Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-CASing

ABSTRACT: The specificity of the RNA-CASing process was analysed by Next-Generation Sequencing. Therfor small RNAs were isolated from purified proteins of Escherichia coli and subjected to Illumina sequencing or nanopore sequencing.

ORGANISM(S): Escherichia coli

PROVIDER: GSE174271 | GEO | 2021/05/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Quantitative Genomic Analysis of RecA Protein Binding During DNA Double-Strand Break Repair Reveals RecBCD Action in vivo

Project description:Here we have developed a method that combines chromatin immunoprecipitation with next-generation sequencing (ChIP-Seq) and mathematical modeling to quantify RecA protein binding during the active repair of a single DSB in the chromosome of Escherichia coli. Examination of RecA binding during double-strand break repair in Escherichia coli

2015-08-11 | E-GEOD-71249 | biostudies-arrayexpress

Quantitative Genomic Analysis of RecA Protein Binding During DNA Double-Strand Break Repair Reveals RecBCD Action in vivo

2015-08-11 | GSE71249 | GEO

CpG underrepresentation and the new bacterial CpG specific DNA methyltransferase M.MpeI

Project description:The CpG depleted Mycoplasma penetrans harbors a CpG specific C5 methyltransferase. The aim of this experiment was to confirm the specificity of the methyltransferase in vivo and in vitro. Genomic DNA from Mycoplasma penetrans and Escherichia coli genomic DNA that either was or was not methylated in vitro by M.MpeI were subjected to Illumina MiSeq bisulfite sequencing.

2012-11-29 | E-GEOD-41022 | biostudies-arrayexpress

Identification of collateral RNA cleavage mediated by Type VI CRISPR-Cas system from Leptotrichia shahiii

Project description:We investigated the in vivo and in vitro specificity of collateral RNA degradation mediated by LshCas13a protein encoded by Type VI CRISPR-Cas system derived from L. shahii. In our experimental system, we used Escherichia coli strain harboring Type VI spacer matching inducible transcript ("targeting" cells) or strain that does not encode spacers matching any E. coli transcripts ("nontargeting" cells). After the induction of the target transcription, cells were collected, total RNA samples were extracted from the cells and subjected to high throughput RNA sequencing with a specific protocol allowing to capture RNA degradation products. To investigate the influence of RNase toxins encoded in E. coli genome on the observed RNA degradation pattern, we repeated the described experiment on E. coli strain lacking ten known ribonuclease-encoding toxin-antitoxin loci. To investigate in vitro specificity of LshCas13a protein, we analyzed products of the degradation on total E. coli RNA by purified LshCas13a supplemented with crRNA and targeted or nontargeted transcripts. The obtained samples were processed as it was described above. All experiments were independently performed in triplicate. To detect transcript degradation sites, the obtained read pairs were filtered using trimmomatic tool and then mapped onto reference sequences using bowtie2. Next, for each nucleotide position of each strand of reference sequences the number of 5’ ends of aligned fragments were counted producing corresponding tables. The differences between the numbers of mapped 5’ ends in targeting and nontargeting samples were analyzed using edgeR package. Using this data, we identified target preferences for collateral RNA degradation by LshCas13a effectors.

2022-08-31 | GSE183061 | GEO

Construction of an artificial diploid Escherichia coli using a CRISPR-based chromosome-doubling technique

Project description:we designed a CRISPR-based chromosome-doubling technique to construct an artificial diploid Escherichia coli cell. The stable diploid E. coli was confirmed by quantitative PCR and third-generation genome sequencing.

2022-12-29 | GSE192799 | GEO

Bacterial RNase III cleaves long dsRNA at preferred sites

Project description:Members of the ribonuclease (RNase) III family regulate gene expression by processing double-stranded (ds) RNA. The founding member of the family, Escherichia coli (Ec) RNase III, is the most comprehensively studied and its E38A mutant (EcE38A) is an economical reagent for the preparation of small interfering (si) RNA cocktails. Previously, it was shown that EcRNase III recognizes dsRNA with little specificity and that EcE38A mainly produces 23-nucleotide (nt) siRNAs. To characterize substrate specificity and product size, we performed in vitro cleavage of dsRNAs by bacterial RNase IIIs and delineated the cleavage products by next generation sequencing. Surprisingly, we found that RNase III cleaves dsRNA at preferred sites and most siRNAs produced by EcE38A are 22 nt long. We eliminated the sequence specificity of EcE38A through the introduction of additional mutations, thereby creating a reagent that is ideally suited for producing heterogeneous siRNA cocktails to be used in gene silencing studies.

2019-05-26 | GSE120052 | GEO

Normalization of whole-genome SNP data from acute monocytic leukemia patients for exome sequencing

Project description:With the whole genome SNPs array information, we could evaluate the sensitivity and specificity of the point mutation we conclude from the next-generation sequencing data. Furthermore, we could use the true positive mutation as our guidance to exclude the most unreliable single nucleotide variation detected from sequence. After the process, we could promise a very high specificity under minimum loss of sensitivity. To evaluate the sensitivity and specificity of point mutaions detected through the next-generation sequencing data from nine cases of M5 leukemia patients.

2011-02-12 | E-GEOD-27193 | biostudies-arrayexpress

Expression of long non-coding RNAs during spermatogenesis

Project description:Total RNA from purified stages of spermatogenesis were subjected to next generation RNA-seq (100bp, paired-end, strand-specific). The expression of mRNAs and lncRNAs was calculated as FPKM values.

2017-09-04 | GSE100964 | GEO

Escherichia coli DH5alpha Transcriptome Sequencing under Wi-Fi radiofrequency radiation

Project description:Purpose: In this study, Escherichia coli DH5alpha whole transcriptome sequencing was performed in order to compare the different gene expression profiles between control and exposed to Wi-Fi radiofrequency radiations. Methods:Escherichia coli DH5alpha were exposed to Wi-Fi radiations. Total RNA samples( control and exposed ) were extracted by bacteria protect-Rneasy kit,treated with DNAase and subjected to sequnecing using an Illumina-NovaSeq 6000 platform. Library preparation and sequencing were performed by Macrogen (south korea).Trimmed reads are mapped to reference genome with Bowtie. HTseq was used for expression profiling. Expression profile was calculated for each sample and gene as read count.

2019-10-21 | GSE126584 | GEO

Post-translational modification mapping - CRK10 WT and crk10-A397T kinase domain

Project description:We have analysed the recombinant kinase domain of AtCRK10 (At4g23180) purified as an N-terminal His-tag from Escherichia coli cells by LC-MS/MS. Both the WT and the crk10-A39T7 mutant allele of the CRK10 kinase domain were analysed. Post-translational modifications were identified, and a MASCOT search was carried out.

2023-07-20 | PXD023831 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data