The RIN: an RNA integrity number for assigning integrity values to RNA measurements
Andreas Schroeder,Odilo Mueller,Susanne Dr. Stocker,Susanne Dr. Stocker,Ruediger Salowsky,Michael Leiber,Marcus Gassmann,Samar Lightfoot,Wolfram Menzel,Martin Granzow,Thomas Ragg +10 more
TLDR
The results show the importance of taking characteristics of several regions of the recorded electropherogram into account in order to get a robust and reliable prediction of RNA integrity, especially if compared to traditional methods.Abstract:
The integrity of RNA molecules is of paramount importance for experiments that try to reflect the snapshot of gene expression at the moment of RNA extraction. Until recently, there has been no reliable standard for estimating the integrity of RNA samples and the ratio of 28S:18S ribosomal RNA, the common measure for this purpose, has been shown to be inconsistent. The advent of microcapillary electrophoretic RNA separation provides the basis for an automated high-throughput approach, in order to estimate the integrity of RNA samples in an unambiguous way. A method is introduced that automatically selects features from signal measurements and constructs regression models based on a Bayesian learning technique. Feature spaces of different dimensionality are compared in the Bayesian framework, which allows selecting a final feature combination corresponding to models with high posterior probability. This approach is applied to a large collection of electrophoretic RNA measurements recorded with an Agilent 2100 bioanalyzer to extract an algorithm that describes RNA integrity. The resulting algorithm is a user-independent, automated and reliable procedure for standardization of RNA quality control that allows the calculation of an RNA integrity number (RIN). Our results show the importance of taking characteristics of several regions of the recorded electropherogram into account in order to get a robust and reliable prediction of RNA integrity, especially if compared to traditional methods.read more
Citations
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Quantification of mRNA using real-time RT-PCR
TL;DR: A series of RT-qPCR protocols are described that illustrate the essential technical steps required to generate quantitative data that are reliable and reproducible in molecular medicine, biotechnology, microbiology and diagnostics.
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Hereditary parkinsonism with dementia is caused by mutations in ATP13A2, encoding a lysosomal type 5 P-type ATPase.
Alfredo Ramirez,André Heimbach,Jan Gründemann,Barbara Stiller,Daniel J. Hampshire,L. Pablo Cid,Ingrid Goebel,Ammar F. Mubaidin,Abdul-Latif Wriekat,Jochen Roeper,Amir S. Najim Al-Din,Axel M. Hillmer,Meliha Karsak,Birgit Liss,C. Geoffrey Woods,Maria I. Behrens,Christian Kubisch +16 more
TL;DR: Loss-of-function mutations in a previously uncharacterized, predominantly neuronal P-type ATPase gene, ATP13A2, underlying an autosomal recessive form of early-onset parkinsonism with pyramidal degeneration and dementia are described.
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Review: Activation patterns of microglia and their identification in the human brain
TL;DR: The question as to what extent different activation states of microglia exist in the human central nervous system is discussed, which tools can be used to identify them and emerging evidence for such changes in ageing and in Alzheimer's disease is discussed.
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Cell-type-specific isolation of ribosome-associated mRNA from complex tissues
TL;DR: A strategy to rapidly and efficiently isolate ribosome-associated mRNA transcripts from any cell type in vivo is described and the application of this technique is demonstrated in brain using neuron-specific Cre recombinase-expressing mice and in testis using a Sertoli cell Cre recomb inase- expressing mouse.
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A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project
Latarsha J. Carithers,Kristin G. Ardlie,Mary Barcus,Philip A. Branton,Angela Britton,Stephen A. Buia,Carolyn C. Compton,David S. DeLuca,Joanne Peter-Demchok,Ellen Gelfand,Ping Guan,Greg E. Korzeniewski,Nicole C. Lockhart,Chana A. Rabiner,Abhi Rao,Karna Robinson,Nancy Roche,Sherilyn Sawyer,Ayellet V. Segrè,Charles Shive,Anna M. Smith,Leslie H. Sobin,Anita H. Undale,Kimberly M. Valentino,Jim Vaught,Taylor Young,Helen M. Moore +26 more
TL;DR: How a successful infrastructure for biospecimen procurement was developed and implemented by multiple research partners to support the prospective collection, annotation, and distribution of blood, tissues, and cell lines for the GTEx project is described.
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