ArticleJournal of neuropathology and experimental neurology2025
An analysis of RNA quality metrics in human brain tissue.
Article in Journal of neuropathology and experimental neurology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Transcriptomic Convergence in Autism Spectrum Disorder: Synaptic, Immune-Glial and RNA-Regulatory Axes in the Human Cerebral Cortex.International journal of developmental neuroscience : the official journal of the International Society for Developmental Neuroscience · 2026Review
- [Half a century of gene expression analysis : The path to modern spatial transcriptomics in autopsy tissue].Pathologie (Heidelberg, Germany) · 2026Review
- Spatial transcriptomics in Alzheimer's disease: technologies, challenges and discoveries.Molecular neurodegeneration advances · 2026Review
- Identifying transcriptomic signatures that mediate the causal effect of genotype on Alzheimer's disease.Frontiers in neuroscience · 2026Article
- UC Irvine's Brain Initiative Cell Atlas Network (BICAN) Brain Procurement Program for the Center for Multiomic Human Brain Cell Atlas Project.bioRxiv : the preprint server for biology · 2025Article
- Article
- Impact of Confounding Factors in Human Postmortem Brain Tissues on Gene Expression Profiles: A Comparison of Patients With Schizophrenia, Bipolar Disorder, and Nonpsychiatric Controls.Neuropsychopharmacology reports · 2025Article
- Transcriptional signatures of hippocampal tau pathology in primary age-related tauopathy and Alzheimer's disease.Cell reports · 2025Article
- Current Status and Future Perspective of Seoul National University Hospital-Dementia Brain Bank with Concordance of Clinical and Neuropathological Diagnosis.Experimental neurobiology · 2024Article
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11 authors.
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Abstract
Human brain tissue studies have used a range of metrics to assess RNA quality but there are few large-scale cross-comparisons of presequencing quality metrics with RNA-seq quality. We analyzed how postmortem interval (PMI) and RNA integrity number (RIN) before RNA-seq relate to RNA quality after sequencing (percent of counts in top 10 genes [PTT], 5' bias, and 3' bias), and with individual gene counts across the transcriptome. We analyzed 4 human cerebrocortical tissue sets (1 surgical, 3 autopsy), sequenced with varying protocols. Postmortem interval and RIN had a low inverse correlation (down to r = -0.258, P < .001 across the autopsy cohorts); both PMI and RIN showed consistent and opposing correlations with PTT (up to r = 0.215, P < .001 for PMI and down to r = -0.677, P < .001 for RIN across the autopsy cohorts). Unlike PMI, RIN showed consistent correlations with measurements of 3' and 5' bias in autopsies (r = -0.366, P < .001 with 3' bias). RNA integrity number correlated with 3933 genes across the 4 datasets vs 138 genes for PMI. Neuronal and immune response genes correlated positively and negatively with RIN, respectively. Thus, different gene sets have divergent relationships with RIN. These analyses suggest that conventional metrics of RNA quality have varying values and that PMI has an overall modest effect on RNA quality.
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