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Single cell RNA seq

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https://www.readbyqxmd.com/read/28431229/functional-enhancer-screening-in-single-cells
#1
Joris van Arensbergen, Bas van Steensel
In this issue of Molecular Cell, Xie et al. (2017) introduce Mosaic-seq, a powerful technology that combines CRISPRi and single-cell RNA-seq. This method enables the high-throughput assessment of contributions of enhancers to gene regulation.
April 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28428369/single-cell-rna-seq-reveals-new-types-of-human-blood-dendritic-cells-monocytes-and-progenitors
#2
Alexandra-Chloé Villani, Rahul Satija, Gary Reynolds, Siranush Sarkizova, Karthik Shekhar, James Fletcher, Morgane Griesbeck, Andrew Butler, Shiwei Zheng, Suzan Lazo, Laura Jardine, David Dixon, Emily Stephenson, Emil Nilsson, Ida Grundberg, David McDonald, Andrew Filby, Weibo Li, Philip L De Jager, Orit Rozenblatt-Rosen, Andrew A Lane, Muzlifah Haniffa, Aviv Regev, Nir Hacohen
Dendritic cells (DCs) and monocytes play a central role in pathogen sensing, phagocytosis, and antigen presentation and consist of multiple specialized subtypes. However, their identities and interrelationships are not fully understood. Using unbiased single-cell RNA sequencing (RNA-seq) of ~2400 cells, we identified six human DCs and four monocyte subtypes in human blood. Our study reveals a new DC subset that shares properties with plasmacytoid DCs (pDCs) but potently activates T cells, thus redefining pDCs; a new subdivision within the CD1C(+) subset of DCs; the relationship between blastic plasmacytoid DC neoplasia cells and healthy DCs; and circulating progenitor of conventional DCs (cDCs)...
April 21, 2017: Science
https://www.readbyqxmd.com/read/28421044/comparative-genomics-of-glossina-palpalis-gambiensis-and-g-morsitans-morsitans-to-reveal-gene-orthologs-involved-in-infection-by-trypanosoma-brucei-gambiense
#3
Illiassou Hamidou Soumana, Bernadette Tchicaya, Stéphanie Rialle, Hugues Parrinello, Anne Geiger
Blood-feeding Glossina palpalis gambiense (Gpg) fly transmits the single-celled eukaryotic parasite Trypanosoma brucei gambiense (Tbg), the second Glossina fly African trypanosome pair being Glossina morsitans/T.brucei rhodesiense. Whatever the T. brucei subspecies, whereas the onset of their developmental program in the zoo-anthropophilic blood feeding flies does unfold in the fly midgut, its completion is taking place in the fly salivary gland where does emerge a low size metacyclic trypomastigote population displaying features that account for its establishment in mammals-human individuals included...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28419223/removal-of-batch-effects-using-distribution-matching-residual-networks
#4
Uri Shaham, Kelly P Stanton, Jun Zhao, Huamin Li, Khadir Raddassi, Ruth Montgomery, Yuval Kluger
Motivation: Sources of variability in experimentally derived data include measurement error in addition to the physical phenomena of interest. This measurement error is a combination of systematic components, originating from the measuring instrument, and random measurement errors. Several novel biological technologies, such as mass cytometry and single-cell RNA-seq, are plagued with systematic errors that may severely affect statistical analysis if the data is not properly calibrated...
April 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28418000/scnorm-robust-normalization-of-single-cell-rna-seq-data
#5
Rhonda Bacher, Li-Fang Chu, Ning Leng, Audrey P Gasch, James A Thomson, Ron M Stewart, Michael Newton, Christina Kendziorski
The normalization of RNA-seq data is essential for accurate downstream inference, but the assumptions upon which most normalization methods are based are not applicable in the single-cell setting. Consequently, applying existing normalization methods to single-cell RNA-seq data introduces artifacts that bias downstream analyses. To address this, we introduce SCnorm for accurate and efficient normalization of single-cell RNA-seq data.
April 17, 2017: Nature Methods
https://www.readbyqxmd.com/read/28416714/jinglebells-a-repository-of-immune-related-single-cell-rna-sequencing-datasets
#6
Hadas Ner-Gaon, Ariel Melchior, Nili Golan, Yael Ben-Haim, Tal Shay
Recent advances in single-cell RNA-sequencing (scRNA-seq) technology increase the understanding of immune differentiation and activation processes, as well as the heterogeneity of immune cell types. Although the number of available immune-related scRNA-seq datasets increases rapidly, their large size and various formats render them hard for the wider immunology community to use, and read-level data are practically inaccessible to the non-computational immunologist. To facilitate datasets reuse, we created the JingleBells repository for immune-related scRNA-seq datasets ready for analysis and visualization of reads at the single-cell level (http://jinglebells...
May 1, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28413616/-a-curated-transcriptomic-dataset-collection-relevant-to-embryonic-development-associated-with-in-vitro-fertilization-in-healthy-individuals-and-patients-with-polycystic-ovary-syndrome
#7
Rafah Mackeh, Sabri Boughorbel, Damien Chaussabel, Tomoshige Kino
The collection of large-scale datasets available in public repositories is rapidly growing and providing opportunities to identify and fill gaps in different fields of biomedical research. However, users of these datasets should be able to selectively browse datasets related to their field of interest. Here we made available a collection of transcriptome datasets related to human follicular cells from normal individuals or patients with polycystic ovary syndrome, in the process of their development, during in vitro fertilization...
2017: F1000Research
https://www.readbyqxmd.com/read/28413068/epithelial-mesenchymal-micro-niches-govern-stem-cell-lineage-choices
#8
Hanseul Yang, Rene C Adam, Yejing Ge, Zhong L Hua, Elaine Fuchs
Adult tissue stem cells (SCs) reside in niches, which, through intercellular contacts and signaling, influence SC behavior. Once activated, SCs typically give rise to short-lived transit-amplifying cells (TACs), which then progress to differentiate into their lineages. Here, using single-cell RNA-seq, we unearth unexpected heterogeneity among SCs and TACs of hair follicles. We trace the roots of this heterogeneity to micro-niches along epithelial-mesenchymal interfaces, where progenitors display molecular signatures reflective of spatially distinct local signals and intercellular interactions...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28408205/temporal-spatial-and-phenotypical-changes-of-pdgfr%C3%AE-expressing-fibroblasts-during-late-lung-development
#9
Mehari Endale, Shawn Ahlfeld, Erik Bao, Xiaoting Chen, Jenna Green, Zach Bess, Matthew T Weirauch, Yan Xu, Anne Karina Perl
Many studies have investigated the source and role of epithelial progenitors during lung development; such information is limited for fibroblast populations and their complex role in the developing lung. In this study, we characterized the spatial location, mRNA expression and Immunophenotyping of PDGFRα(+) fibroblasts during sacculation and alveolarization. Confocal microscopy identified spatial association of PDGFRα expressing fibroblasts with proximal epithelial cells of the branching bronchioles and the dilating acinar tubules at E16...
April 11, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28404604/unusual-semi-extractability-as-a-hallmark-of-nuclear-body-associated-architectural-noncoding-rnas
#10
Takeshi Chujo, Tomohiro Yamazaki, Tetsuya Kawaguchi, Satoshi Kurosaka, Toru Takumi, Shinichi Nakagawa, Tetsuro Hirose
NEAT1_2 long noncoding RNA (lncRNA) is the molecular scaffold of paraspeckle nuclear bodies. Here, we report an improved RNA extraction method: extensive needle shearing or heating of cell lysate in RNA extraction reagent improved NEAT1_2 extraction by 20-fold (a property we term "semi-extractability"), whereas using a conventional method NEAT1_2 was trapped in the protein phase. The improved extraction method enabled us to estimate that approximately 50 NEAT1_2 molecules are present in a single paraspeckle...
April 12, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28400492/the-molecular-dialog-between-flowering-plant-reproductive-partners-defined-by-snp-informed-rna-sequencing
#11
Alexander R Leydon, Caleb Weinreb, Elena Venable, Anke Reinders, John M Ward, Mark A Johnson
The molecular interactions between reproductive cells are critical for determining whether sexual reproduction between individuals results in fertilization and can result in barriers to interspecific hybridization. However, it is a challenge to define the complete molecular exchange between reproductive partners because parents contribute to a complex mixture of cells during reproduction. We unambiguously defined male- and female-specific patterns of gene expression during Arabidopsis reproduction using single nucleotide polymorphism-informed RNA-seq analysis...
April 11, 2017: Plant Cell
https://www.readbyqxmd.com/read/28396000/measuring-signaling-and-rna-seq-in-the-same-cell-links-gene-expression-to-dynamic-patterns-of-nf-%C3%AE%C2%BAb-activation
#12
Keara Lane, David Van Valen, Mialy M DeFelice, Derek N Macklin, Takamasa Kudo, Ariel Jaimovich, Ambrose Carr, Tobias Meyer, Dana Pe'er, Stéphane C Boutet, Markus W Covert
Signaling proteins display remarkable cell-to-cell heterogeneity in their dynamic responses to stimuli, but the consequences of this heterogeneity remain largely unknown. For instance, the contribution of the dynamics of the innate immune transcription factor nuclear factor κB (NF-κB) to gene expression output is disputed. Here we explore these questions by integrating live-cell imaging approaches with single-cell sequencing technologies. We used this approach to measure both the dynamics of lipopolysaccharide-induced NF-κB activation and the global transcriptional response in the same individual cell...
April 4, 2017: Cell Systems
https://www.readbyqxmd.com/read/28379537/tasic-determining-branching-models-from-time-series-single-cell-data
#13
Sabrina Rashid, Darrell N Kotton, Ziv Bar-Joseph
Motivation: Single cell RNA-Seq analysis holds great promise for elucidating the networks and pathways controlling cellular differentiation and disease. However, the analysis of time series single cell RNA-Seq data raises several new computational challenges. Cells at each time point are often sampled from a mixture of cell types, each of which may be a progenitor of one, or several, specific fates making it hard to determine which cells should be used to reconstruct temporal trajectories...
April 4, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28379368/scode-an-efficient-regulatory-network-inference-algorithm-from-single-cell-rna-seq-during-differentiation
#14
Hirotaka Matsumoto, Hisanori Kiryu, Chikara Furusawa, Minoru S H Ko, Shigeru B H Ko, Norio Gouda, Tetsutaro Hayashi, Itoshi Nikaido
Motivation: The analysis of RNA-Seq data from individual differentiating cells enables us to reconstruct the differentiation process and the degree of differentiation (in pseudo-time) of each cell. Such analyses can reveal detailed expression dynamics and functional relationships for differentiation. To further elucidate differentiation processes, more insight into gene regulatory networks is required. The pseudo-time can be regarded as time information and, therefore, single-cell RNA-Seq data are time-course data with high time resolution...
April 4, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28369676/transcriptome-wide-identification-of-rna-binding-protein-binding-sites-using-photoactivatable-ribonucleoside-enhanced-crosslinking-immunoprecipitation-par-clip
#15
Henrike Maatz, Marcin Kolinski, Norbert Hubner, Markus Landthaler
RNA-binding proteins (RBPs) mediate important co- and post-transcriptional gene regulation by binding pre-mRNA in a sequence- and/or structure-specific manner. For a comprehensive understanding of RBP function, transcriptome-wide mapping of the RNA-binding sites is essential, and CLIP-seq methods have been developed to elucidate protein/RNA interactions at high resolution. CLIP-seq combines protein/RNA UV-crosslinking with immunoprecipitation (CLIP) followed by high-throughput sequencing of crosslinked RNA fragments...
April 3, 2017: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/28369524/ngscheckmate-software-for-validating-sample-identity-in-next-generation-sequencing-studies-within-and-across-data-types
#16
Sejoon Lee, Soohyun Lee, Scott Ouellette, Woong-Yang Park, Eunjung A Lee, Peter J Park
In many next-generation sequencing (NGS) studies, multiple samples or data types are profiled for each individual. An important quality control (QC) step in these studies is to ensure that datasets from the same subject are properly paired. Given the heterogeneity of data types, file types and sequencing depths in a multi-dimensional study, a robust program that provides a standardized metric for genotype comparisons would be useful. Here, we describe NGSCheckMate, a user-friendly software package for verifying sample identities from FASTQ, BAM or VCF files...
March 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28369191/the-rnaseq-er-api-a-gateway-to-systematically-updated-analysis-of-public-rna-seq-data
#17
Robert Petryszak, Nuno A Fonseca, Anja Füllgrabe, Laura Huerta, Maria Keays, Y Amy Tang, Alvis Brazma
Motivation: The exponential growth of publicly available RNA sequencing (RNA-Seq) data poses an increasing challenge to researchers wishing to discover, analyse and store such data, particularly those based in institutions with limited computational resources. EMBL-EBI is in an ideal position to address these challenges and to allow the scientific community easy access to not just raw, but also processed RNA-Seq data. We present a Web service to access the results of a systematically and continually updated standardised alignment as well as gene and exon expression quantification of all public bulk (and in the near future also single-cell) RNA-Seq runs in 264 species in European Nucleotide Archive, using Representational State Transfer...
March 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28367160/neural-stem-cell-heterogeneity-through-time-and-space-in-the-ventricular-subventricular-zone
#18
Gabrielle Rushing, Rebecca A Ihrie
BACKGROUND: The origin and classification of neural stem cells (NSCs) has been a subject of intense investigation for the past two decades. Efforts to categorize NSCs based on their location, function and expression have established that these cells are a heterogeneous pool in both the embryonic and adult brain. The discovery and additional characterization of adult NSCs has introduced the possibility of using these cells as a source for neuronal and glial replacement following injury or disease...
August 2016: Frontiers in Biology
https://www.readbyqxmd.com/read/28361706/comprehensive-evaluation-of-rna-seq-quantification-methods-for-linearity
#19
Haijing Jin, Ying-Wooi Wan, Zhandong Liu
BACKGROUND: Deconvolution is a mathematical process of resolving an observed function into its constituent elements. In the field of biomedical research, deconvolution analysis is applied to obtain single cell-type or tissue specific signatures from a mixed signal and most of them follow the linearity assumption. Although recent development of next generation sequencing technology suggests RNA-seq as a fast and accurate method for obtaining transcriptomic profiles, few studies have been conducted to investigate best RNA-seq quantification methods that yield the optimum linear space for deconvolution analysis...
March 22, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28360267/decoupling-genetics-lineages-and-microenvironment-in-idh-mutant-gliomas-by-single-cell-rna-seq
#20
Andrew S Venteicher, Itay Tirosh, Christine Hebert, Keren Yizhak, Cyril Neftel, Mariella G Filbin, Volker Hovestadt, Leah E Escalante, McKenzie L Shaw, Christopher Rodman, Shawn M Gillespie, Danielle Dionne, Christina C Luo, Hiranmayi Ravichandran, Ravindra Mylvaganam, Christopher Mount, Maristela L Onozato, Brian V Nahed, Hiroaki Wakimoto, William T Curry, A John Iafrate, Miguel N Rivera, Matthew P Frosch, Todd R Golub, Priscilla K Brastianos, Gad Getz, Anoop P Patel, Michelle Monje, Daniel P Cahill, Orit Rozenblatt-Rosen, David N Louis, Bradley E Bernstein, Aviv Regev, Mario L Suvà
Tumor subclasses differ according to the genotypes and phenotypes of malignant cells as well as the composition of the tumor microenvironment (TME). We dissected these influences in isocitrate dehydrogenase (IDH)-mutant gliomas by combining 14,226 single-cell RNA sequencing (RNA-seq) profiles from 16 patient samples with bulk RNA-seq profiles from 165 patient samples. Differences in bulk profiles between IDH-mutant astrocytoma and oligodendroglioma can be primarily explained by distinct TME and signature genetic events, whereas both tumor types share similar developmental hierarchies and lineages of glial differentiation...
March 31, 2017: Science
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