Similar studies for GEO DataSets (Select 200209901) - GEO DataSets

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Items: 4

Select item 2002099011.

RNA-DNA interactome of a prokaryotic cell uncovered by proximity ligation

(Submitter supplied) We used one of the RNA-DNA proximity ligation approaches, RedC, for the analysis of an RNA-DNA interactome of microbial cells. We assess the distribution of main RNA types — mRNA, tRNA and rRNA — along the genomes of E.coli, B.subtilis, and thermophilic archaea T. adornatum.

Organism:: Thermofilum adornatum; Escherichia coli; Bacillus subtilis

Type:: Other

Platforms:: GPL32512 GPL30886 GPL25368
6 Samples

Download data: TSV

Series

Accession:: GSE209901

ID:: 200209901

PubMed Full text in PMC Similar studies

Select item 2000520592.

Unexpected complexity of the Escherichia coli K-12 transcriptome architecture revealed by single nucleotide resolution RNA sequencing

(Submitter supplied) To investigate the architecture of the E. coli K-12 transcriptome, we used two RNA-Seq technologies to analyze strand-specific transcription at single-nucleotide resolution. We analyzed the data by using an organizational schema to annotate the promoters and terminators that define transcription units across the genome. Our results showed that most (ca. two-thirds) operons have a single promoter and terminator, whereas one-third of operons contain multiple transcription units. more...

Organism:: Escherichia coli K-12

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17884
26 Samples

Download data: TXT, WIG

Series

Accession:: GSE52059

ID:: 200052059

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001361413.

Studying RNA-DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics

(Submitter supplied) Noncoding RNAs (ncRNAs) participate in various biological processes, including regulation of transcription and sustaining genome 3D organization. Here, we present a method called Red-C, which exploits proximity ligation to identify contacts with the genome for all RNA molecules present in the nucleus. Using Red-C, we uncover RNA-DNA interactome of human K562 cells and identify hundreds of ncRNAs enriched in active or repressed chromatin. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Other

Platforms:: GPL16791 GPL15520 GPL18573
10 Samples

Download data: TSV

Series

Accession:: GSE136141

ID:: 200136141

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001986064.

YAMAT-seq of mature tRNA pools in the bacterium Escherichia coli str. K-12 substr. MG1655 and derivatives

(Submitter supplied) Mature tRNA pools were measured using an adaptation of YAMAT-seq (Shigematsu et al., 2017; doi:10.1093/nar/gkx005 ) and further described in (Ayan et al., 2020; doi:10.7554/eLife.57947) in 10 strain-medium combinations (all strains dervied from the model bacterium E. coli MG1655). The aim of the experiment was to investigate the effect of reducing tRNA gene copy number on mature tRNA pools in rich and poor media.