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Single cell RNA seq

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https://www.readbyqxmd.com/read/28214646/new-rna-seq-approaches-for-the-study-of-bacterial-pathogens
#1
REVIEW
Antoine-Emmanuel Saliba, Sara C Santos, Jörg Vogel
Understanding how bacteria cause disease requires knowledge of which genes are expressed and how they are regulated during infection. While RNA-seq is now a routine method for gene expression analysis in bacterial pathogens, the past years have also witnessed a surge of novel RNA-seq based approaches going beyond standard mRNA profiling. These include variations of the technique to capture post-transcriptional networks controlled by small RNAs and to discover associated RNA-binding proteins in the pathogen itself...
February 16, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28212749/comparative-analysis-of-single-cell-rna-sequencing-methods
#2
Christoph Ziegenhain, Beate Vieth, Swati Parekh, Björn Reinius, Amy Guillaumet-Adkins, Martha Smets, Heinrich Leonhardt, Holger Heyn, Ines Hellmann, Wolfgang Enard
Single-cell RNA sequencing (scRNA-seq) offers new possibilities to address biological and medical questions. However, systematic comparisons of the performance of diverse scRNA-seq protocols are lacking. We generated data from 583 mouse embryonic stem cells to evaluate six prominent scRNA-seq methods: CEL-seq2, Drop-seq, MARS-seq, SCRB-seq, Smart-seq, and Smart-seq2. While Smart-seq2 detected the most genes per cell and across cells, CEL-seq2, Drop-seq, MARS-seq, and SCRB-seq quantified mRNA levels with less amplification noise due to the use of unique molecular identifiers (UMIs)...
February 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28211524/epigenetic-and-genetic-dissections-of-uv-induced-global-gene-dysregulation-in-skin-cells-through-multi-omics-analyses
#3
Yao Shen, Milda Stanislauskas, Gen Li, Deyou Zheng, Liang Liu
To elucidate the complex molecular mechanisms underlying the adverse effects UV radiation (UVR) on skin homeostasis, we performed multi-omics studies to characterize UV-induced genetic and epigenetic changes. Human keratinocytes from a single donor treated with or without UVR were analyzed by RNA-seq, exome-seq, and H3K27ac ChIP-seq at 4 h and 72 h following UVR. Compared to the relatively moderate mutagenic effects of UVR, acute UV exposure induced substantial epigenomic and transcriptomic alterations, illuminating a previously underappreciated role of epigenomic and transcriptomic instability in skin pathogenesis...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28207000/spatial-transcriptomic-analysis-of-cryosectioned-tissue-samples-with-geo-seq
#4
Jun Chen, Shengbao Suo, Patrick Pl Tam, Jing-Dong J Han, Guangdun Peng, Naihe Jing
Conventional gene expression studies analyze multiple cells simultaneously or single cells, for which the exact in vivo or in situ position is unknown. Although cellular heterogeneity can be discerned when analyzing single cells, any spatially defined attributes that underpin the heterogeneous nature of the cells cannot be identified. Here, we describe how to use Geo-seq, a method that combines laser capture microdissection (LCM) and single-cell RNA-seq technology. The combination of these two methods enables the elucidation of cellular heterogeneity and spatial variance simultaneously...
March 2017: Nature Protocols
https://www.readbyqxmd.com/read/28202516/modeling-the-genetic-regulation-of-cancer-metabolism-interplay-between-glycolysis-and-oxidative-phosphorylation
#5
Linglin Yu, Mingyang Lu, Dongya Jia, Jianpeng Ma, Eshel Ben-Jacob, Herbert Levine, Benny A Kaipparettu, Jose' N Onuchic
Abnormal metabolism is a hallmark of cancer, yet its regulation remains poorly understood. Cancer cells were considered to utilize primarily glycolysis for ATP production, referred to as the Warburg effect. However, recent evidence suggests that oxidative phosphorylation (OXPHOS) plays a crucial role during cancer progression. Here we utilized a systems biology approach to decipher the regulatory principle of glycolysis and OXPHOS. Integrating information from literature, we constructed a regulatory network of genes and metabolites from which we extracted a core circuit containing HIF-1, AMPK, and ROS...
February 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28192419/seq-well-portable-low-cost-rna-sequencing-of-single-cells-at-high-throughput
#6
Todd M Gierahn, Marc H Wadsworth, Travis K Hughes, Bryan D Bryson, Andrew Butler, Rahul Satija, Sarah Fortune, J Christopher Love, Alex K Shalek
Single-cell RNA-seq can precisely resolve cellular states, but applying this method to low-input samples is challenging. Here, we present Seq-Well, a portable, low-cost platform for massively parallel single-cell RNA-seq. Barcoded mRNA capture beads and single cells are sealed in an array of subnanoliter wells using a semipermeable membrane, enabling efficient cell lysis and transcript capture. We use Seq-Well to profile thousands of primary human macrophages exposed to Mycobacterium tuberculosis.
February 13, 2017: Nature Methods
https://www.readbyqxmd.com/read/28190458/detection-of-imprinted-genes-by-single-cell-allele-specific-gene-expression
#7
Federico A Santoni, Georgios Stamoulis, Marco Garieri, Emilie Falconnet, Pascale Ribaux, Christelle Borel, Stylianos E Antonarakis
Genomic imprinting results in parental-specific gene expression. Imprinted genes are involved in the etiology of rare syndromes and have been associated with common diseases such as diabetes and cancer. Standard RNA bulk cell sequencing applied to whole-tissue samples has been used to detect imprinted genes in human and mouse models. However, lowly expressed genes cannot be detected by using RNA bulk approaches. Here, we report an original and robust method that combines single-cell RNA-seq and whole-genome sequencing into an optimized statistical framework to analyze genomic imprinting in specific cell types and in different individuals...
February 6, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28181495/expression-of-%C3%AE-globin-by-cancer-cells-promotes-cell-survival-during-blood-borne-dissemination
#8
Yu Zheng, David T Miyamoto, Ben S Wittner, James P Sullivan, Nicola Aceto, Nicole Vincent Jordan, Min Yu, Nezihi Murat Karabacak, Valentine Comaills, Robert Morris, Rushil Desai, Niyati Desai, Erin Emmons, John D Milner, Richard J Lee, Chin-Lee Wu, Lecia V Sequist, Wilhelm Haas, David T Ting, Mehmet Toner, Sridhar Ramaswamy, Shyamala Maheswaran, Daniel A Haber
Metastasis-competent circulating tumour cells (CTCs) experience oxidative stress in the bloodstream, but their survival mechanisms are not well defined. Here, comparing single-cell RNA-Seq profiles of CTCs from breast, prostate and lung cancers, we observe consistent induction of β-globin (HBB), but not its partner α-globin (HBA). The tumour-specific origin of HBB is confirmed by sequence polymorphisms within human xenograft-derived CTCs in mouse models. Increased intracellular reactive oxygen species (ROS) in cultured breast CTCs triggers HBB induction, mediated through the transcriptional regulator KLF4...
February 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28181481/dpath-software-reveals-hierarchical-haemato-endothelial-lineages-of-etv2-progenitors-based-on-single-cell-transcriptome-analysis
#9
Wuming Gong, Tara L Rasmussen, Bhairab N Singh, Naoko Koyano-Nakagawa, Wei Pan, Daniel J Garry
Developmental, stem cell and cancer biologists are interested in the molecular definition of cellular differentiation. Although single-cell RNA sequencing represents a transformational advance for global gene analyses, novel obstacles have emerged, including the computational management of dropout events, the reconstruction of biological pathways and the isolation of target cell populations. We develop an algorithm named dpath that applies the concept of metagene entropy and allows the ranking of cells based on their differentiation potential...
February 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28176806/a-putative-myb35-ortholog-is-a-candidate-for-the-sex-determining-genes-in-asparagus-officinalis
#10
Daisuke Tsugama, Kohei Matsuyama, Mayui Ide, Masato Hayashi, Kaien Fujino, Kiyoshi Masuda
Asparagus officinalis (garden asparagus) is a dioecious perennial crop. For agricultural production of A. officinalis, male plants have advantages over female plants. The dioecism of A. officinalis is determined by the single dominant masculinizing M locus, which is involved in tapetal cell development in stamens, but thus far no specific M locus genes have been identified. We re-analyzed previously published RNA-Seq data for the A. officinalis transcriptome, cloned some genes, and discovered that a putative ortholog of MYB35, which is indispensable for tapetal cell development in Arabidopsis thaliana, is absent in the genome of female plants in A...
February 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28166822/disruption-of-the-m949_rs01915-gene-changed-the-bacterial-lipopolysaccharide-pattern-pathogenicity-and-gene-expression-of-riemerella-anatipestifer
#11
Yafeng Dou, Xiaolan Wang, Guijing Yu, Shaohui Wang, Mingxing Tian, Jingjing Qi, Tao Li, Chan Ding, Shengqing Yu
Riemerella anatipestifer is an important pathogen that causes septicemia anserum exsudativa in ducks. Lipopolysaccharide (LPS) is considered to be a major virulence factor of R. anatipestifer. To identify genes involved in LPS biosynthesis, we screened a library of random Tn4351 transposon mutants using a monoclonal antibody against R. anatipestifer serotype 1 LPS (anti-LPS MAb). A mutant strain RA1067 which lost the reactivity in an indirect ELISA was obtained. Southern blot and sequencing analyses indicated a single Tn4351 was inserted at 116 bp in the M949_RS01915 gene in the RA1067 chromosomal DNA...
February 6, 2017: Veterinary Research
https://www.readbyqxmd.com/read/28155657/a-machine-learning-approach-for-the-identification-of-key-markers-involved-in-brain-development-from-single-cell-transcriptomic-data
#12
Yongli Hu, Takeshi Hase, Hui Peng Li, Shyam Prabhakar, Hiroaki Kitano, See Kiong Ng, Samik Ghosh, Lawrence Jin Kiat Wee
BACKGROUND: The ability to sequence the transcriptomes of single cells using single-cell RNA-seq sequencing technologies presents a shift in the scientific paradigm where scientists, now, are able to concurrently investigate the complex biology of a heterogeneous population of cells, one at a time. However, till date, there has not been a suitable computational methodology for the analysis of such intricate deluge of data, in particular techniques which will aid the identification of the unique transcriptomic profiles difference between the different cellular subtypes...
December 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28145452/testis-specific-transcriptional-regulators-selectively-occupy-boris-bound-ctcf-target-regions-in-mouse-male-germ-cells
#13
Samuel Rivero-Hinojosa, Sungyun Kang, Victor V Lobanenkov, Gabriel E Zentner
Despite sharing the same sequence specificity in vitro and in vivo, CCCTC-binding factor (CTCF) and its paralog brother of the regulator of imprinted sites (BORIS) are simultaneously expressed in germ cells. Recently, ChIP-seq analysis revealed two classes of CTCF/BORIS-bound regions: single CTCF target sites (1xCTSes) that are bound by CTCF alone (CTCF-only) or double CTCF target sites (2xCTSes) simultaneously bound by CTCF and BORIS (CTCF&BORIS) or BORIS alone (BORIS-only) in germ cells and in BORIS-positive somatic cancer cells...
February 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28143951/single-molecule-sequencing-of-the-drosophila-serrata-genome
#14
Scott L Allen, Emily K Delaney, Artyom Kopp, Stephen F Chenoweth
Long read sequencing technology promises to greatly enhance de novo assembly of genomes for non-model species. Although the high error rates of long reads have been a stumbling block, sequencing at high coverage permits the self-correction of many errors. Here we sequence and de novo assemble the genome of Drosophila serrata, a species from the montium subgroup that has been well studied for latitudinal clines, sexual selection, and gene expression but which lacks a reference genome. Using 11 PacBio SMRT cells, we generated 12 Gbp of raw sequence data comprising approximately 65x whole genome coverage...
January 30, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28134613/dna-methylation-and-gene-expression-changes-derived-from-assisted-reproductive-technologies-can-be-decreased-by-reproductive-fluids
#15
Sebastian Canovas, Elena Ivanova, Raquel Romar, Soledad García-Martínez, Cristina Soriano-Úbeda, Francisco Alberto A García-Vázquez, Heba Saadeh, Simon Andrews, Gavin Kelsey, Pilar Coy
The number of children born since the origin of Assisted Reproductive Technologies (ART) exceeds 5 million. The majority seem healthy, but a higher frequency of defects has been reported among ART-conceived infants, suggesting an epigenetic cost. We report the first whole-genome DNA methylation datasets from single pig blastocysts showing differences between in vivo and in vitro produced embryos. Blastocysts were produced in vitro either without (C-IVF) or in the presence of natural reproductive fluids (Natur-IVF)...
January 30, 2017: ELife
https://www.readbyqxmd.com/read/28133571/detecting-heterogeneity-in-single-cell-rna-seq-data-by-non-negative-matrix-factorization
#16
Xun Zhu, Travers Ching, Xinghua Pan, Sherman M Weissman, Lana Garmire
Single-cell RNA-Sequencing (scRNA-Seq) is a fast-evolving technology that enables the understanding of biological processes at an unprecedentedly high resolution. However, well-suited bioinformatics tools to analyze the data generated from this new technology are still lacking. Here we investigate the performance of non-negative matrix factorization (NMF) method to analyze a wide variety of scRNA-Seq datasets, ranging from mouse hematopoietic stem cells to human glioblastoma data. In comparison to other unsupervised clustering methods including K-means and hierarchical clustering, NMF has higher accuracy in separating similar groups in various datasets...
2017: PeerJ
https://www.readbyqxmd.com/read/28132643/comparative-transcriptomics-of-elasmobranchs-and-teleosts-highlight-important-processes-in-adaptive-immunity-and-regional-endothermy
#17
Nicholas J Marra, Vincent P Richards, Angela Early, Steve M Bogdanowicz, Paulina D Pavinski Bitar, Michael J Stanhope, Mahmood S Shivji
BACKGROUND: Comparative genomic and/or transcriptomic analyses involving elasmobranchs remain limited, with genome level comparisons of the elasmobranch immune system to that of higher vertebrates, non-existent. This paper reports a comparative RNA-seq analysis of heart tissue from seven species, including four elasmobranchs and three teleosts, focusing on immunity, but concomitantly seeking to identify genetic similarities shared by the two lamnid sharks and the single billfish in our study, which could be linked to convergent evolution of regional endothermy...
January 30, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28118844/single-cell-epigenomic-variability-reveals-functional-cancer-heterogeneity
#18
Ulrike M Litzenburger, Jason D Buenrostro, Beijing Wu, Ying Shen, Nathan C Sheffield, Arwa Kathiria, William J Greenleaf, Howard Y Chang
BACKGROUND: Cell-to-cell heterogeneity is a major driver of cancer evolution, progression, and emergence of drug resistance. Epigenomic variation at the single-cell level can rapidly create cancer heterogeneity but is difficult to detect and assess functionally. RESULTS: We develop a strategy to bridge the gap between measurement and function in single-cell epigenomics. Using single-cell chromatin accessibility and RNA-seq data in K562 leukemic cells, we identify the cell surface marker CD24 as co-varying with chromatin accessibility changes linked to GATA transcription factors in single cells...
January 24, 2017: Genome Biology
https://www.readbyqxmd.com/read/28114287/single-cell-mrna-quantification-and-differential-analysis-with-census
#19
Xiaojie Qiu, Andrew Hill, Jonathan Packer, Dejun Lin, Yi-An Ma, Cole Trapnell
Single-cell gene expression studies promise to reveal rare cell types and cryptic states, but the high variability of single-cell RNA-seq measurements frustrates efforts to assay transcriptional differences between cells. We introduce the Census algorithm to convert relative RNA-seq expression levels into relative transcript counts without the need for experimental spike-in controls. Analyzing changes in relative transcript counts led to dramatic improvements in accuracy compared to normalized read counts and enabled new statistical tests for identifying developmentally regulated genes...
January 23, 2017: Nature Methods
https://www.readbyqxmd.com/read/28108447/mirmine-a-database-of-human-mirna-expression-profiles
#20
Bharat Panwar, Gilbert S Omenn, Yuanfang Guan
MOTIVATION: MicroRNAs (miRNAs) are small non-coding RNAs that are involved in post-transcriptional regulation of gene expression. In this high-throughput sequencing era, a tremendous amount of RNA-seq data is accumulating, and full utilization of publicly available miRNA data is an important challenge. These data are useful to determine expression values for each miRNA, but quantification pipelines are in a primitive stage and still evolving; there are many factors that affect expression values significantly...
January 19, 2017: Bioinformatics
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