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Single cell RNA seq

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https://www.readbyqxmd.com/read/28934929/single-molecule-counting-and-assessment-of-random-molecular-tagging-errors-with-transposable-giga-scale-error-correcting-barcodes
#1
Billy T Lau, Hanlee P Ji
BACKGROUND: RNA-Seq measures gene expression by counting sequence reads belonging to unique cDNA fragments. Molecular barcodes commonly in the form of random nucleotides were recently introduced to improve gene expression measures by detecting amplification duplicates, but are susceptible to errors generated during PCR and sequencing. This results in false positive counts, leading to inaccurate transcriptome quantification especially at low input and single-cell RNA amounts where the total number of molecules present is minuscule...
September 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28934479/targeted-reconstruction-of-t-cell-receptor-sequence-from-single-cell-rna-seq-links-cdr3-length-to-t-cell-differentiation-state
#2
Shaked Afik, Kathleen B Yates, Kevin Bi, Samuel Darko, Jernej Godec, Ulrike Gerdemann, Leo Swadling, Daniel C Douek, Paul Klenerman, Eleanor J Barnes, Arlene H Sharpe, W Nicholas Haining, Nir Yosef
The T cell compartment must contain diversity in both T cell receptor (TCR) repertoire and cell state to provide effective immunity against pathogens. However, it remains unclear how differences in the TCR contribute to heterogeneity in T cell state. Single cell RNA-sequencing (scRNA-seq) can allow simultaneous measurement of TCR sequence and global transcriptional profile from single cells. However, current methods for TCR inference from scRNA-seq are limited in their sensitivity and require long sequencing reads, thus increasing the cost and decreasing the number of cells that can be feasibly analyzed...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28931656/single-cell-analyses-to-tailor-treatments
#3
REVIEW
Alex K Shalek, Mikael Benson
Single-cell RNA-seq could play a key role in personalized medicine by facilitating characterization of cells, pathways, and genes associated with human diseases such as cancer.
September 20, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28923089/dna-epigenome-editing-using-crispr-cas-suntag-directed-dnmt3a
#4
Yung-Hsin Huang, Jianzhong Su, Yong Lei, Lorenzo Brunetti, Michael C Gundry, Xiaotian Zhang, Mira Jeong, Wei Li, Margaret A Goodell
BACKGROUND: DNA methylation has widespread effects on gene expression during development. However, our ability to assign specific function to regions of DNA methylation is limited by the poor correlation between global patterns of DNA methylation and gene expression. RESULTS: Here, we utilize nuclease-deactivated Cas9 protein fused to repetitive peptide epitopes (SunTag) recruiting multiple copies of antibody-fused de novo DNA methyltransferase 3A (DNMT3A) (dCas9-SunTag-DNMT3A) to amplify the local DNMT3A concentration to methylate genomic sites of interest...
September 18, 2017: Genome Biology
https://www.readbyqxmd.com/read/28899397/splatter-simulation-of-single-cell-rna-sequencing-data
#5
Luke Zappia, Belinda Phipson, Alicia Oshlack
As single-cell RNA sequencing (scRNA-seq) technologies have rapidly developed, so have analysis methods. Many methods have been tested, developed, and validated using simulated datasets. Unfortunately, current simulations are often poorly documented, their similarity to real data is not demonstrated, or reproducible code is not available. Here, we present the Splatter Bioconductor package for simple, reproducible, and well-documented simulation of scRNA-seq data. Splatter provides an interface to multiple simulation methods including Splat, our own simulation, based on a gamma-Poisson distribution...
September 12, 2017: Genome Biology
https://www.readbyqxmd.com/read/28893664/single-cell-transcriptome-analysis-of-muscle-satellite-cells-reveals-widespread-transcriptional-heterogeneity
#6
Dong Seong Cho, Jason D Doles
Tissue specific stem cells are indispensable contributors to adult tissue maintenance, repair, and regeneration. In skeletal muscle, satellite cells (SCs) are the resident muscle stem cell population and are required to maintain skeletal muscle homeostasis throughout life. Increasing evidence suggests that SCs are a heterogeneous cell population with substantial biochemical and functional diversity. A major limitation in the field is an incomplete understanding of the nature and extent of this cellular heterogeneity...
September 8, 2017: Gene
https://www.readbyqxmd.com/read/28893418/the-promise-of-single-cell-rna-sequencing-for-kidney-disease-investigation
#7
Haojia Wu, Benjamin D Humphreys
Recent techniques for single-cell RNA sequencing (scRNA-seq) at high throughput are leading to profound new discoveries in biology. The ability to generate vast amounts of transcriptomic data at cellular resolution represents a transformative advance, allowing the identification of novel cell types, states, and dynamics. In this review, we summarize the development of scRNA-seq methodologies and highlight their advantages and drawbacks. We discuss available software tools for analyzing scRNA-Seq data and summarize current computational challenges...
September 8, 2017: Kidney International
https://www.readbyqxmd.com/read/28893133/rale051-a-novel-established-cell-line-of-sporadic-burkitt-lymphoma
#8
Alberto L'Abbate, Ilaria Iacobucci, Angelo Lonoce, Antonella Turchiano, Elisa Ficarra, Giulia Paciello, Federica Cattina, Anna Ferrari, Enrica Imbrogno, Claudio Agostinelli, Pierluigi Zinzani, Giovanni Martinelli, Enrico Derenzini, Clelia Tiziana Storlazzi
To date, the lack of chemo-naive cell models limited exploratory studies to define novel therapies for Burkitt lymphoma (BL). To obtain a useful tool for biological and translational studies for this tumor, we established the RALE051 cell line from the malignant ascitic fluid cells of a patient at initial diagnosis, not previously exposed to any treatment. The cell line was characterized by karyotyping, fluorescence in situ hybridization (FISH), single nucleotide polymorphism (SNP) array, immunohistochemistry, and RNA-Seq, revealing the persistence of biological and molecular features observed in the primary ascitic fluid, such as the cell morphology and immunophenotype, the occurrence of a t(8;22) translocation deregulating MYC, knock-out ID3 mutations in a compound homozygous state, and a mutated TP53...
September 11, 2017: Leukemia & Lymphoma
https://www.readbyqxmd.com/read/28888129/leveraging-blood-and-tissue-cd4-t-cell-heterogeneity-at-the-single-cell-level-to-identify-mechanisms-of-disease-in-rheumatoid-arthritis
#9
REVIEW
Chamith Y Fonseka, Deepak A Rao, Soumya Raychaudhuri
CD4+ T cells have been long known to play an important role in the pathogenesis of rheumatoid arthritis (RA), but the specific cell populations and states that drive the disease have been challenging to identify with low dimensional single cell data and bulk assays. The advent of high dimensional single cell technologies-like single cell RNA-seq or mass cytometry-has offered promise to defining key populations, but brings new methodological and statistical challenges. Recent single cell profiling studies have revealed a broad diversity of cell types among CD4+ T cells, identifying novel populations that are expanded or altered in RA...
September 6, 2017: Current Opinion in Immunology
https://www.readbyqxmd.com/read/28887696/lessons-from-single-cell-transcriptome-analysis-of-oxygen-sensing-cells
#10
REVIEW
Ting Zhou, Hiroaki Matsunami
The advent of single-cell RNA-sequencing (RNA-Seq) technology has enabled transcriptome profiling of individual cells. Comprehensive gene expression analysis at the single-cell level has proven to be effective in characterizing the most fundamental aspects of cellular function and identity. This unbiased approach is revolutionary for small and/or heterogeneous tissues like oxygen-sensing cells in identifying key molecules. Here, we review the major methods of current single-cell RNA-Seq technology. We discuss how this technology has advanced the understanding of oxygen-sensing glomus cells in the carotid body and helped uncover novel oxygen-sensing cells and mechanisms in the mice olfactory system...
September 8, 2017: Cell and Tissue Research
https://www.readbyqxmd.com/read/28885179/dual-rna-sequencing-to-elucidate-the-plant-pathogen-duel
#11
Sanushka Naidoo, Erik Andrei Visser, Lizahn Zwart, Yves du Toit, Vijai Bhadauria, Louise Simone Shuey
RNA-sequencing technology has been widely adopted to investigate host responses during infection with pathogens. Dual RNA-sequencing (RNA-seq) allows the simultaneous capture of pathogen specific transcripts during infection, providing a more complete view of the interaction. In this review, we focus on the design of dual RNA-seq experiments and the application of downstream data analysis to gain biological insight into both sides of the interaction. Recent literature in this area demonstrates the power of the dual RNA-seq approach and shows that it is not limited to model systems where genomic resources are available...
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28884792/profiling-of-single-cell-transcriptomes
#12
Wanze Chen, Vincent Gardeux, Antonio Meireles-Filho, Bart Deplancke
Complex biological systems are composed of multiple cell types whose transcriptional activity can vary due to differences in cell state, environmental stimulation, or intrinsic programs. Conventional bulk analysis methods capture the average transcriptional programs of the cell population, thus missing the unique cellular signature of each single cell. In recent years, the development of single-cell RNA-sequencing (scRNA-seq) technologies has provided a powerful approach to dissect the cellular heterogeneity of complex biological systems...
September 8, 2017: Current Protocols in Mouse Biology
https://www.readbyqxmd.com/read/28883481/early-x-chromosome-inactivation-during-human-preimplantation-development-revealed-by-single-cell-rna-sequencing
#13
Joana C Moreira de Mello, Gustavo R Fernandes, Maria D Vibranovski, Lygia V Pereira
In female mammals, one X chromosome is transcriptionally inactivated (XCI), leading to dosage compensation between sexes, fundamental for embryo viability. A previous study using single-cell RNA-sequencing (scRNA-seq) data proposed that female human preimplantation embryos achieve dosage compensation by downregulating both Xs, a phenomenon named dampening of X expression. Using a novel pipeline on those data, we identified a decrease in the proportion of biallelically expressed X-linked genes during development, consistent with XCI...
September 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28881849/advances-in-single-cell-rna-sequencing-and-its-applications-in-cancer-research
#14
REVIEW
Sibo Zhu, Tao Qing, Yuanting Zheng, Li Jin, Leming Shi
Unlike population-level approaches, single-cell RNA sequencing enables transcriptomic analysis of an individual cell. Through the combination of high-throughput sequencing and bioinformatic tools, single-cell RNA-seq can detect more than 10,000 transcripts in one cell to distinguish cell subsets and dynamic cellular changes. After several years' development, single-cell RNA-seq can now achieve massively parallel, full-length mRNA sequencing as well as in situ sequencing and even has potential for multi-omic detection...
August 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28868248/the-window-of-implantation-is-closed-by-estrogen-via-insulin-like-growth-factor-1-pathway
#15
Ryosuke Kobayashi, Jumpei Terakawa, Tsutomu Omatsu, Yupadee Hengjan, Tetsuya Mizutani, Yasushige Ohmori, Eiichi Hondo
BACKGROUND: The opening and closing of the implantation window is important for successful pregnancy in eutherians. The recent study demonstrated that the window of uterine receptivity was prepared by the sole action of progesterone in mice, but the mechanism to close the window remained to be elucidated. METHODS: The pregnant mice were ovariectomized on the evening on the third day of pregnancy with a single injection of medroxyprogesterone acetate to induce delayed implantation (DI)...
April 2017: Journal of Reproduction & Infertility
https://www.readbyqxmd.com/read/28855263/an-atlas-of-alternative-splicing-profiles-and-functional-associations-reveals-new-regulatory-programs-and-genes-that-simultaneously-express-multiple-major-isoforms
#16
Javier Tapial, Kevin C H Ha, Timothy Sterne-Weiler, Andre Gohr, Ulrich Braunschweig, Antonio Hermoso-Pulido, Mathieu Quesnel-Vallières, Jon Permanyer, Reza Sodaei, Yamile Marquez, Luca Cozzuto, Xinchen Wang, Melisa Gómez-Velázquez, Teresa Rayon, Miguel Manzanares, Julia Ponomarenko, Benjamin Blencowe, Manuel Irimia
Alternative splicing (AS) generates remarkable regulatory and proteomic complexity in metazoans. However, the functions of most AS events are not known and programs of regulated splicing remain to be identified. To address these challenges, we describe the Vertebrate Alternative Splicing and Transcription Database (VastDB), the largest resource of genome-wide, quantitative profiles of AS events assembled to date. VastDB provides readily accessible quantitative information on the inclusion levels and functional associations of AS events detected in RNA-seq data from diverse vertebrate cell and tissue types, as well as developmental stages...
August 30, 2017: Genome Research
https://www.readbyqxmd.com/read/28854975/ruxolitinib-nilotinib-cotreatment-inhibits-leukemia-propagating-cells-in-philadelphia-chromosome-positive-all
#17
Yuan Kong, Yi-Lin Wu, Yang Song, Min-Min Shi, Xie-Na Cao, Hong-Yan Zhao, Ya-Zhen Qin, Yue-Yun Lai, Hao Jiang, Qian Jiang, Xiao-Jun Huang
BACKGROUND: As one of the major treatment obstacles in Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph(+)ALL), relapse of Ph(+)ALL may result from the persistence of leukemia-propagating cells (LPCs). Research using a xenograft mouse assay recently determined that LPCs were enriched in the CD34(+)CD38(-)CD58(-) fraction in human Ph(+)ALL. Additionally, a cohort study demonstrated that Ph(+)ALL patients with a LPCs phenotype at diagnosis exhibited a significantly higher cumulative incidence of relapse than those with the other cell phenotypes even with uniform front-line imatinib-based therapy pre- and post-allotransplant, thus highlighting the need for novel LPCs-based therapeutic strategies...
August 30, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28854175/multiplexed-quantification-of-proteins-and-transcripts-in-single-cells
#18
Vanessa M Peterson, Kelvin Xi Zhang, Namit Kumar, Jerelyn Wong, Lixia Li, Douglas C Wilson, Renee Moore, Terrill K McClanahan, Svetlana Sadekova, Joel A Klappenbach
We present a tool to measure gene and protein expression levels in single cells with DNA-labeled antibodies and droplet microfluidics. Using the RNA expression and protein sequencing assay (REAP-seq), we quantified proteins with 82 barcoded antibodies and >20,000 genes in a single workflow. We used REAP-seq to assess the costimulatory effects of a CD27 agonist on human CD8(+) lymphocytes and to identify and characterize an unknown cell type.
August 30, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28851751/mrna-pseudouridylation-affects-rna-metabolism-in-the-parasite-toxoplasma-gondii
#19
Margaret A Nakamoto, Alexander F Lovejoy, Alicja M Cygan, John C Boothroyd
RNA contains over 100 modified nucleotides that are created post-transcriptionally, among which pseudouridine (Ψ) is one of the most abundant. Although it was one of the first modifications discovered, the biological role of this modification is still not fully understood. Recently, we reported that a pseudouridine synthase (TgPUS1) is necessary for differentiation of the single-celled eukaryotic parasite Toxoplasma gondii from active to chronic infection. To better understand the biological role of pseudouridylation we report here gel-based and deep-sequencing methods to identify TgPUS1-dependent Ψs in Toxoplasma RNA, and the use of TgPUS1 mutants to examine the effect of this modification on mRNAs...
August 29, 2017: RNA
https://www.readbyqxmd.com/read/28851704/psychrophilic-proteases-dramatically-reduce-single-cell-rna-seq-artifacts-a-molecular-atlas-of-kidney-development
#20
Mike Adam, Andrew S Potter, S Steven Potter
Single cell RNA-seq is a powerful methodology. Nevertheless there are important limitations, including the technical challenges of breaking down an organ or tissue into a single cell suspension. Invariably this has required enzymatic incubation at 37°C, which can be expected to result in artifact changes in gene expression patterns. We here describe a dissociation method that uses a protease with high activity in the cold, purified from a psychrophilic microorganism. The entire procedure is carried out at 6°C or colder, where mammalian transcriptional machinery is largely inactive, thereby effectively "freezing in" the in vivo gene expression patterns...
August 29, 2017: Development
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