Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Influence of RNA Labeling on Expression Profiling of MicroRNAs

ABSTRACT: Influence of RNA Labeling on Expression Profiling of MicroRNAs

PROVIDER: PRJNA144079 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Influence of RNA Labeling on Expression Profiling of MicroRNAs

2012-05-22 | GSE30045 | GEO

Influence of RNA Labeling on Expression Profiling of MicroRNAs

Project description:Several technical parameters are now being optimized for microRNA expression profiling experiments, but the finite amount of total RNA available continues to bottleneck clinical investigations. We used microarrays to determine the influence of the labeling reagent on total RNA requirements and data quality. Human brain/lung samples were each labeled in duplicate, at 1.0ug, 0.5ug, 0.2ug, and 0.1ug of total RNA, using two microRNA labeling kits (Genisphere Biotin and Biotin-HSR) that utilize the same labeling procedure but differ in the composition of the labeling reagent used to label the microRNA molecules in the samples. A total of 32 arrays were used for this experiment. Additionally, synthetic microRNA spike-in experiments were also performed to establish the signal dynamic range of the microarray using the Biotin-HSR labeling kit. Two-fold serial dilution samples were prepared that contained from 5000 to 4.88 attomoles of miRNA. A total of 12 arrays were used for this experiment, including a negative control sample.

2012-05-21 | E-GEOD-30045 | biostudies-arrayexpress

Influence of RNA labeling on expression profiling of microRNAs.

Project description:Although a number of technical parameters are now being examined to optimize microRNA profiling experiments, it is unknown whether reagent or component changes to the labeling step affect starting RNA requirements or microarray performance. Human brain/lung samples were each labeled in duplicate, at 1.0, 0.5, 0.2, and 0.1 ?g of total RNA, by means of two kits that use the same labeling procedure but differ in the reagent composition used to label microRNAs. Statistical measures of reliability and validity were used to evaluate microarray data. Cross-platform confirmation was accomplished using TaqMan microRNA assays. Synthetic microRNA spike-in experiments were also performed to establish the microarray signal dynamic range using the ligation-modified kit. Technical replicate correlations of signal intensity values were high using both kits, but improved with the ligation-modified assay. The drop in detection call sensitivity and miRNA gene list correlations, when using reduced amounts of standard-labeled RNA, was considerably improved with the ligation-modified kit. Microarray signal dynamic range was found to be linear across three orders of magnitude from 4.88 to 5000 attomoles. Thus, optimization of the microRNA labeling reagent can result in at least a 10-fold decrease in microarray total RNA requirements with little compromise to data quality. Clinical investigations bottlenecked by the amount of starting material may use a ligation mix modification strategy to reduce total RNA requirements.

| S-EPMC3338349 | biostudies-literature

Profiling stress-triggered RNA condensation with photocatalytic proximity labeling

Project description:Profiling stress-triggered RNA condensation with photocatalytic proximity labeling

| PRJNA925537 | ENA

A chromatin integration labeling method enables lower-input epigenomic profiling

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

| PRJNA473561 | ENA

Microarray profiling analysis of microRNAs expression in Hypertrophic scar

Project description:Microarray profiling analysis of microRNAs expression in Hypertrophic scar

| PRJNA781618 | ENA

Microarray profiling analysis of microRNAs expression in glioblastoma cells

Project description:Microarray profiling analysis of microRNAs expression in glioblastoma cells

| PRJNA625711 | ENA

Microarray profiling analysis of microRNAs expression in diabetes samples

Project description:Microarray profiling analysis of microRNAs expression in diabetes samples

| PRJNA780905 | ENA

Off-the-shelf proximity labeling

Project description:Off-the-shelf proximity labeling

| PRJNA716256 | ENA

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

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