Anti-bias training for (sc) RNA-seq: experimental and computational approaches to improve precision

P Davies, M Jones, J Liu… - Briefings in …, 2021 - academic.oup.com
RNA-seq, including single cell RNA-seq (scRNA-seq), is plagued by insufficient sensitivity
and lack of precision. As a result, the full potential of (sc) RNA-seq is limited. Major factors in …

[HTML][HTML] Gene expression in the dorsolateral and ventromedial prefrontal cortices implicates immune-related gene networks in PTSD

MW Logue, Z Zhou, FG Morrison, EJ Wolf… - Neurobiology of …, 2021 - Elsevier
Studies evaluating neuroimaging, genetically predicted gene expression, and pre-clinical
genetic models of PTSD, have identified PTSD-related abnormalities in the prefrontal cortex …

[HTML][HTML] Investigating post-translational modifications in neuropsychiatric disease: The next frontier in human post-mortem brain research

MJ Grubisha, RA Sweet… - Frontiers in Molecular …, 2021 - frontiersin.org
Gene expression and translation have been extensively studied in human post-mortem
brain tissue from subjects with psychiatric disease. Post-translational modifications (PTMs) …

[HTML][HTML] Multiple freeze-thaw cycles lead to a loss of consistency in poly (A)-enriched RNA sequencing

BP Kellman, HM Baghdassarian, T Pramparo, I Shamie… - BMC genomics, 2021 - Springer
Abstract Background Both RNA-Seq and sample freeze-thaw are ubiquitous. However,
knowledge about the impact of freeze-thaw on downstream analyses is limited. The lack of …

[HTML][HTML] SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses

NJ Eagles, EE Burke, J Leonard, BK Barry, JM Stolz… - BMC …, 2021 - Springer
Background RNA sequencing (RNA-seq) is a common and widespread biological assay,
and an increasing amount of data is generated with it. In practice, there are a large number …

Timedependent changes in placental mRNA expression after delivery due to delayed specimen collection

AA Freedman, BP Smart… - American Journal of …, 2021 - Wiley Online Library
Problem Current scientific guidelines recommend collecting placental specimens within two
hours of delivery for gene expression analysis. However, collecting samples in a narrow …

Declining RNA integrity in control autopsy brain tissue is robustly and asymmetrically associated with selective neuronal mRNA signal loss

ES Johnson, KE Stenzel, S Lee, EM Blalock - bioRxiv, 2021 - biorxiv.org
RNA integrity numbers (RINs) are a standardized method for semi-quantification of RNA
degradation, and are used in quality control prior to transcriptional profiling analysis. Recent …

Leveraging the whole methylome to elucidate the relationship between schizophrenia and DNA methylation in the human brain

K Perzel Mandell - 2021 - jscholarship.library.jhu.edu
Schizophrenia is a serious, complex psychiatric illness that affects around 1% of people
globally, costing billions of dollars and negatively impacting quality of life. It's exact causes …

Investigating trait variability of gene co-expression network architecture in brain by manipulating genomic signatures of schizophrenia risk

E Radulescu, Q Chen, G Pergola, NJ Eagles, JM Stolz… - bioRxiv, 2021 - biorxiv.org
While the role of genomic risk for schizophrenia on brain gene co-expression networks has
been described, the patterns of its manifestations are varied and complex. To acquire a …

Robust RNA Integrity-to-Neuronal Gene Expression Association in Autopsy Brain Tissue Not Explained by Post-Mortem Variables; and Acute Behavioral Stress Does …

ES Johnson - 2021 - uknowledge.uky.edu
Transcriptional profiling (TP) is a common tool to determine RNA expression levels. It allows
for thousands of genes to be analyzed simultaneously, and determines differences in gene …