.

Differential RNA-Seq (dRNA-seq) data from Sphingopyxis granuli strain TFA grown in two different carbon sources and RNA-seq from Hfq-coIP experiment.

(Submitter supplied) We performed differential RNA-sequencing (dRNA-seq) experiments in both minimal medium (MM) plus β-hydroxybutyrate (β-HB) and MM plus tetralin (THN) of Sphingopyxis granuli strain TFA. The objective was mapping the Transcription Start Site (TSS) of each gene in the genome in both conditions, detecting non-coding RNAs (ncRNAs) and comparing the gene expression profile in a preferential carbon source (β-HB) versus tetralin (an aromatic pollutant). more...
Organism:
Sphingopyxis granuli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24666
6 Samples
Download data: WIG
Series
Accession:
GSE111181
ID:
200111181
11.

rne Rhodobacter sphaeroides

(Submitter supplied) Comparison of wild type and mutant strain with temperature-sensitive RNase E. Goal: to study the effect of RNase E on the transcriptome
Organism:
Rhodobacter sphaeroides
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24048
12 Samples
Download data: WIG
Series
Accession:
GSE104278
ID:
200104278
12.

The probiotic Escherichia coli strain Nissle 1917 combats the lambdoid bacteriophages stx and λ

(Submitter supplied) The Escherichia coli strain Nissle 1917 (EcN) is used as a probiotic for the treatment of certain gastrointestinal diseases in several European and non-European countries. In vitro studies showed EcN to efficiently inhibit the production of Shiga toxin (Stx) by Stx producing E. coli (STEC) such as Enterohemorrhagic E. coli (EHEC). The occurrence of the latest EHEC serotype (O104:H4) responsible for the great outbreak in 2011 in Germany was due to the infection of an enteroaggregative E. more...
Organism:
Escherichia coli Nissle 1917
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24564
6 Samples
Download data: TXT, WIG
Series
Accession:
GSE109932
ID:
200109932
13.

RNA-Seq based comparison of Staphylococcus aureus strains resistent and sensitive to MT02

(Submitter supplied) A MT02 sensitive and resistant strain of Staphylococcus LAC USA300 JE2 were exposed to MT02. From those cell RNA was extracted and anylsed by RNA-Seq
Organism:
Staphylococcus aureus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16057
4 Samples
Download data: WIG
Series
Accession:
GSE87572
ID:
200087572
14.

Transcriptomic profiling of BRC+, BRC-, DRC+ and DRC- FACS-sorted samples

(Submitter supplied) BRcells and DRcells show distinct transcriptomic profiles. We assessed transcriptome changes, by deep-sequencing, of different subpopulations of Staphylococcus aureus strain Newman from multicellular aggregates.
Organism:
Staphylococcus aureus subsp. aureus str. Newman
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20326
4 Samples
Download data: WIG
Series
Accession:
GSE69835
ID:
200069835
15.

RNA-seq Transcriptional Profiling of the FK506 Biosynthetic Gene Cluster in Streptomyces tsukubaensis NRRL18488 and General Analysis of the Transcriptome

(Submitter supplied) FK506 (tacrolimus) is a valuable immunosuppressant produced by several Streptomyces strains. In the genome of the wild type producer Streptomyces tsukubaensis NRRL18488 FK506 biosynthesis is encoded by a gene cluster that spans 83.5 kilobases. A whole transcriptome differential shotgun sequencing of S. tsukubaensis was performed to analyze transcription at two different time points; before and during active FK506 production. more...
Organism:
Streptomyces tsukubensis NRRL18488
Type:
Expression profiling by high throughput sequencing
Platform:
GPL22802
8 Samples
Download data: WIG
Series
Accession:
GSE92480
ID:
200092480
16.

GT-rich promoters can drive RNA pol II transcription and deposition of H2A.Z in African trypanosomes

(Submitter supplied) Genome-wide transcription studies are revealing increasing examples of ‘dispersed promoters’ that unlike ‘focused promoters’, lack well-conserved sequence motifs and tight regulation. Dispersed promoters are nevertheless marked by well-defined chromatin structures, suggesting that specific sequence elements must exist in these unregulated promoters. Here, we have analyzed regions of transcription initiation in the eukaryotic parasite Trypanosoma brucei, in which RNA polymerase II transcription initiation and occurs over broad regions without distinct promoter motifs and lacks regulation. more...
Organism:
Trypanosoma brucei brucei
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL21682 GPL22141
16 Samples
Download data: WIG
Series
Accession:
GSE98061
ID:
200098061
17.

Salmonella Cascade assembles on both cis- and -trans encoded CRISPR RNAs

(Submitter supplied) CRISPR/Cas loci commonly encode both proteins and small guide RNAs (crRNAs) to assemble ribonucleoproteins particles (RNPs) that confer a sequence-based, adaptive immunity against viruses and plasmids in prokaryotes. However, it has not been established whether this conserved synteny of RNA and protein genes is needed for the efficient RNP production in vivo. We show that the pathogenic bacterium Salmonella Typhimurium harbours two physically unlinked loci, CRISPR01 and CRISPR02, both of which produce mature crRNAs, although CRISPR02 lacks the protein genes for the type I-specific Cascade complex. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18823
16 Samples
Download data: WIG
Series
Accession:
GSE58602
ID:
200058602
18.

Growth-phase dependent gene regulation in the alpha-proteobacterium Rhodobacter sphaeroides

(Submitter supplied) Global transcriptome analyses at different stages of growth were applied to monitor growth phase-dependent gene expression in the alpha-proteobacterium Rhodobacter sphaeroides. Cultures with low aeration, which underwent strong changes in levels of dissolved oxygen during growth, were compared to aerated cultures, which showed little variation in levels of dissolved oxygen. Cells were in stationary phase for 12 h or for 57 h before dilution into fresh medium. more...
Organism:
Rhodobacter sphaeroides 2.4.1
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17213
8 Samples
Download data: WIG
Series
Accession:
GSE71844
ID:
200071844
19.

The absence of quorum sensing signals triggers the expression of the symbiotic genes in broad host range rhizobia

(Submitter supplied) Plant-released flavonoids induce the transcription of symbiotic genes in rhizobia and one of the first bacterial responses is the synthesis of so called Nod factors. They are responsible for the initial root hair curling during onset of root nodule development. This signal exchange is believed to be essential for initiating the plant symbiosis with rhizobia affiliated with the alphaproteobacteria. Here, we provide evidence that in broad host range rhizobia the complete lack of quorum sensing molecules results in an elevated copy number of its symbiotic plasmid (pNGR234a). more...
Organism:
Sinorhizobium fredii NGR234
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21474
12 Samples
Download data: TXT
Series
Accession:
GSE78039
ID:
200078039
20.

RNA-Seq of Bacillus subtilis and its phage AR9 during the infection

(Submitter supplied) Time course of after infection (5 min, 20 min and 40 min) of Bacillus subtilis by phage AR9
Organism:
Bacillus phage AR9; Bacillus subtilis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL22521
4 Samples
Download data: WIG
Series
Accession:
GSE87573
ID:
200087573
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