Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

An Optimized Chemical-Genetic Method for Cell-Specific Metabolic Labeling of RNA

ABSTRACT: An Optimized Chemical-Genetic Method for Cell-Specific Metabolic Labeling of RNA

PROVIDER: PRJNA562914 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10043563.fastq.gz	Fastqsanger.gz
	SRR10043564.fastq.gz	Fastqsanger.gz
	SRR10043565.fastq.gz	Fastqsanger.gz
	SRR10043566.fastq.gz	Fastqsanger.gz
	SRR10043567.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

An Optimized Chemical-Genetic Method for Cell-Specific Metabolic Labeling of RNA

Project description:We demonstrate that mammalian cells are able to salvage uracil analogs, yielding high background incorporation into cellular RNA. We also discover the enzymatic pathways responsible for this background. To overcome these limitations, we have developed a novel small-molecule/enzyme pair consisting of uridine/cytidine kinase 2 (UCK2) and 2'-azidouridine (2'AzUd).

2020-04-01 | GSE136638 | GEO

Transcriptome-wide Profiling of N6‑Methyladenosine via a Selective Chemical Labeling Method

Project description:Transcriptome-wide Profiling of N6‑Methyladenosine via a Selective Chemical Labeling Method

| PRJNA770671 | ENA

An optimized chemical-genetic method for cell-specific metabolic labeling of RNA.

Project description:Tissues and organs are composed of diverse cell types, which poses a major challenge for cell-type-specific profiling of gene expression. Current metabolic labeling methods rely on exogenous pyrimidine analogs that are only incorporated into RNA in cells expressing an exogenous enzyme. This approach assumes that off-target cells cannot incorporate these analogs. We disprove this assumption and identify and characterize the enzymatic pathways responsible for high background incorporation. We demonstrate that mammalian cells can incorporate uracil analogs and characterize the enzymatic pathways responsible for high background incorporation. To overcome these limitations, we developed a new small molecule-enzyme pair consisting of uridine/cytidine kinase 2 and 2'-azidouridine. We demonstrate that 2'-azidouridine is only incorporated in cells expressing uridine/cytidine kinase 2 and characterize selectivity mechanisms using molecular dynamics and X-ray crystallography. Furthermore, this pair can be used to purify and track RNA from specific cellular populations, making it ideal for high-resolution cell-specific RNA labeling. Overall, these results reveal new aspects of mammalian salvage pathways and serve as a new benchmark for designing, characterizing and evaluating methodologies for cell-specific labeling of biomolecules.

| S-EPMC8518020 | biostudies-literature

Transcriptome-wide Profiling of N6‑Methyladenosine via a Selective Chemical Labeling Method

Project description:We present a chemical method (m6A-ORL-Seq) for transcriptome-wide m6A profiling , and compared its results with MeRIP-seq.

2021-10-15 | GSE185753 | GEO

Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion (SCL-exo)

Project description:We report the setup of a new method to map 5-hydroxymethylcytosine (5hmC) genome-wide at CpG resolution. The method combines selective chemical labeling by 5hmC b-glucosyltransferase and exonuclease digestion of the DNA molecules bound to streptavidin beads after biotinylation of the 5-glucosylmethylcytosines. Associated with a straightforward bioinformatic analysis, this new procedure provides a cost-effective and fast method for mapping 5hmC at high resolution.

2016-03-04 | GSE70635 | GEO

An optimized RNA amplification method for prokaryotic expression profiling analysis

2009-07-25 | GSE17074 | GEO

An optimized RNA amplification method for prokaryotic expression profiling analysis

Project description:Conventional prokaryotic RNA labeling method usually requires large amounts of starting materials and tends to generate high background signals. Recently, two novel methods based on amplification systems were introduced. Here, we compared three alternative strategies: direct labeling method, ployadenylation-involved oligo-dT priming amplification method and random priming amplification method (hereafter referred to as DL, PAOD and RPA method in this article) for prokaryotic RNA labeling employing the expression profiling investigation in Escherichia coli (E. coli) heat shock model. To identify an optimal RNA labeling method for prokaryotic microarray analysis, experiments were performed with starting RNA obtained from E.coli growing at control (37Â°C) or heat shock (43Â°C) condition. We employed 0.5 Î¼g of total RNA for a single round of amplification using PAOD and RPA methods coupling to IVT to generate cDNA targets. In addition, an approach using DL method was also performed. Three types of cDNA mixtures containing Cy5-labeled (or Cy3-labeled) control DNA and Cy3-labeled (or Cy5-labeled) DNA targets were hybridized with E.coli microarrays in a dye-swap strategy. Replicate experiments were conducted from the same batch of total RNA to assess technique reproducibility of each approach.

2010-05-15 | E-GEOD-17074 | biostudies-arrayexpress

A chromatin integration labeling method enables lower-input epigenomic profiling

Project description:A chromatin integration labeling method enables lower-input epigenomic profiling

| PRJNA473561 | ENA

Selective chemical labeling reveals intragenic enrichment of 5-hydroxymethylcytosine in mouse cerebellum

Project description:5-Methylcytosine (5-mC) is an important DNA modification found in eukaryotes that impacts gene regulation and disease pathogenesis. Recently, 5-hydroxymethylcytosine (5-hmC), another form of DNA modification, has been identified in substantial amounts in certain mammalian cell types; however, its roles as well as its distribution in mammalian genomes are unknown. Here we present a selective chemical labeling method for 5-hmC by utilizing T4 bacteriophage BGT-glucosyltransferase to transfer an engineered glucose moiety containing an azide group onto the hydroxyl group of 5-hmC, which in turn can chemically incorporate a biotin group for detection, affinity enrichment, and sequencing of 5-hmC in mammalian genomes. Using this highly effective method, we demonstrate that 5-hmC is present in human cell lines beyond those previously recognized. We also find a gene expression level-dependent enrichment of intragenic 5-hmC in mouse cerebellum and an age-dependent acquisition of this modification in specific gene bodies linked to neurodegenerative disorders

2010-12-12 | GSE25398 | GEO

Selective chemical labeling reveals intragenic enrichment of 5-hydroxymethylcytosine in mouse cerebellum

2010-12-12 | E-GEOD-25398 | biostudies-arrayexpress