WG2: Best practices and experimental standards
WG2 will focus on the best practices for cardiovascular transcriptomic studies from the crucial issue of sample collection and processing, which directly impacts final results, to the main techniques used to study the transcriptome (qPCR, microarray and RNA sequencing) and the statistical analysis. Protocols, technologies, and procedures will be assessed, and standard strategies will be delineated for better quality control and study comparison, tackling all the steps along the process.
Comparison of protocols and data from different laboratories is necessary to facilitate the comprehension of results and advance knowledge in CVD transcriptomics. It also directly impacts the development of tools that can be used for diagnosis and monitoring of CVD. In order to compare results, generated data must meet common standards, which should be from the collection of samples to the generation and analysis of data, so that variations are minimized and results are accurate and reproducible. Sample collection, storage, and quality testing are critical, particularly when dealing with RNA due to its sensitive nature. Although guidelines exist for separate steps of sample collection, data generation, and analysis, a complete guideline comprising all steps that are specific for CVD is still lacking.
WG2 will focus on the best practices for cardiovascular transcriptomic studies from the crucial issue of sample collection and processing, which directly impacts final results, to the main techniques used to study the transcriptome (qPCR, microarray and RNA sequencing) and the statistical analysis. Protocols, technologies, and procedures will be assessed, and standard strategies will be delineated for better quality control and study comparison, tackling all the steps along the process. This Action aims to bring together in WG2 experts from relevant disciplines to discuss and come up with guidelines to generate reference materials for CVD and also for the production of internal quality control materials that can be used in CVD transcriptome analyses. Participating members with unique knowledge will share their expertise through meetings, STSMs, and training schools.
Propose guidelines for collection and processing of biological material for cardiovascular transcriptomics analysis, including quality testing and storage, and define strategies for their implementation among different laboratories;
Review standard protocols and suggest refinements for the generation of data on RNA from specific types of samples;
Choose standard protocols for each analysis methodology (qPCR, microarray, and RNA-seq), including sample type and handling that offer the greatest potential for CVD transcriptomics studies;
Generate guidelines to produce reference materials for CVD and for the production of normalizers and internal quality control materials for CVD RNA analyses;
Organize WG2 meetings, provide training for ECI and students through STSMs and/or training schools.
1) Devise best practices guidelines towards sample collection, handling, storage and quality testing for cardiovascular transcriptomics analysis;
2) review current pipelines for RNA analysis using qPCR, microarray and RNA-seq to draft a document suggesting improved pipelines for each in the context of CVD;
3) identify lacking experimental details in CVD transcriptomics publications and suggest criteria of critical information that should be published to enable reproducibility of results;
4) find the best normalization targets and their reference ranges for normalization in CVD transcriptomics;
5) write a technical report with guidelines to generate reference materials for CVD transcriptomics studies;
6) organize WG2 meetings, STSMs and/or training schools;
7) provide progress reports for WG4.
1) Initial meeting to define strategies for the design of best practices and experimental standards and their implementation;
2) WG2 meetings to review and discuss guidelines;
3) STSMs and/or training schools on best practices and experimental standards in CVD transcriptome.
1) Consensus document/publication with best practices for sample collection, handling, and storage for CVD transcriptomics research;
2) consensus document/publication with experimental standards for all steps of RNA analysis using qPCR, microarray, and RNA-seq for CVD transcriptomics research;
3) refinement of guidelines for publishing minimum information regarding CVD transcriptomics;
4) a peer-reviewed publication with the guidelines developed by WG2 and the relative advantages of adopting them, so that the CVD community at large will benefit;
5) a peer-reviewed publication / technical report on the production of reference materials for CVD and for the production of internal quality control materials applied for CVD;
6) WG2 Meetings, STSMs, training schools.
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