The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

The recent development of high-throughput technologies based on RNA sequencing has allowed a better description of the role of post-transcriptional regulation in gene expression. In particular, the development of degradome approaches based on the capture of 5′monophosphate decay intermediates allows the discovery of a new decay pathway called co-translational mRNA decay. Thanks to these approaches, ribosome dynamics could now be revealed by analysis of 5′P reads accumulation. However, library preparation could be difficult to set-up for non-specialists. Here, we present a fast and efficient 5′P degradome library preparation for Arabidopsis samples. Our protocol was designed without commercial kit and gel purification and can be easily done in one working day. We demonstrated the robustness and the reproducibility of our protocol. Finally, we present the bioinformatic reads-outs necessary to assess library quality control.

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Quality control in biobank samples: The impact of pre-freezing storage time and temperature on gene expression of blood collected in EDTA tubes

Journal of the Neurological Sciences ◽

10.1016/j.jns.2021.119937 ◽

2021 ◽

Vol 429 ◽

pp. 119937

Author(s):

Paola Valentino ◽

Serena Martire ◽

Fabiana Marnetto ◽

Luca Mirabile ◽

Antonio Bertolotto

Keyword(s):

Gene Expression ◽

Quality Control ◽

Storage Time ◽

The Impact ◽

Freezing Storage

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IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics

Bioinformatics ◽

10.1093/bioinformatics/btu027 ◽

2014 ◽

Vol 30 (10) ◽

pp. 1392-1399 ◽

Cited By ~ 7

Author(s):

Marta Rosikiewicz ◽

Marc Robinson-Rechavi

Keyword(s):

Quality Control ◽

Conservation Score ◽

New Method ◽

Microarray Quality Control ◽

Affymetrix Microarray ◽

Quality Control Metrics ◽

Homologous Organ

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GEView (Gene Expression View) Tool for Intuitive and High Accessible Visualization of Expression Data for Non-Programmer Biologists

Data Analytics in Medicine ◽

10.4018/978-1-7998-1204-3.ch032 ◽

2020 ◽

pp. 580-592

Author(s):

Libi Hertzberg ◽

Assif Yitzhaky ◽

Metsada Pasmanik-Chor

Keyword(s):

Gene Expression ◽

Quality Control ◽

User Interface ◽

High Throughput ◽

Graphical User Interface ◽

Differential Expression Analysis ◽

Biological Data ◽

Expression Data ◽

Batch Correction ◽

User Friendly

This article describes how the last decade has been characterized by the production of huge amounts of different types of biological data. Following that, a flood of bioinformatics tools have been published. However, many of these tools are commercial, or require computational skills. In addition, not all tools provide intuitive and highly accessible visualization of the results. The authors have developed GEView (Gene Expression View), which is a free, user-friendly tool harboring several existing algorithms and statistical methods for the analysis of high-throughput gene, microRNA or protein expression data. It can be used to perform basic analysis such as quality control, outlier detection, batch correction and differential expression analysis, through a single intuitive graphical user interface. GEView is unique in its simplicity and highly accessible visualization it provides. Together with its basic and intuitive functionality it allows Bio-Medical scientists with no computational skills to independently analyze and visualize high-throughput data produced in their own labs.

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Fidelity and Quality Control in Gene Expression

10.1016/c2010-0-68393-3 ◽

2012 ◽

Keyword(s):

Gene Expression ◽

Quality Control

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Fidelity in Archaeal Information Processing

Archaea ◽

10.1155/2010/960298 ◽

2010 ◽

Vol 2010 ◽

pp. 1-15 ◽

Cited By ~ 2

Author(s):

Bart de Koning ◽

Fabian Blombach ◽

Stan J. J. Brouns ◽

John van der Oost

Keyword(s):

Gene Expression ◽

Quality Control ◽

Information Processing ◽

Genome Size ◽

Genetic Information ◽

Important Determinant ◽

Current Knowledge ◽

The Other ◽

Living Systems ◽

Evolution Of Life

A key element during the flow of genetic information in living systems is fidelity. The accuracy of DNA replication influences the genome size as well as the rate of genome evolution. The large amount of energy invested in gene expression implies that fidelity plays a major role in fitness. On the other hand, an increase in fidelity generally coincides with a decrease in velocity. Hence, an important determinant of the evolution of life has been the establishment of a delicate balance between fidelity and variability. This paper reviews the current knowledge on quality control in archaeal information processing. While the majority of these processes are homologous in Archaea, Bacteria, and Eukaryotes, examples are provided of nonorthologous factors and processes operating in the archaeal domain. In some instances, evidence for the existence of certain fidelity mechanisms has been provided, but the factors involved still remain to be identified.

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