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single cell RNAseq

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https://www.readbyqxmd.com/read/28151934/hepatitis-b-virus-modulates-store-operated-calcium-entry-to-enhance-viral-replication-in-primary-hepatocytes
#1
Jessica C Casciano, Nicholas J Duchemin, R Jason Lamontagne, Laura F Steel, Michael J Bouchard
Many viruses modulate calcium (Ca2+) signaling to create a cellular environment that is more permissive to viral replication, but for most viruses that regulate Ca2+ signaling, the mechanism underlying this regulation is not well understood. The hepatitis B virus (HBV) HBx protein modulates cytosolic Ca2+ levels to stimulate HBV replication in some liver cell lines. A chronic HBV infection is associated with life-threatening liver diseases, including hepatocellular carcinoma (HCC), and HBx modulation of cytosolic Ca2+ levels could have an important role in HBV pathogenesis...
2017: PloS One
https://www.readbyqxmd.com/read/28107386/regulation-of-pi-2b-pilus-expression-in-hypervirulent-streptococcus-agalactiae-st-17-bm110
#2
Bruno Périchon, Noémi Szili, Laurence du Merle, Isabelle Rosinski-Chupin, Myriam Gominet, Samuel Bellais, Claire Poyart, Patrick Trieu-Cuot, Shaynoor Dramsi
The widely spread Streptococcus agalactiae (also known as Group B Streptococcus, GBS) "hypervirulent" ST17 clone is strongly associated with neonatal meningitis. The PI-2b locus is mainly found in ST17 strains but is also present in a few non ST17 human isolates such as the ST-7 prototype strain A909. Here, we analysed the expression of the PI-2b pilus in the ST17 strain BM110 as compared to the non ST17 A909. Comparative genome analyses revealed the presence of a 43-base pair (bp) hairpin-like structure in the upstream region of PI-2b operon in all 26 ST17 genomes, which was absent in the 8 non-ST17 strains carrying the PI-2b locus...
2017: PloS One
https://www.readbyqxmd.com/read/28086790/rna-sequencing-for-global-gene-expression-associated-with-muscle-growth-in-a-single-male-modern-broiler-line-compared-to-a-foundational-barred-plymouth-rock-chicken-line
#3
Byung-Whi Kong, Nicholas Hudson, Dongwon Seo, Seok Lee, Bhuwan Khatri, Kentu Lassiter, Devin Cook, Alissa Piekarski, Sami Dridi, Nicholas Anthony, Walter Bottje
BACKGROUND: Modern broiler chickens exhibit very rapid growth and high feed efficiency compared to unselected chicken breeds. The improved production efficiency in modern broiler chickens was achieved by the intensive genetic selection for meat production. This study was designed to investigate the genetic alterations accumulated in modern broiler breeder lines during selective breeding conducted over several decades. METHODS: To identify genes important in determining muscle growth and feed efficiency in broilers, RNA sequencing (RNAseq) was conducted with breast muscle in modern pedigree male (PeM) broilers (n = 6 per group), and with an unselected foundation broiler line (Barred Plymouth Rock; BPR)...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/27864379/foxn4-promotes-gene-expression-required-for-the-formation-of-multiple-motile-cilia
#4
Evan P Campbell, Ian K Quigley, Chris Kintner
Multiciliated cell (MCC) differentiation involves extensive organelle biogenesis required to extend hundreds of motile cilia. Key transcriptional regulators known to drive the gene expression required for this organelle biogenesis are activated by the related coiled-coil proteins Multicilin and Gemc1. Here we identify foxn4 as a new downstream target of Multicilin required for MCC differentiation in Xenopus skin. When Foxn4 activity is inhibited in Xenopus embryos, MCCs show transient ciliogenesis defects similar to those seen in mutants of Foxj1, a known key regulator of genes required for motile ciliation...
December 15, 2016: Development
https://www.readbyqxmd.com/read/27716520/out-of-many-one-computational-reconstruction-of-mouse-skin-using-single-cell-transcriptomics
#5
James C Chen, Angela M Christiano
Mammalian skin is a complex and heterogeneous tissue with several distinct compartments and stem cell populations. Joost et al. (2016) now use single-cell RNaseq to comprehensively reconstruct this complexity, revealing spatial and pseudotemporal differences between transcriptional programs in distinct compartments and a common basal program in skin stem cell populations.
October 6, 2016: Cell Stem Cell
https://www.readbyqxmd.com/read/27694193/the-start-app-a-web-based-rnaseq-analysis-and-visualization-resource
#6
Jonathan W Nelson, Jiri Sklenar, Anthony P Barnes, Jessica Minnier
Transcriptional profiling using RNA sequencing (RNAseq) has emerged as a powerful methodology to quantify global gene expression patterns in various contexts from single cells to whole tissues. The tremendous amount of data generated by this profiling technology presents a daunting challenge in terms of effectively visualizing and interpreting results. Convenient and intuitive data interfaces are critical for researchers to easily upload, analyze and visualize their RNAseq data. We designed the START (Shiny Transcriptome Analysis Resource Tool) App with these requirements in mind...
September 30, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27585245/targeted-rna-sequencing-assay-to-characterize-gene-expression-and-genomic-alterations
#7
Dorrelyn P Martin, Jharna Miya, Julie W Reeser, Sameek Roychowdhury
RNA sequencing (RNAseq) is a versatile method that can be utilized to detect and characterize gene expression, mutations, gene fusions, and noncoding RNAs. Standard RNAseq requires 30 - 100 million sequencing reads and can include multiple RNA products such as mRNA and noncoding RNAs. We demonstrate how targeted RNAseq (capture) permits a focused study on selected RNA products using a desktop sequencer. RNAseq capture can characterize unannotated, low, or transiently expressed transcripts that may otherwise be missed using traditional RNAseq methods...
2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27531958/single-cell-rnaseq-reveals-cell-adhesion-molecule-profiles-in-electrophysiologically-defined-neurons
#8
Csaba Földy, Spyros Darmanis, Jason Aoto, Robert C Malenka, Stephen R Quake, Thomas C Südhof
In brain, signaling mediated by cell adhesion molecules defines the identity and functional properties of synapses. The specificity of presynaptic and postsynaptic interactions that is presumably mediated by cell adhesion molecules suggests that there exists a logic that could explain neuronal connectivity at the molecular level. Despite its importance, however, the nature of such logic is poorly understood, and even basic parameters, such as the number, identity, and single-cell expression profiles of candidate synaptic cell adhesion molecules, are not known...
August 30, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27466694/single-cell-rnaseq-reveals-that-pancreatic-%C3%AE-cells-from-very-old-male-mice-have-a-young-gene-signature
#9
Yurong Xin, Haruka Okamoto, Jinrang Kim, Min Ni, Christina Adler, Katie Cavino, Erqian Na, Andrew J Murphy, George D Yancopoulos, Calvin Lin, Jesper Gromada
Aging improves pancreatic β-cell function in mice. This is a surprising finding because aging is typically associated with functional decline. We performed single-cell RNA sequencing of β-cells from 3- and 26-month-old mice to explore how changes in gene expression contribute to improved function with age. The old mice were healthy and had reduced blood glucose levels and increased β-cell mass, which correlated to their body weight. β-Cells from young and old mice had similar transcriptome profiles. In fact, only 193 genes (0...
September 2016: Endocrinology
https://www.readbyqxmd.com/read/27460926/single-cell-tcrseq-paired-recovery-of-entire-t-cell-alpha-and-beta-chain-transcripts-in-t-cell-receptors-from-single-cell-rnaseq
#10
David Redmond, Asaf Poran, Olivier Elemento
Accurate characterization of the repertoire of the T-cell receptor (TCR) alpha and beta chains is critical to understanding adaptive immunity. Such characterization has many applications across such fields as vaccine development and response, clone-tracking in cancer, and immunotherapy. Here we present a new methodology called single-cell TCRseq (scTCRseq) for the identification and assembly of full-length rearranged V(D)J T-cell receptor sequences from paired-end single-cell RNA sequencing reads. The method allows accurate identification of the V(D)J rearrangements for each individual T-cell and has the novel ability to recover paired alpha and beta segments...
July 27, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27036964/proton-irradiation-induces-persistent-and-tissue-specific-dna-methylation-changes-in-the-left-ventricle-and-hippocampus
#11
Soren Impey, Carl Pelz, Amanuel Tafessu, Tessa Marzulla, Mitchell S Turker, Jacob Raber
BACKGROUND: Proton irradiation poses a potential hazard to astronauts during and following a mission, with post-mitotic cells at most risk because they cannot dilute resultant epigenetic changes via cell division. Persistent epigenetic changes that result from environmental exposures include gains or losses of DNA methylation of cytosine, which can impact gene expression. In the present study, we compared the long-term epigenetic effects of whole body proton irradiation in the mouse hippocampus and left ventricle...
March 31, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27025767/droplet-based-microfluidics-in-drug-discovery-transcriptomics-and-high-throughput-molecular-genetics
#12
REVIEW
Nachiket Shembekar, Chawaree Chaipan, Ramesh Utharala, Christoph A Merten
Droplet-based microfluidics enables assays to be carried out at very high throughput (up to thousands of samples per second) and enables researchers to work with very limited material, such as primary cells, patient's biopsies or expensive reagents. An additional strength of the technology is the possibility to perform large-scale genotypic or phenotypic screens at the single-cell level. Here we critically review the latest developments in antibody screening, drug discovery and highly multiplexed genomic applications such as targeted genetic workflows, single-cell RNAseq and single-cell ChIPseq...
April 21, 2016: Lab on a Chip
https://www.readbyqxmd.com/read/26956645/mitochondria-single-nucleotide-variation-across-six-blood-cell-types
#13
Pan Zhang, David C Samuels, Jing Wang, Shilin Zhao, Yu Shyr, Yan Guo
It has been shown that heteroplasmic mitochondrial DNA variants can be tissue specific. However, whether mitochondrial DNA variants are specific by blood cell types has not been investigated. Motivated by this question and using mitochondria sequences extracted from RNAseq data from six distinct blood cell types (neutrophil, monocyte, myeloid dendritic, natural killer, T and B), we thoroughly compared SNPs and heteroplasmies among these cell types. Each cell type from each subject was sequenced at four time points used as biological replicates...
May 2016: Mitochondrion
https://www.readbyqxmd.com/read/26598538/seeking-the-driver-in-tumours-with-apparent-normal-molecular-profile-on-comparative-genomic-hybridization-and-targeted-gene-panel-sequencing-what-is-the-added-value-of-whole-exome-sequencing
#14
S Postel-Vinay, Y Boursin, C Massard, A Hollebecque, E Ileana, M Chiron, J Jung, J S Lee, Z Balogh, J Adam, P Vielh, E Angevin, L Lacroix, J-C Soria
BACKGROUND: Molecular tumour profiling technologies have become increasingly important in the era of precision medicine, but their routine use is limited by their accessibility, cost, and tumour material availability. It is therefore crucial to assess their relative added value to optimize the sequence and combination of such technologies. PATIENTS AND METHODS: Within the MOSCATO-01 trial, we investigated the added value of whole exome sequencing (WES) in patients that did not present any molecular abnormality on array comparative genomic hybridization (aCGH) and targeted gene panel sequencing (TGPS) using cancer specific panels...
February 2016: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/26458527/a-full-genomic-characterization-of-the-development-of-a-stable-small-colony-variant-cell-type-by-a-clinical-staphylococcus-aureus-strain
#15
Long M G Bui, Stephen P Kidd
A key to persistent and recurrent Staphylococcus aureus infections is its ability to adapt to diverse and toxic conditions. This ability includes a switch into a biofilm or to the quasi-dormant Small Colony Variant (SCV). The development and molecular attributes of SCVs have been difficult to study due to their rapid reversion to their parental cell-type. We recently described the unique induction of a matrix-embedded and stable SCV cell-type in a clinical S. aureus strain (WCH-SK2) by growing the cells with limiting conditions for a prolonged timeframe...
December 2015: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/26397140/characterization-of-pancreatic-ductal-adenocarcinoma-using-whole-transcriptome-sequencing-and-copy-number-analysis-by-single-nucleotide-polymorphism-array
#16
Mariacristina Di Marco, Annalisa Astolfi, Elisa Grassi, Silvia Vecchiarelli, Marina Macchini, Valentina Indio, Riccardo Casadei, Claudio Ricci, Marielda D'Ambra, Giovanni Taffurelli, Carla Serra, Giorgio Ercolani, Donatella Santini, Antonia D'Errico, Antonio Daniele Pinna, Francesco Minni, Sandra Durante, Laura Raffaella Martella, Guido Biasco
The aim of the current study was to implement whole transcriptome massively parallel sequencing (RNASeq) and copy number analysis to investigate the molecular biology of pancreatic ductal adenocarcinoma (PDAC). Samples from 16 patients with PDAC were collected by ultrasound‑guided biopsy or from surgical specimens for DNA and RNA extraction. All samples were analyzed by RNASeq performed at 75x2 base pairs on a HiScanSQ Illumina platform. Single‑nucleotide variants (SNVs) were detected with SNVMix and filtered on dbSNP, 1000 Genomes and Cosmic...
November 2015: Molecular Medicine Reports
https://www.readbyqxmd.com/read/26271746/transcriptional-maturation-of-the-mouse-auditory-forebrain
#17
Troy A Hackett, Yan Guo, Amanda Clause, Nicholas J Hackett, Krassimira Garbett, Pan Zhang, Daniel B Polley, Karoly Mirnics
BACKGROUND: The maturation of the brain involves the coordinated expression of thousands of genes, proteins and regulatory elements over time. In sensory pathways, gene expression profiles are modified by age and sensory experience in a manner that differs between brain regions and cell types. In the auditory system of altricial animals, neuronal activity increases markedly after the opening of the ear canals, initiating events that culminate in the maturation of auditory circuitry in the brain...
2015: BMC Genomics
https://www.readbyqxmd.com/read/26249222/mitochondria-sequence-mapping-strategies-and-practicability-of-mitochondria-variant-detection-from-exome-and-rna-sequencing-data
#18
Pan Zhang, David C Samuels, Brian Lehmann, Thomas Stricker, Jennifer Pietenpol, Yu Shyr, Yan Guo
The rapid progress in high-throughput sequencing has significantly enriched our capacity for studying the mitochondrial DNA (mtDNA). In addition to performing specific mitochondrial targeted sequencing, an increasingly popular alternative approach is using the off-target reads from exome sequencing to infer mtDNA variants, including single nucleotide polymorphisms (SNPs) and heteroplasmy. However, the effectiveness and practicality of this approach have not been tested. Recently, RNAseq data have also been suggested as a good source for alternative data mining, but whether mitochondrial variants can be detected from RNAseq data has not been validated...
March 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/26167162/cautions-about-the-reliability-of-pairwise-gene-correlations-based-on-expression-data
#19
Scott Powers, Matt DeJongh, Aaron A Best, Nathan L Tintle
BACKGROUND: Rapid growth in the availability of genome-wide transcript abundance levels through gene expression microarrays and RNAseq promises to provide deep biological insights into the complex, genome-wide transcriptional behavior of single-celled organisms. However, this promise has not yet been fully realized. RESULTS: We find that computation of pairwise gene associations (correlation; mutual information) across a set of 2782 total genome-wide expression samples from six diverse bacteria produces unexpectedly large variation in estimates of pairwise gene association-regardless of the metric used, the organism under study, or the number and source of the samples...
2015: Frontiers in Microbiology
https://www.readbyqxmd.com/read/26148505/mecp2-a-gene-associated-with-rett-syndrome-in-humans-shows-conserved-coding-regions-independent-alu-insertions-and-a-novel-transcript-across-primate-evolution
#20
Maria Carolina Viana, Albert Nobre Menezes, Miguel Angelo M Moreira, Alcides Pissinatti, Héctor N Seuánez
BACKGROUND: The methyl-CpG Binding Protein two gene (MECP2) encodes a multifunctional protein comprising two isoforms involved in nuclear organization and regulation of splicing and mRNA template activity. This gene is normally expressed in all tissues, with a higher expression level in the brain during neuronal maturation. Loss of MECP2 function is the primary cause of Rett syndrome (RTT) in humans, a dominant, X-linked disorder dramatically affecting neural and motor development. RESULTS: We investigated the molecular evolution of MECP2 in several primate taxa including 36 species in 16 genera of neotropical (platyrrhine) primates...
2015: BMC Genetics
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