RNA Sequencing of Formalin-Fixed and Paraffin-Embedded Tissue as a Complementary Method in Ophthalmopathology

Schlunck, Günther; Boneva, Stefaniya; Wolf, Julian; Schlecht, Anja; Reinhard, Thomas; Auw-Hädrich, Claudia; Lange, Clemens

doi:10.1055/a-1187-1590

Cited by 4 publications

(3 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…RNA sequencing allows the nucleotide sequences of millions of RNA molecules in a sample to be analyzed [ 24 ]. By comparing these sequences with the known reference genome, it is possible to identify and quantify different RNA molecules.…”

Section: Principle Of Rna Sequencingmentioning

confidence: 99%

Web-based gene expression analysis—paving the way to decode healthy and diseased ocular tissue

et al. 2022

Self Cite

View full text Add to dashboard Cite

Background Gene expression analysis using RNA sequencing has helped to improve the understanding of many diseases. Databases, such as the Gene Expression Omnibus database of the National Center for Biotechnology Information provide RNA sequencing raw data from various diseased tissue types but their analysis requires advanced bioinformatics skills. Therefore, specific ocular databases provide the transcriptional profiles of different ocular tissues and in addition enable intuitive web-based data analysis. Objective The aim of this narrative review is to provide an overview of ocular transcriptome databases and to compare them with the Human Eye Transcriptome Atlas newly established in Freiburg. Methods PubMed literature search. Results A total of nine ocular transcriptome databases focusing on different aspects were identified. The iSyTE and Express platforms specialize in gene expression during lens and retinal development in mice, whereas retina.tigem.it, Eye in a Disk, and Spectacle focus on selected ocular tissues such as the retina. Spectacle, UCSC Cell Browser and Single Cell Portal allow intuitive exploration of single cell RNA sequencing data derived from retinal, choroid, cornea, iris, trabecular meshwork and sclera specimens. The microarray profiles of a variety of healthy ocular tissues are included in the Ocular Tissue Database. The Human Eye Transcriptome Atlas provides the largest collection of different ocular tissue types, contains the highest number of ocular diseases and is characterized by a high level of quality achieved by methodological consistency. Conclusion Ocular transcriptome databases provide comprehensive and intuitive insights into the transcriptional profiles of a variety of healthy and diseased ocular tissues. Thus, they improve our understanding of the underlying molecular mediators, support hypothesis generation and help in the search for new diagnostic and therapeutic targets for various ocular diseases.

show abstract

Section: Principle Of Rna Sequencingmentioning

confidence: 99%

Web-based gene expression analysis—paving the way to decode healthy and diseased ocular tissue

et al. 2022

Self Cite

View full text Add to dashboard Cite

show abstract

“…Die RNA-Sequenzierung erlaubt die Entschlüsselung der Nukleotidsequenzen von Millionen von RNA-Molekülen in einer Probe [ 24 ]. Durch Vergleich dieser Sequenzen mit dem bekannten Referenzgenom können unterschiedliche RNA-Moleküle identifiziert und quantifiziert werden.…”

Section: Prinzip Der Rna-sequenzierungunclassified

Webbasierte Genexpressionsanalysen – auf dem Weg zur molekularen Entschlüsselung gesunder und erkrankter Augengewebe

et al. 2022

Self Cite

View full text Add to dashboard Cite

Zusammenfassung Hintergrund Die Entschlüsselung des Transkriptoms hat in den letzten Jahren unser Verständnis zahlreicher Erkrankungen verbessert. Öffentlich zugängliche Datenbanken, wie z. B. die Gene Expression Omnibus-Datenbank des National Center for Biotechnology Information, sammeln Transkriptomrohdaten aus einer Vielfalt von Proben, ohne jedoch dem bioinformatischen Laien einen intuitiven Zugang zu den Daten zu gewähren. Daher wurden in den vergangenen Jahren spezielle Transkriptomdatenbanken programmiert, die eine benutzerfreundliche Web-basierte Datenanalyse ermöglichen und damit niederschwellig molekulare Einblicke in okuläre Gewebe ermöglichen. Fragestellung Ziel dieser Arbeit ist es, einen Überblick über die aktuell verfügbaren okulären Transkriptomdatenbanken zu geben und diese mit dem in Freiburg neu etablierten Human Eye Transcriptome Atlas zu vergleichen. Methoden Literatursuche in PubMed. Ergebnisse Neun okuläre Transkriptomdatenbanken mit unterschiedlichem Anwendungsschwerpunkt wurden identifiziert. Die Plattformen iSyTE und Express spezialisieren sich auf die Genexpression während der Linsen- und Netzhautentwicklung der Maus, wohingegen retina.tigem.it, Eye in a Disk und Spectacle ihren Fokus auf einzelne okuläre Gewebe wie die Netzhaut legen. Spectacle, UCSC Cell Browser und Single Cell Portal erlauben die intuitive Exploration von Einzelzell-RNA-Sequenzierungsdaten von Netzhaut‑, Aderhaut‑, Kornea‑, Iris‑, Trabekelmaschenwerk- und Skleragewebe. Die Microarray-Profile verschiedener gesunder okulärer Gewebe werden in der Ocular Tissue Database bereitgestellt. Der Human Eye Transcriptome Atlas erfasst derzeit die größte Vielfalt an Augengeweben und Erkrankungen des Auges. Er zeichnet sich durch einen hohen Qualitätsstandard aus, der durch methodische Homogenität erreicht wird. Schlussfolgerungen Okuläre Transkriptomdatenbanken bieten einen umfassenden und intuitiven Einblick in die Transkriptionsprofile verschiedener gesunder und erkrankter Augengewebe. So verbessern sie unser Verständnis der zugrunde liegenden molekularen Krankheitsprozesse, unterstützen die Hypothesengenerierung und helfen bei der Suche nach neuen diagnostischen und therapeutischen Zielen für verschiedene Augenerkrankungen.

show abstract

“…compared different RNA extraction methods and could show that the fully automated bead-based method provided the overall best yield and reproducibility for high-throughput RNA expression analysis [ 11 ]. Most RNA extraction methods from FFPE (mainly using PCR) were performed from non-bone tissue rather than decalcified bone tissue [ 17 ]. Traditionally, quantification of RNA yield analyses was measured by RT-PCR.…”

Section: Introductionmentioning

confidence: 99%

Cracking it - successful mRNA extraction for digital gene expression analysis from decalcified, formalin-fixed and paraffin-embedded bone tissue

et al. 2021

View full text Add to dashboard Cite

With the advance of precision medicine, the availability of tumor tissue for molecular analysis has become a limiting factor. This is particularly the case for bone metastases which are frequently occurring in cancer types such as prostate cancer. Due to the necessary decalcification process it was long thought that transcriptome analysis will not be feasible from decalcified formalin-fixed, paraffin-embedded (DFFPE) in a large manner. Here we demonstrate that mRNA extraction from DFFPE is feasible, quick, robust and reproducible and that decalcification does not hamper subsequent gene expression analysis. This might assist in implementing transcriptome analysis from DFFPE into every day practice.

show abstract

RNA Sequencing of Formalin-Fixed and Paraffin-Embedded Tissue as a Complementary Method in Ophthalmopathology

Cited by 4 publications

References 10 publications

Web-based gene expression analysis—paving the way to decode healthy and diseased ocular tissue

Web-based gene expression analysis—paving the way to decode healthy and diseased ocular tissue

Webbasierte Genexpressionsanalysen – auf dem Weg zur molekularen Entschlüsselung gesunder und erkrankter Augengewebe

Cracking it - successful mRNA extraction for digital gene expression analysis from decalcified, formalin-fixed and paraffin-embedded bone tissue

Contact Info

Product

Resources

About