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single cell rna-seq

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https://www.readbyqxmd.com/read/28630177/integrated-genome-and-transcriptome-sequencing-identifies-a-noncoding-mutation-in-the-genome-replication-factor-donson-as-the-cause-of-microcephaly-micromelia-syndrome
#1
Gilad D Evrony, Dwight R Cordero, Jun Shen, Jennifer N Partlow, Timothy W Yu, Rachel E Rodin, R Sean Hill, Michael E Coulter, Anh-Thu N Lam, Divya Jayaraman, Dianne Gerrelli, Diana G Diaz, Chloe Santos, Victoria Morrison, Antonella Galli, Ulrich Tschulena, Stefan Wiemann, M Jocelyne Martel, Betty Spooner, Steven C Ryu, Princess C Elhosary, Jillian M Richardson, Danielle Tierney, Christopher A Robinson, Rajni Chibbar, Dana Diudea, Rebecca Folkerth, Sheldon Wiebe, A James Barkovich, Ganeshwaran H Mochida, James Irvine, Edmond G Lemire, Patricia Blakley, Christopher A Walsh
While next-generation sequencing has accelerated the discovery of human disease genes, progress has been largely limited to the "low hanging fruit" of mutations with obvious exonic coding or canonical splice site impact. In contrast, the lack of high-throughput, unbiased approaches for functional assessment of most noncoding variants has bottlenecked gene discovery. We report the integration of transcriptome sequencing (RNA-seq), which surveys all mRNAs to reveal functional impacts of variants at the transcription level, into the gene discovery framework for a unique human disease, microcephaly-micromelia syndrome (MMS)...
June 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28623283/dosage-compensation-in-the-process-of-inactivation-reactivation-during-both-germ-cell-development-and-early-embryogenesis-in-mouse
#2
Xiaoyong Li, Zhiqiang Hu, Xuelin Yu, Chen Zhang, Binbin Ma, Lin He, Chaochun Wei, Ji Wu
Ohno proposed that dosage compensation in mammals evolved as a two-step mechanism involving X-inactivation and X-upregulation. While X-inactivation is well characterized, it remains to further analysis whether upregulation of the single activated X chromosome in mammals occurs. We obtained RNA-seq data, including single-cell RNA-seq data, from cells undergoing inactivation/reactivation in both germ cell development and early embryogenesis stages in mouse and calculated the X: A ratio from the gene expression...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28620184/transcriptomic-analysis-of-the-regulation-of-lipid-fraction-migration-and-fatty-acid-biosynthesis-in-schizochytrium-sp
#3
Lujing Ren, Xuechao Hu, Xiaoyan Zhao, Shenglan Chen, Yi Wu, Dan Li, Yadong Yu, Lingjun Geng, Xiaojun Ji, He Huang
Schizochytrium sp. is the main source of docosahexaenoic acid-rich oil, which is widely used in food additive and pharmaceutical industry. In this study, using RNA-seq, comparative transcriptomic analyses were performed at four stages of DHA fermentation by Schizochytrium sp to get potential genes related to cell transition from cell growth to lipid accumulation and then to lipid turnover. 1406, 385, 1384 differently expressed genes were identified by comparisons in pairs of S2 vs S1, S3 vs S2 and S4 vs S3...
June 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28600559/transcriptome-of-pterospermum-kingtungense-provides-implications-on-the-mechanism-underlying-its-rapid-vegetative-growth-and-limestone-adaption
#4
Yandong Ren, Yanan Zhu, Qi Wang, Hui Xiang, Boyi Wang
Pterospermum kingtungense C.Y.Wu ex Hsue is a typical tree species living in the relatively adverse limestone habitat. Due to its excellent wood quality and big size, it is an important timber resource which caused its endangered. We firstly provide the data resources by reporting an annotated transcriptome assembly. 203 million unique Illumina RNA-seq reads were produced with totally 50,333 transcripts, among which 48,778 transcripts were annotated. By a global comparison of homology between P. kingtungense and cacao, we identified 9,507 single copy orthologues and 990 P...
June 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28597408/single-cell-rna-sequencing-of-the-brain
#5
REVIEW
Raquel Cuevas-Diaz Duran, Haichao Wei, Jia Qian Wu
Single-cell RNA-sequencing (scRNA-seq) is revolutionizing our understanding of the genomic, transcriptomic and epigenomic landscapes of cells within organs. The mammalian brain is composed of a complex network of millions to billions of diverse cells with either highly specialized functions or support functions. With scRNA-seq it is possible to comprehensively dissect the cellular heterogeneity of brain cells, and elucidate their specific functions and state. In this review, we describe the current experimental methods used for scRNA-seq...
December 2017: Clinical and Translational Medicine
https://www.readbyqxmd.com/read/28592854/transcriptomic-analysis-of-short-fruit-1-sf1-reveals-new-insights-into-the-variation-of-fruit-related-traits-in-cucumis-sativus
#6
Lina Wang, Chenxing Cao, Shuangshuang Zheng, Haiyang Zhang, Panjing Liu, Qian Ge, Jinrui Li, Zhonghai Ren
Fruit size is an important quality trait in different market classes of Cucumis sativus L., an economically important vegetable cultivated worldwide, but the genetic and molecular mechanisms that control fruit size are largely unknown. In this study, we isolated a natural cucumber mutant, short fruit 1 (sf1), caused by a single recessive Mendelian factor, from the North China-type inbred line CNS2. In addition to significantly decreased fruit length, other fruit-related phenotypic variations were also observed in sf1 compared to the wild-type (WT) phenotype, indicating that sf1 might have pleiotropic effects...
June 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28589853/n-of-1-pathways-mixenrich-advancing-precision-medicine-via-single-subject-analysis-in-discovering-dynamic-changes-of-transcriptomes
#7
Qike Li, A Grant Schissler, Vincent Gardeux, Ikbel Achour, Colleen Kenost, Joanne Berghout, Haiquan Li, Hao Helen Zhang, Yves A Lussier
BACKGROUND: Transcriptome analytic tools are commonly used across patient cohorts to develop drugs and predict clinical outcomes. However, as precision medicine pursues more accurate and individualized treatment decisions, these methods are not designed to address single-patient transcriptome analyses. We previously developed and validated the N-of-1-pathways framework using two methods, Wilcoxon and Mahalanobis Distance (MD), for personal transcriptome analysis derived from a pair of samples of a single patient...
May 24, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28586482/determination-of-trna-aminoacylation-levels-by-high-throughput-sequencing
#8
Molly E Evans, Wesley C Clark, Guanqun Zheng, Tao Pan
Transfer RNA (tRNA) decodes mRNA codons when aminoacylated (charged) with an amino acid at its 3΄ end. Charged tRNAs turn over rapidly in cells, and variations in charged tRNA fractions are known to be a useful parameter in cellular responses to stress. tRNA charging fractions can be measured for individual tRNA species using acid denaturing gels, or comparatively at the genome level using microarrays. These hybridization-based approaches cannot be used for high resolution analysis of mammalian tRNAs due to their large sequence diversity...
June 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28582478/model-based-branching-point-detection-in-single-cell-data-by-k-branches-clustering
#9
Nikolaos K Chlis, F Alexander Wolf, Fabian J Theis
Motivation: The identification of heterogeneities in cell populations by utilizing single-cell technologies such as single-cell RNA-Seq, enables inference of cellular development and lineage trees. Several methods have been proposed for such inference from high-dimensional single-cell data. They typically assign each cell to a branch in a differentiation trajectory. However, they commonly assume specific geometries such as tree-like developmental hierarchies and lack statistically sound methods to decide on the number of branching events...
June 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28578186/revealing-allele-specific-gene-expression-by-single-cell-transcriptomics
#10
Julio Aguila Benitez, Shangli Cheng, Qiaolin Deng
Single-cell sequencing has emerged as a revolutionary method that reveals biological processes with unprecedented resolution and scale, and has already greatly impacted biology and medicine. To investigate processes such as alternative splicing, novel exon detection and allele-specific expression (ASE), full-length based single-cell RNA-seq methods are required for broad sequence coverage and single nucleotide polymorphism (SNP) identification. In this review, we revisit recent achievements from studies that used single-cell RNA-seq to advance our understanding of ASE in the context of both autosomal and X-chromosome genes...
May 31, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28575695/single-cell-rna-seq-analysis-maps-development-of-human-germline-cells-and-gonadal-niche-interactions
#11
Li Li, Ji Dong, Liying Yan, Jun Yong, Xixi Liu, Yuqiong Hu, Xiaoying Fan, Xinglong Wu, Hongshan Guo, Xiaoye Wang, Xiaohui Zhu, Rong Li, Jie Yan, Yuan Wei, Yangyu Zhao, Wei Wang, Yixin Ren, Peng Yuan, Zhiqiang Yan, Boqiang Hu, Fan Guo, Lu Wen, Fuchou Tang, Jie Qiao
No abstract text is available yet for this article.
June 1, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28574839/advances-in-single-cell-rna-sequencing-and-its-applications-in-cancer-research
#12
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...
May 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28570514/single-cell-rna-seq-of-defined-subsets-of-retinal-ganglion-cells
#13
Lauren A Laboissonniere, Takuma Sonoda, Seul Ki Lee, Jeffrey M Trimarchi, Tiffany M Schmidt
The discovery of cell type-specific markers can provide insight into cellular function and the origins of cellular heterogeneity. With a recent push for the improved understanding of neuronal diversity, it is important to identify genes whose expression defines various subpopulations of cells. The retina serves as an excellent model for the study of central nervous system diversity, as it is composed of multiple major cell types. The study of each major class of cells has yielded genetic markers that facilitate the identification of these populations...
May 22, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28569836/single-cell-entropy-for-accurate-estimation-of-differentiation-potency-from-a-cell-s-transcriptome
#14
Andrew E Teschendorff, Tariq Enver
The ability to quantify differentiation potential of single cells is a task of critical importance. Here we demonstrate, using over 7,000 single-cell RNA-Seq profiles, that differentiation potency of a single cell can be approximated by computing the signalling promiscuity, or entropy, of a cell's transcriptome in the context of an interaction network, without the need for feature selection. We show that signalling entropy provides a more accurate and robust potency estimate than other entropy-based measures, driven in part by a subtle positive correlation between the transcriptome and connectome...
June 1, 2017: Nature Communications
https://www.readbyqxmd.com/read/28569138/identification-of-candidate-genes-for-fiber-length-quantitative-trait-loci-through-rna-seq-and-linkage-and-physical-mapping-in-cotton
#15
Xihua Li, Man Wu, Guoyuan Liu, Wenfeng Pei, Honghong Zhai, Jiwen Yu, Jinfa Zhang, Shuxun Yu
BACKGROUND: Cotton (Gossypium spp.) fibers are single-celled elongated trichomes, the molecular aspects of genetic variation in fiber length (FL) among genotypes are currently unknown. In this study, two backcross inbred lines (BILs), i.e., NMGA-062 ("Long") and NMGA-105 ("Short") with 32.1 vs. 27.2 mm in FL, respectively, were chosen to perform RNA-Seq on developing fibers at 10 days post anthesis (DPA). The two BILs differed in 4 quantitative trait loci (QTL) for FL and were developed from backcrosses between G...
May 31, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28558694/accurate-characterization-of-the-ifitm-locus-using-miseq-and-pacbio-sequencing-shows-genetic-variation-in-galliformes
#16
Irene Bassano, Swee Hoe Ong, Nathan Lawless, Thomas Whitehead, Mark Fife, Paul Kellam
BACKGROUND: Interferon inducible transmembrane (IFITM) proteins are effectors of the immune system widely characterized for their role in restricting infection by diverse enveloped and non-enveloped viruses. The chicken IFITM (chIFITM) genes are clustered on chromosome 5 and to date four genes have been annotated, namely chIFITM1, chIFITM3, chIFITM5 and chIFITM10. However, due to poor assembly of this locus in the Gallus Gallus v4 genome, accurate characterization has so far proven problematic...
May 30, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28542535/a-trichostatin-a-expression-signature-identified-by-tempo-seq-targeted-whole-transcriptome-profiling
#17
Joanne M Yeakley, Peter J Shepard, Diana E Goyena, Harper C VanSteenhouse, Joel D McComb, Bruce E Seligmann
The use of gene expression signatures to classify compounds, identify efficacy or toxicity, and differentiate close analogs relies on the sensitivity of the method to identify modulated genes. We used a novel ligation-based targeted whole transcriptome expression profiling assay, TempO-Seq®, to determine whether previously unreported compound-responsive genes could be identified and incorporated into a broad but specific compound signature. TempO-Seq exhibits 99.6% specificity, single cell sensitivity, and excellent correlation with fold differences measured by RNA-Seq (R2 = 0...
2017: PloS One
https://www.readbyqxmd.com/read/28542205/rots-an-r-package-for-reproducibility-optimized-statistical-testing
#18
Tomi Suomi, Fatemeh Seyednasrollah, Maria K Jaakkola, Thomas Faux, Laura L Elo
Differential expression analysis is one of the most common types of analyses performed on various biological data (e.g. RNA-seq or mass spectrometry proteomics). It is the process that detects features, such as genes or proteins, showing statistically significant differences between the sample groups under comparison. A major challenge in the analysis is the choice of an appropriate test statistic, as different statistics have been shown to perform well in different datasets. To this end, the reproducibility-optimized test statistic (ROTS) adjusts a modified t-statistic according to the inherent properties of the data and provides a ranking of the features based on their statistical evidence for differential expression between two groups...
May 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28541377/asap-a-web-based-platform-for-the-analysis-and-interactive-visualization-of-single-cell-rna-seq-data
#19
Vincent Gardeux, Fabrice P A David, Adrian Shajkofci, Petra C Schwalie, Bart Deplancke
Motivation: Single-cell RNA-sequencing (scRNA-seq) allows whole transcriptome profiling of thousands of individual cells, enabling the molecular exploration of tissues at the cellular level. Such analytical capacity is of great interest to many research groups in the world, yet these groups often lack the expertise to handle complex scRNA-seq data sets. Results: We developed a fully integrated, web-based platform aimed at the complete analysis of scRNA-seq data post genome alignment: from the parsing, filtering, and normalization of the input count data files, to the visual representation of the data, identification of cell clusters, differentially expressed genes (including cluster-specific marker genes), and functional gene set enrichment...
May 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28539161/single-cell-rna-seq-unveils-tumor-microenvironment
#20
Hae-Ock Lee, Woong-Yang Park
Single cell transcriptome analysis became an essential tool to define cell types or sub-populations within a heterogeneous bulk population. Tumor-associated microenvironment is a complex ecosystem with numerous cell types, supporting the tumor growth, angiogenesis, immune evasion, and metastasis. With the success of checkpoint inhibitors targeting the immune cell compartment, tumor microenvironment is an emerging anti-cancer target and its understanding becomes an imminent issue in the cancer biology.
May 25, 2017: BMB Reports
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