Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RppH can faithfully replace TAP to allow cloning of 5’-triphosphate carrying small RNAs

ABSTRACT: RppH can faithfully replace TAP to allow cloning of 5’-triphosphate carrying small RNAs

PROVIDER: PRJNA438901 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6854650.fastq.gz	Fastqsanger.gz
	SRR6854651.fastq.gz	Fastqsanger.gz
	SRR6854652.fastq.gz	Fastqsanger.gz
	SRR6854653.fastq.gz	Fastqsanger.gz
	SRR6854654.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

RppH can faithfully replace TAP to allow cloning of 5’-triphosphate carrying small RNAs

Project description:RNA interference was first described in the nematode Caenorhabditis elegans. Ever since, several new endogenous small RNA pathways have been described and characterized to different degrees. Much like plants, but unlike Drosophila and mammals, worms have RNA-dependent RNA Polymerases (RdRPs) that directly synthesize small RNAs using other transcripts as a template. The very prominent secondary small interfering RNAs, also called 22G-RNAs, produced by the RdRPs RRF-1 and EGO-1 in C. elegans, maintain the 5’ triphosphate group, stemming from RdRP activity, also after loading into an Argonaute protein. This creates a technical issue, since 5’PPP groups decrease cloning efficiency for small RNA sequencing. To increase cloning efficiency of these small RNA species, a common practice in the field is the treatment of RNA samples, prior to library preparation, with Tobacco Acid pyrophosphatase (TAP). Recently, TAP production and supply was discontinued, so an alternative must be devised. We turned to RNA 5’ pyrophosphohydrolase (RppH), a commercially available pyrophosphatase isolated from E. coli. Here we directly compare TAP and RppH in their use for small RNA library preparation.

2018-03-20 | GSE111995 | GEO

RppH can faithfully replace TAP to allow cloning of 5'-triphosphate carrying small RNAs.

Project description:RNA interference was first described in the nematode Caenorhabditis elegans. Ever since, several new endogenous small RNA pathways have been described and characterized to different degrees. The very prominent secondary small interfering RNAs, also called 22G-RNAs, bear a 5' triphosphate group after loading into an Argonaute protein. This creates a technical issue, since 5'PPP groups decrease cloning efficiency for small RNA sequencing. To increase cloning efficiency of these small RNA species, a common practice in the field is the treatment of RNA samples, prior to library preparation, with Tobacco Acid pyrophosphatase (TAP). Recently, TAP production and supply was discontinued, so an alternative must be devised. We turned to RNA 5' pyrophosphohydrolase (RppH), a commercially available pyrophosphatase isolated from E. coli. Here we directly compare TAP and RppH in their use for small RNA library preparation. We show that RppH-treated samples faithfully recapitulate TAP-treated samples. Specifically, there is enrichment for 22G-RNAs and mapped small RNA reads show no small RNA transcriptome-wide differences between RppH and TAP treatment. We propose that RppH can be used as a small RNA pyrophosphatase to enrich for triphosphorylated small RNA species and show that RppH- and TAP-derived datasets can be used in direct comparison. •We show that treatment of small RNA samples with RppH prior to sequencing library preparation increases the cloning efficiency of 5' triphosphorylated small RNAs;•RppH treatment is a valid alternative to TAP treatment.

| S-EPMC6369235 | biostudies-literature

Organic fertilizer replace

Project description:Organic fertilizer replace Raw sequence reads

| PRJNA735545 | ENA

Engineering transcriptional regulators using REPLACE

Project description:Engineering transcriptional regulators using REPLACE

| PRJNA1133800 | ENA

Engineering transcriptional regulators using REPLACE

Project description:Transcriptional regulators are fundamental elements in synthetic biology. We sought to use REPLACE to evolve synthetic transcriptional regulators. Through weeks of directed evolution experiments, we succesufuly modified the sensitivity of TetR and PadR to ligand molecules.

2024-09-30 | GSE271879 | GEO

Blue‐shifting green fluorescent proteins using REPLACE

Project description:Blue‐shifting green fluorescent proteins using REPLACE

| PRJNA1133788 | ENA

Escaping from a dominant‐negative KRAS using REPLACE

Project description:Escaping from a dominant‐negative KRAS using REPLACE

| PRJNA1133794 | ENA

Blue‐shifting green fluorescent proteins using REPLACE

Project description:In the directed evolution experiments of EGFP or StayGold, the objective was to blue-shift the excitation light spectrum of GFP towards shorter wavelengths, resulting in an enhancement of fluorescence intensity upon 405 nm laser excitation. This facilitates the advancement of novel fluorescent proteins. These experiments represent a category of experiments that utilize REPLACE to achieve discontinuous directed evolution through FACS sorting (screening).

2024-09-30 | GSE271876 | GEO

Adenosine 5’-tetraphosphate and adenosine triphosphate signaling in THP-1 macrophages.

Project description:The endogenous nucleotide adenosine 5’-tetraphosphate (Ap4) has emerged as a potent vasoconstrictor. Despite its structural similarity to the danger signal adenosine triphosphate (ATP), the immunomodulatory effects of Ap4 remain unclear. To gain a deeper insight into the biological processes underlying Ap4- and ATP-mediated responses, RNA-sequence analysis of transcriptional changes in THP-1 macropahges was performed. After 3 hours of stimulation with Ap4 or ATP, THP-1 macrophages showed significant changes in RNA expression compared to the unstimulated control.

2025-02-21 | GSE272546 | GEO

Escaping from a dominant‐negative KRAS using REPLACE

Project description:A dominant-negative gene therapy approach has been proposed and tested on proto-oncogene KRAS, wherein the oncogenic activity (and cell proliferation) of KRAS can be suppressed by introducing a dominant-negative KRAS allele (S17N). We employed REPLACE to conduct continuous evolution on KRAS (S17N) and examined its potential pathways for conferring resistance in this gene therapy methodology.

2024-09-30 | GSE271877 | GEO

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