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Single cell RNA seq

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https://www.readbyqxmd.com/read/29321653/integrated-sequencing-of-exome-and-mrna-of-large-sized-single-cells
#1
Lily Yan Wang, Jiajie Guo, Wei Cao, Meng Zhang, Jiankui He, Zhoufang Li
Current approaches of single cell DNA-RNA integrated sequencing are difficult to call SNPs, because a large amount of DNA and RNA is lost during DNA-RNA separation. Here, we performed simultaneous single-cell exome and transcriptome sequencing on individual mouse oocytes. Using microinjection, we kept the nuclei intact to avoid DNA loss, while retaining the cytoplasm inside the cell membrane, to maximize the amount of DNA and RNA captured from the single cell. We then conducted exome-sequencing on the isolated nuclei and mRNA-sequencing on the enucleated cytoplasm...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29317474/reconstructing-differentiation-networks-and-their-regulation-from-time-series-single-cell-expression-data
#2
Jun Ding, Bruce Aronow, Naftali Kaminski, Joseph Kitzmiller, Jeffrey Whitsett, Ziv Bar-Joseph
Generating detailed and accurate organogenesis models using single cell RNA-seq data remains a major challenge. Current methods have relied primarily on the assumption that decedent cells are similar to their parents in terms of gene expression levels. These assumptions do not always hold for in-vivo studies which often include infrequently sampled, un-synchronized and diverse cell populations. Thus, additional information may be needed to determine the correct ordering and branching of progenitor cells and the set of transcription factors (TFs) that are active during advancing stages of organogenesis...
January 9, 2018: Genome Research
https://www.readbyqxmd.com/read/29299873/single-cell-expression-profiling-and-proteomics-of-primordial-germ-cells-spermatogonial-stem-cells-adult-germ-stem-cells-and-oocytes
#3
Sabine Conrad, Hossein Azizi, Thomas Skutella
The mammalian germ cells, cell assemblies, tissues, and organs during development and maturation have been extensively studied at the tissue level. However, to investigate and understand the fundamental insights at the molecular basis of germ and stem cells, their cell fate plasticity, and determination, it is of most importance to analyze at the large scale on the single-cell level through different biological windows. Here, modern molecular techniques optimized for single-cell analysis, including single fluorescence-activated cell sorting (FACS) and single-cell RNA sequencing (scRNA-seq) or microfluidic high-throughput quantitative real-time polymerase chain reaction (qRT-PCR) for single-cell gene expression and liquid chromatography coupled to tandem mass spectrometry (LC-MSMS) for protein profiling, have been established and are still getting optimized...
January 4, 2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29287307/effects-of-hla-b27-on-gut-microbiota-in-experimental-spondyloarthritis-implicate-an-ecological-model-of-dysbiosis
#4
Tejpal Gill, Mark Asquith, Stephen R Brooks, James T Rosenbaum, Robert A Colbert
OBJECTIVES: We investigated whether HLA-B27-mediated experimental spondyloarthritis (SpA) is associated with a common gut microbial signature to identify potential drivers of pathogenesis. METHODS: Effects of HLA-B27 on three genetic backgrounds, Dark Agouti (DA), Lewis, and Fischer were compared, using wild-type littermates and HLA-B7 transgenic Lewis rats as controls. At 2, 3-4, and 6-8 months of age, cecal and colonic tissue or contents were analyzed by histology for inflammation, RNA-Seq for gene expression differences, and 16S rRNA gene sequencing for microbiota differences...
December 29, 2017: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/29284484/platform-independent-gene-expression-signature-differentiates-sessile-serrated-adenomas-polyps-and-hyperplastic-polyps-of-the-colon
#5
Yasir Rahmatallah, Magomed Khaidakov, Keith K Lai, Hannah E Goyne, Laura W Lamps, Curt H Hagedorn, Galina Glazko
BACKGROUND: Sessile serrated adenomas/polyps are distinguished from hyperplastic colonic polyps subjectively by their endoscopic appearance and histological morphology. However, hyperplastic and sessile serrated polyps can have overlapping morphological features resulting in sessile serrated polyps diagnosed as hyperplastic. While sessile serrated polyps can progress into colon cancer, hyperplastic polyps have virtually no risk for colon cancer. Objective measures, differentiating these types of polyps would improve cancer prevention and treatment outcome...
December 28, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29283424/integrated-microrna-mrna-analysis-reveals-mir-204-inhibits-cell-proliferation-in-gastric-cancer-by-targeting-cks1b-cxcl1-and-gprc5a
#6
Sirjana Shrestha, Chi-Dung Yang, Hsiao-Chin Hong, Chih-Hung Chou, Chun-San Tai, Men-Yee Chiew, Wen-Liang Chen, Shun-Long Weng, Chung-Chu Chen, Yi-An Chang, Meng-Lin Lee, Wei-Yun Huang, Sheng-Da Hsu, Yi-Chang Chen, Hsien-Da Huang
Gastric cancer (GC) is the second most frequent cause of cancer-related deaths worldwide. MicroRNAs are single-stranded RNA molecules of 21-23 nucleotides that regulate target gene expression through specific base-pairing interactions between miRNA and untranslated regions of targeted mRNAs. In this study, we generated a multistep approach for the integrated analysis of miRNA and mRNA expression. First, both miRNA and mRNA expression profiling datasets in gastric cancer from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) identified 79 and 1042 differentially expressed miRNAs and mRNAs, respectively, in gastric cancer...
December 28, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29280088/visnormsc-a-graphical-user-interface-to-normalize-single-cell-rna-sequencing-data
#7
Lijun Tang, Nan Zhou
Single-cell RNA sequencing (RNA-seq) allows the analysis of gene expression with high resolution. The intrinsic defects of this promising technology imports technical noise into the single-cell RNA-seq data, increasing the difficulty of accurate downstream inference. Normalization is a crucial step in single-cell RNA-seq data pre-processing. SCnorm is an accurate and efficient method that can be used for this purpose. An R implementation of this method is currently available. On one hand, the R package possesses many excellent features from R...
December 26, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29273784/integrated-transcriptional-analysis-unveils-the-dynamics-of-cellular-differentiation-in-the-developing-mouse-hippocampus
#8
Giovanni Iacono, Marco Benevento, Aline Dubos, Yann Herault, Hans van Bokhoven, Nael Nadif Kasri, Hendrik G Stunnenberg
The ability to assign expression patterns to the individual cell types that constitute a tissue is a major challenge. This especially applies to brain, given its plethora of different, functionally interconnected cell types. Here, we derived cell type-specific transcriptome signatures from existing single cell RNA data and integrated these signatures with a newly generated dataset of expression (bulk RNA-Seq) of the postnatal developing mouse hippocampus. This integrated analysis allowed us to provide a comprehensive and unbiased prediction of the differentiation drivers for 11 different hippocampal cell types and describe how the different cell types interact to support crucial developmental stages...
December 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29261120/high-throughput-rna-seq-data-analysis-of-the-single-nucleotide-polymorphisms-snps-and-zygomorphic-flower-development-in-pea-pisum-sativum-l
#9
Keyuan Jiao, Xin Li, Wuxiu Guo, Shihao Su, Da Luo
Pea (Pisum sativum L.) is a model plant that has been used in classical genetics and organ development studies. However, its large and complex genome has hindered research investigations in pea. Here, we generated transcriptomes from different tissues or organs of three pea accessions using next-generation sequencing to assess single nucleotide polymorphisms (SNPs), and further investigated petal differentially expressed genes to elucidate the mechanisms regulating floral zygomorphy. Eighteen samples were sequenced, which yielded a total of 617 million clean reads, and de novo assembly resulted in 87,137 unigenes...
December 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29249941/correlating-anatomy-and-function-with-gene-expression-in-individual-neurons-by-combining-in-vivo-labeling-patch-clamp-and-single-cell-rna-seq
#10
Carsten K Pfeffer, Riccardo Beltramo
The classification of neurons into distinct types is an ongoing effort aimed at revealing and understanding the diversity of the components of the nervous system. Recently available methods allow us to determine the gene expression pattern of individual neurons in the mammalian cerebral cortex to generate powerful categorization schemes. For a thorough understanding of neuronal diversity such genetic categorization schemes need to be combined with traditional classification parameters like position, axonal projection or response properties to sensory stimulation...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/29247800/de-novo-rna-seq-based-transcriptome-analysis-of-papiliotrema-laurentii-strain-ry1-under-nitrogen-starvation
#11
Soumyadev Sarkar, Somnath Chakravorty, Avishek Mukherjee, Debanjana Bhattacharya, Semantee Bhattacharya, Ratan Gachhui
Nitrogen is a key nutrient for all cell forms. Most organisms respond to nitrogen scarcity by slowing down their growth rate. On the contrary, our previous studies have shown that Papiliotrema laurentii strain RY1 has a robust growth under nitrogen starvation. To understand the global regulation that leads to such an extraordinary response, we undertook a de novo approach for transcriptome analysis of the yeast. Close to 33 million sequence reads of high quality for nitrogen limited and enriched condition were generated using Illumina NextSeq500...
December 13, 2017: Gene
https://www.readbyqxmd.com/read/29246115/training-the-salmon-s-genes-influence-of-aerobic-exercise-swimming-performance-and-selection-on-gene-expression-in-atlantic-salmon
#12
Nicholas A Robinson, Gerrit Timmerhaus, Matthew Baranski, Øivind Andersen, Harald Takle, Aleksei Krasnov
BACKGROUND: Farmed and wild Atlantic salmon are exposed to many infectious and non-infectious challenges that can cause mortality when they enter the sea. Exercise before transfer promotes growth, health and survival in the sea. Swimming performance in juveniles at the freshwater parr stage is positively associated with resistance to some diseases. Genetic variation is likely to affect response to exercise. In this study we map genetic differences associated with aerobic exercise, swimming performance and genetic origin...
December 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29244808/fgmd-a-novel-approach-for-functional-gene-module-detection-in-cancer
#13
Daeyong Jin, Hyunju Lee
With the increasing availability of multi-dimensional biological datasets for the same samples (i.e., gene expression, microRNAs, copy numbers, mutations, methylations), it has now become possible to systematically understand the regulatory mechanisms operating in a cancer cell. For this task, it is important to discover a set of co-expressed genes with functions, representing a so-called functional gene module, because co-expressed genes tend to be co-regulated by the same regulators, including transcription factors, microRNAs, and copy number aberrations...
2017: PloS One
https://www.readbyqxmd.com/read/29236955/clustering-single-cells-a-review-of-approaches-on-high-and-low-depth-single-cell-rna-seq-data
#14
Vilas Menon
Advances in single-cell RNA-sequencing technology have resulted in a wealth of studies aiming to identify transcriptomic cell types in various biological systems. There are multiple experimental approaches to isolate and profile single cells, which provide different levels of cellular and tissue coverage. In addition, multiple computational strategies have been proposed to identify putative cell types from single-cell data. From a data generation perspective, recent single-cell studies can be classified into two groups: those that distribute reads shallowly over large numbers of cells and those that distribute reads more deeply over a smaller cell population...
December 11, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29236248/determining-mrna-decay-rates-using-rna-approach-to-equilibrium-sequencing-rate-seq
#15
Farah Abdul-Rahman, David Gresham
RATE-seq is a 4-thiouracil (4-tU)-based method that enables the in vivo measurement of transcriptome-wide RNA degradation rates. 4-tU is an analog of uracil that is rapidly incorporated into newly synthesized RNA and facilitates the conjugation of a biotinylated molecule containing a reactive thiol group. The biotinylated RNA can then be fractionated from the unlabeled RNA with streptavidin magnetic beads. By adding 4-tU to a culture of cells growing in steady-state conditions, fractionating the labeled population of RNA at multiple time points following 4-tU addition, and quantifying the abundance of newly transcribed RNAs using RNAseq, it is possible to estimate the degradation rates of all transcripts in a single experiment...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29233929/single-cell-rna-seq-reveals-a-subpopulation-of-prostate-cancer-cells-with-enhanced-cell-cycle-related-transcription-and-attenuated-androgen-response
#16
Aaron M Horning, Yao Wang, Che-Kuang Lin, Anna D Louie, Rohit R Jadhav, Chia-Nung Hung, Chiou-Miin Wang, Chun-Lin Lin, Nameer B Kirma, Michael A Liss, Addanki P Kumar, LuZhe Sun, Zhijie Liu, Wei-Ting Chao, Qianben Wang, Victor X Jin, Chun-Liang Chen, Tim H-M Huang
Increasing evidence suggests the presence of minor cell subpopulations in prostate cancer that are androgen independent and poised for selection as dominant clones after androgen-deprivation therapy. In this study, we investigated this phenomenon by stratifying cell subpopulations based on transcriptome profiling of 144 single LNCaP prostate cancer cells treated or untreated with androgen after cell cycle synchronization. Model-based clustering of 397 differentially expressed genes identified eight potential subpopulations of LNCaP cells, revealing a previously unappreciable level of cellular heterogeneity to androgen stimulation...
December 12, 2017: Cancer Research
https://www.readbyqxmd.com/read/29230913/a-novel-approach-to-single-cell-rna-seq-analysis-facilitates-in-silico-gene-reporting-of-human-pluripotent-stem-cell-derived-retinal-cell-types
#17
M Joseph Phillips, Peng Jiang, Sara Howden, Patrick Barney, Jee Min, Nathaniel W York, Li-Fang Chu, Elizabeth E Capowski, Abigail Cash, Shivani Jain, Katherine Barlow, Tasnia Tabassum, Ron Stewart, Bikash R Pattnaik, James A Thomson, David M Gamm
Cell type-specific investigations commonly employ gene reporters or single-cell (sc) analytical techniques. However, reporter line development is arduous and generally limited to a single gene of interest, while scRNA-seq frequently yields equivocal results that preclude definitive cell identification. To examine gene expression profiles of multiple retinal cell types derived from human pluripotent stem cells (hPSCs), we performed scRNA-seq on optic vesicle-like structures (OVs) cultured under cGMP-compatible conditions...
December 12, 2017: Stem Cells
https://www.readbyqxmd.com/read/29230012/estimation-of-immune-cell-content-in-tumour-tissue-using-single-cell-rna-seq-data
#18
Max Schelker, Sonia Feau, Jinyan Du, Nav Ranu, Edda Klipp, Gavin MacBeath, Birgit Schoeberl, Andreas Raue
As interactions between the immune system and tumour cells are governed by a complex network of cell-cell interactions, knowing the specific immune cell composition of a solid tumour may be essential to predict a patient's response to immunotherapy. Here, we analyse in depth how to derive the cellular composition of a solid tumour from bulk gene expression data by mathematical deconvolution, using indication-specific and cell type-specific reference gene expression profiles (RGEPs) from tumour-derived single-cell RNA sequencing data...
December 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/29227470/multiplexed-droplet-single-cell-rna-sequencing-using-natural-genetic-variation
#19
Hyun Min Kang, Meena Subramaniam, Sasha Targ, Michelle Nguyen, Lenka Maliskova, Elizabeth McCarthy, Eunice Wan, Simon Wong, Lauren Byrnes, Cristina M Lanata, Rachel E Gate, Sara Mostafavi, Alexander Marson, Noah Zaitlen, Lindsey A Criswell, Chun Jimmie Ye
Droplet single-cell RNA-sequencing (dscRNA-seq) has enabled rapid, massively parallel profiling of transcriptomes. However, assessing differential expression across multiple individuals has been hampered by inefficient sample processing and technical batch effects. Here we describe a computational tool, demuxlet, that harnesses natural genetic variation to determine the sample identity of each droplet containing a single cell (singlet) and detect droplets containing two cells (doublets). These capabilities enable multiplexed dscRNA-seq experiments in which cells from unrelated individuals are pooled and captured at higher throughput than in standard workflows...
December 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29227193/ddx5-p68-associated-lncrna-loc284454-is-differentially-expressed-in-human-cancers-and-modulates-gene-expression
#20
Monalisa Das, Arun Renganathan, Shrinivas Nivrutti Dighe, Utsa Bhaduri, Abhijith Shettar, Geetashree Mukherjee, Paturu Kondaiah, Manchanahalli R Satyanarayana Rao
Long non-coding RNAs (lncRNAs) are emerging as important players in regulation of gene expression in higher eukaryotes. DDX5/p68 RNA helicase protein which is involved in splicing of precursor mRNAs also interacts with lncRNAs like, SRA and mrhl, to modulate gene expression. We performed RIP-seq analysis in HEK293T cells to identify the complete repertoire of DDX5/p68 interacting transcripts including 73 single exonic (SE) lncRNAs. The LOC284454 lncRNA is the second top hit of the list of SE lncRNAs which we have characterized in detail for its molecular features and cellular functions...
December 11, 2017: RNA Biology
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