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Single cell RNA seq

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https://www.readbyqxmd.com/read/29161425/linnorm-improved-statistical-analysis-for-single-cell-rna-seq-expression-data
#1
Shun H Yip, Panwen Wang, Jean-Pierre A Kocher, Pak Chung Sham, Junwen Wang
No abstract text is available yet for this article.
November 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29153838/unsupervised-trajectory-analysis-of-single-cell-rna-seq-and-imaging-data-reveals-alternative-tuft-cell-origins-in-the-gut
#2
Charles A Herring, Amrita Banerjee, Eliot T McKinley, Alan J Simmons, Jie Ping, Joseph T Roland, Jeffrey L Franklin, Qi Liu, Michael J Gerdes, Robert J Coffey, Ken S Lau
Modern single-cell technologies allow multiplexed sampling of cellular states within a tissue. However, computational tools that can infer developmental cell-state transitions reproducibly from such single-cell data are lacking. Here, we introduce p-Creode, an unsupervised algorithm that produces multi-branching graphs from single-cell data, compares graphs with differing topologies, and infers a statistically robust hierarchy of cell-state transitions that define developmental trajectories. We have applied p-Creode to mass cytometry, multiplex immunofluorescence, and single-cell RNA-seq data...
November 7, 2017: Cell Systems
https://www.readbyqxmd.com/read/29152579/streptococcus-pneumoniae-tigr4-phase-locked-opacity-variants-differ-in-virulence-phenotypes
#3
Melissa B Oliver, Ankita Basu Roy, Ranjit Kumar, Elliot J Lefkowitz, W Edward Swords
Streptococcus pneumoniae (pneumococcus) is a leading human pathogen that can cause serious localized and invasive diseases. Pneumococci can undergo a spontaneous and reversible phase variation that is reflected in colony opacity and which allows the population to adapt to different host environments. Generally, transparent variants are adapted for nasopharyngeal colonization, whereas opaque variants are associated with invasive disease. In recent work, colony phase variation was shown to occur by means of recombination events to generate multiple alleles of the hsdS targeting domain of a DNA methylase complex, which mediates epigenetic changes in gene expression...
November 2017: MSphere
https://www.readbyqxmd.com/read/29139170/single-cell-resolution-of-human-hemato-endothelial-cells-defines-transcriptional-signatures-of-hemogenic-endothelium
#4
Mathew G Angelos, Juan E Abrahante, Robert H Blum, Dan S Kaufman
Endothelial-to-hematopoietic transition (EHT) is an important stage in definitive hematopoietic development. However, the genetic mechanisms underlying human EHT remains poorly characterized. We performed single cell RNA-seq using 55 hemogenic endothelial cells (HE: CD31(+) CD144(+) CD41(-) CD43(-) CD45(-) CD73(-) RUNX1c(+) ), 47 vascular endothelial cells without hematopoietic potential (non-HE: CD31(+) CD144(+) CD41(-) CD43(-) CD45(-) CD73(-) RUNX1c(-) ), and 35 hematopoietic progenitor cells (HP: CD34(+) CD43(+) RUNX1c(+) ) derived from human embryonic stem cells (hESCs)...
November 15, 2017: Stem Cells
https://www.readbyqxmd.com/read/29138277/coupling-shrna-screens-with-single-cell-rna-seq-identifies-a-dual-role-for-mtor-in-reprogramming-induced-senescence
#5
Marieke Aarts, Athena Georgilis, Meryam Beniazza, Patrizia Beolchi, Ana Banito, Thomas Carroll, Marizela Kulisic, Daniel F Kaemena, Gopuraja Dharmalingam, Nadine Martin, Wolf Reik, Johannes Zuber, Keisuke Kaji, Tamir Chandra, Jesús Gil
Expression of the transcription factors OCT4, SOX2, KLF4, and cMYC (OSKM) reprograms somatic cells into induced pluripotent stem cells (iPSCs). Reprogramming is a slow and inefficient process, suggesting the presence of safeguarding mechanisms that counteract cell fate conversion. One such mechanism is senescence. To identify modulators of reprogramming-induced senescence, we performed a genome-wide shRNA screen in primary human fibroblasts expressing OSKM. In the screen, we identified novel mediators of OSKM-induced senescence and validated previously implicated genes such as CDKN1A We developed an innovative approach that integrates single-cell RNA sequencing (scRNA-seq) with the shRNA screen to investigate the mechanism of action of the identified candidates...
November 14, 2017: Genes & Development
https://www.readbyqxmd.com/read/29130882/simultaneous-enumeration-of-cancer-and-immune-cell-types-from-bulk-tumor-gene-expression-data
#6
Julien Racle, Kaat de Jonge, Petra Baumgaertner, Daniel E Speiser, David Gfeller
Immune cells infiltrating tumors can have important impact on tumor progression and response to therapy. We present an efficient algorithm to simultaneously estimate the fraction of cancer and immune cell types from bulk tumor gene expression data. Our method integrates novel gene expression profiles from each major non-malignant cell type found in tumors, renormalization based on cell-type specific mRNA content, and the ability to consider uncharacterized and possibly highly variable cell types. Feasibility is demonstrated by validation with flow cytometry, immunohistochemistry and single-cell RNA-Seq analyses of human melanoma and colorectal tumor specimens...
November 13, 2017: ELife
https://www.readbyqxmd.com/read/29130192/lcm-seq-a-method-for-spatial-transcriptomic-profiling-using-laser-capture-microdissection-coupled-with-polya-based-rna-sequencing
#7
Susanne Nichterwitz, Julio Aguila Benitez, Rein Hoogstraaten, Qiaolin Deng, Eva Hedlund
LCM-seq couples laser capture microdissection of cells from frozen tissues with polyA-based RNA sequencing and is applicable to single neurons. The method utilizes off-the-shelf reagents and direct lysis of the cells without RNA purification, making it a simple and relatively cheap method with high reproducibility and sensitivity compared to previous methods. The advantage with LCM-seq is also that tissue sections are kept intact and thus the positional information of each cell is preserved.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29129909/rna-editing-by-adar1-leads-to-context-dependent-transcriptome-wide-changes-in-rna-secondary-structure
#8
Oz Solomon, Ayelet Di Segni, Karen Cesarkas, Hagit T Porath, Victoria Marcu-Malina, Orel Mizrahi, Noam Stern-Ginossar, Nitzan Kol, Sarit Farage-Barhom, Efrat Glick-Saar, Yaniv Lerenthal, Erez Y Levanon, Ninette Amariglio, Ron Unger, Itamar Goldstein, Eran Eyal, Gidi Rechavi
Adenosine deaminase acting on RNA 1 (ADAR1) is the master RNA editor, catalyzing the deamination of adenosine to inosine. RNA editing is vital for preventing abnormal activation of cytosolic nucleic acid sensing pathways by self-double-stranded RNAs. Here we determine, by parallel analysis of RNA secondary structure sequencing (PARS-seq), the global RNA secondary structure changes in ADAR1 deficient cells. Surprisingly, ADAR1 silencing resulted in a lower global double-stranded to single-stranded RNA ratio, suggesting that A-to-I editing can stabilize a large subset of imperfect RNA duplexes...
November 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29129640/the-stress-granule-transcriptome-reveals-principles-of-mrna-accumulation-in-stress-granules
#9
Anthony Khong, Tyler Matheny, Saumya Jain, Sarah F Mitchell, Joshua R Wheeler, Roy Parker
Stress granules are mRNA-protein assemblies formed from nontranslating mRNAs. Stress granules are important in the stress response and may contribute to some degenerative diseases. Here, we describe the stress granule transcriptome of yeast and mammalian cells through RNA-sequencing (RNA-seq) analysis of purified stress granule cores and single-molecule fluorescence in situ hybridization (smFISH) validation. While essentially every mRNA, and some noncoding RNAs (ncRNAs), can be targeted to stress granules, the targeting efficiency varies from <1% to >95%...
November 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29126398/characteristics-of-allelic-gene-expression-in-human-brain-cells-from-single-cell-rna-seq-data-analysis
#10
Dejian Zhao, Mingyan Lin, Erika Pedrosa, Herbert M Lachman, Deyou Zheng
BACKGROUND: Monoallelic expression of autosomal genes has been implicated in human psychiatric disorders. However, there is a paucity of allelic expression studies in human brain cells at the single cell and genome wide levels. RESULTS: In this report, we reanalyzed a previously published single-cell RNA-seq dataset from several postmortem human brains and observed pervasive monoallelic expression in individual cells, largely in a random manner. Examining single nucleotide variants with a predicted functional disruption, we found that the "damaged" alleles were overall expressed in fewer brain cells than their counterparts, and at a lower level in cells where their expression was detected...
November 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29126257/experimental-design-for-single-cell-rna-sequencing
#11
Jeanette Baran-Gale, Tamir Chandra, Kristina Kirschner
Single-cell RNA sequencing (scRNA-seq) has opened new avenues for the characterization of heterogeneity in a large variety of cellular systems. As this is a relatively new technique, the field is fast evolving. Here, we discuss general considerations in experimental design and the two most popular approaches, plate-based Smart-Seq2 and microdroplet-based scRNA-seq at the example of 10x Chromium. We discuss advantages and disadvantages of both methods and point out major factors to consider in designing successful experiments...
November 8, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29121214/missing-data-and-technical-variability-in-single-cell-rna-sequencing-experiments
#12
Stephanie C Hicks, F William Townes, Mingxiang Teng, Rafael A Irizarry
Until recently, high-throughput gene expression technology, such as RNA-Sequencing (RNA-seq) required hundreds of thousands of cells to produce reliable measurements. Recent technical advances permit genome-wide gene expression measurement at the single-cell level. Single-cell RNA-Seq (scRNA-seq) is the most widely used and numerous publications are based on data produced with this technology. However, RNA-seq and scRNA-seq data are markedly different. In particular, unlike RNA-seq, the majority of reported expression levels in scRNA-seq are zeros, which could be either biologically-driven, genes not expressing RNA at the time of measurement, or technically-driven, genes expressing RNA, but not at a sufficient level to be detected by sequencing technology...
November 6, 2017: Biostatistics
https://www.readbyqxmd.com/read/29115968/f-sclvm-scalable-and-versatile-factor-analysis-for-single-cell-rna-seq
#13
Florian Buettner, Naruemon Pratanwanich, Davis J McCarthy, John C Marioni, Oliver Stegle
Single-cell RNA-sequencing (scRNA-seq) allows studying heterogeneity in gene expression in large cell populations. Such heterogeneity can arise due to technical or biological factors, making decomposing sources of variation difficult. We here describe f-scLVM (factorial single-cell latent variable model), a method based on factor analysis that uses pathway annotations to guide the inference of interpretable factors underpinning the heterogeneity. Our model jointly estimates the relevance of individual factors, refines gene set annotations, and infers factors without annotation...
November 7, 2017: Genome Biology
https://www.readbyqxmd.com/read/29114259/identification-of-splicing-quantitative-trait-loci-sqtl-in-drosophila-melanogaster-with-developmental-lead-pb-2-exposure
#14
Wen Qu, Katherine Gurdziel, Roger Pique-Regi, Douglas M Ruden
Lead (Pb) poisoning has been a major public health issue globally and the recent Flint water crisis has drawn nation-wide attention to its effects. To better understand how lead plays a role as a neurotoxin, we utilized the Drosophila melanogaster model to study the genetic effects of lead exposure during development and identified lead-responsive genes. In our previous studies, we have successfully identified hundreds of lead-responsive expression QTLs (eQTLs) by using RNA-seq analysis on heads collected from the Drosophila Synthetic Population Resource...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29106824/inferring-relevant-cell-types-for-complex-traits-by-using-single-cell-gene-expression
#15
Diego Calderon, Anand Bhaskar, David A Knowles, David Golan, Towfique Raj, Audrey Q Fu, Jonathan K Pritchard
Previous studies have prioritized trait-relevant cell types by looking for an enrichment of genome-wide association study (GWAS) signal within functional regions. However, these studies are limited in cell resolution by the lack of functional annotations from difficult-to-characterize or rare cell populations. Measurement of single-cell gene expression has become a popular method for characterizing novel cell types, and yet limited work has linked single-cell RNA sequencing (RNA-seq) to phenotypes of interest...
October 23, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29106401/irf3-and-type-i-interferons-fuel-a-fatal-response-to-myocardial-infarction
#16
Kevin R King, Aaron D Aguirre, Yu-Xiang Ye, Yuan Sun, Jason D Roh, Richard P Ng, Rainer H Kohler, Sean P Arlauckas, Yoshiko Iwamoto, Andrej Savol, Ruslan I Sadreyev, Mark Kelly, Timothy P Fitzgibbons, Katherine A Fitzgerald, Timothy Mitchison, Peter Libby, Matthias Nahrendorf, Ralph Weissleder
Interferon regulatory factor 3 (IRF3) and type I interferons (IFNs) protect against infections and cancer, but excessive IRF3 activation and type I IFN production cause autoinflammatory conditions such as Aicardi-Goutières syndrome and STING-associated vasculopathy of infancy (SAVI). Myocardial infarction (MI) elicits inflammation, but the dominant molecular drivers of MI-associated inflammation remain unclear. Here we show that ischemic cell death and uptake of cell debris by macrophages in the heart fuel a fatal response to MI by activating IRF3 and type I IFN production...
November 6, 2017: Nature Medicine
https://www.readbyqxmd.com/read/29091775/single-cell-rna-seq-analysis-of-infiltrating-neoplastic-cells-at-the-migrating-front-of-human-glioblastoma
#17
Spyros Darmanis, Steven A Sloan, Derek Croote, Marco Mignardi, Sophia Chernikova, Peyman Samghababi, Ye Zhang, Norma Neff, Mark Kowarsky, Christine Caneda, Gordon Li, Steven D Chang, Ian David Connolly, Yingmei Li, Ben A Barres, Melanie Hayden Gephart, Stephen R Quake
Glioblastoma (GBM) is the most common primary brain cancer in adults and is notoriously difficult to treat because of its diffuse nature. We performed single-cell RNA sequencing (RNA-seq) on 3,589 cells in a cohort of four patients. We obtained cells from the tumor core as well as surrounding peripheral tissue. Our analysis revealed cellular variation in the tumor's genome and transcriptome. We were also able to identify infiltrating neoplastic cells in regions peripheral to the core lesions. Despite the existence of significant heterogeneity among neoplastic cells, we found that infiltrating GBM cells share a consistent gene signature between patients, suggesting a common mechanism of infiltration...
October 31, 2017: Cell Reports
https://www.readbyqxmd.com/read/29089539/heterogeneous-circrna-expression-profiles-and-regulatory-functions-among-hek293t-single-cells
#18
Chaofang Zhong, Shaojun Yu, Maozhen Han, Jiahuan Chen, Kang Ning
The single-cell analysis is becoming a powerful method for early detection of the abnormal variant in tissues, especially for profiling a small number of heterogeneous cells. With the advancement of sequencing technologies, many types of non-coding elements including miRNAs and lncRNAs which shed light on their heterogeneous patterns and functions among cells, have been profiled at the single-cell level. However, the complete picture of circRNA profile at single-cell level is still lacking. In this study, RNA-Seq data obtained from single HEK293T cells have been used to analyze expressions and functions of heterogeneous circRNA profiles...
October 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29089413/transcriptomes-of-major-renal-collecting-duct-cell-types-in-mouse-identified-by-single-cell-rna-seq
#19
Lihe Chen, Jae Wook Lee, Chung-Lin Chou, Anil V Nair, Maria A Battistone, Teodor G Păunescu, Maria Merkulova, Sylvie Breton, Jill W Verlander, Susan M Wall, Dennis Brown, Maurice B Burg, Mark A Knepper
Prior RNA sequencing (RNA-seq) studies have identified complete transcriptomes for most renal epithelial cell types. The exceptions are the cell types that make up the renal collecting duct, namely intercalated cells (ICs) and principal cells (PCs), which account for only a small fraction of the kidney mass, but play critical physiological roles in the regulation of blood pressure, extracellular fluid volume, and extracellular fluid composition. To enrich these cell types, we used FACS that employed well-established lectin cell surface markers for PCs and type B ICs, as well as a newly identified cell surface marker for type A ICs, c-Kit...
October 31, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29080679/sfrp2-dpp4-and-fmo1-lsp1-define-major-fibroblast-populations-in-human-skin
#20
Tracy Tabib, Christina Morse, Ting Wang, Wei Chen, Robert Lafyatis
Fibroblasts produce matrix, regulate inflammation, mediate reparative processes, and serve as pluripotent mesenchymal cells. Analyzing digested normal human skin by single cell RNA-seq (scRNA-seq), we explored different fibroblast populations. T-distributed stochastic neighbor embedding and clustering of scRNA-seq data from six biopsies revealed two major fibroblast populations, defined by distinct genes, including SFRP2 and FMO1, expressed exclusively by these two major fibroblast populations. Further subpopulations were defined within each of the SFRP2 and FMO1 populations, as well as five minor fibroblast populations, each expressing discrete genes: CRABP1, COL11A1, FMO2, PRG4 or C2ORF40...
October 25, 2017: Journal of Investigative Dermatology
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