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10X genomics

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https://read.qxmd.com/read/30698692/new-de-novo-assembly-of-the-atlantic-bottlenose-dolphin-tursiops-truncatus-improves-genome-completeness-and-provides-haplotype-phasing
#1
Karine A Martinez-Viaud, Cindy Taylor Lawley, Milmer Martinez Vergara, Gil Ben-Zvi, Tammy Biniashvili, Kobi Baruch, Judy St Leger, Jennie Le, Aparna Natarajan, Marlem Rivera, Marbie Guillergan, Erich Jaeger, Brian Steffy, Aleksey Zimin
High quality genomes are essential to resolve challenges in breeding, comparative biology, medicine and conservation planning. New library preparation techniques along with better assembly algorithms result in continued improvements in assemblies for non-model organisms, moving them toward reference quality genomes. We report on the latest genome assembly of the Atlantic bottlenose dolphin leveraging Illumina sequencing data coupled with a combination of several library preparation techniques. These include Linked-Reads (Chromium, 10x Genomics), mate pairs, long insert paired ends and standard paired ends...
January 29, 2019: GigaScience
https://read.qxmd.com/read/30689848/genome-sequence-of-malania-oleifera-a-tree-with-great-value-for-nervonic-acid-production
#2
Chao-Qun Xu, Hui Liu, Shan-Shan Zhou, Dong-Xu Zhang, Wei Zhao, Sihai Wang, Fu Chen, Yan-Qiang Sun, Shuai Nie, Kai-Hua Jia, Si-Qian Jiao, Ren-Gang Zhang, Quan-Zheng Yun, Wenbin Guan, Xuewen Wang, Qiong Gao, Jeffrey L Bennetzen, Fatemeh Maghuly, Ilga Porth, Yves Van de Peer, Xiao-Ru Wang, Yongpeng Ma, Jian-Feng Mao
Background: Malania oleifera, a member of the Olacaceae family, is an IUCN Red Listed tree, endemic and restricted to the Karst region of South West China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic make-up, and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools. Findings: We generated 51 Gigabases (Gb) and 135 Gb of raw DNA sequences, using PacBio Single-Molecule Real-Time (SMRT) and 10x Genomics sequencing, respectively...
January 24, 2019: GigaScience
https://read.qxmd.com/read/30678108/genome-assembly-and-annotation-of-the-trichoplusia-ni-tni-fnl-insect-cell-line-enabled-by-long-read-technologies
#3
Keyur Talsania, Monika Mehta, Castle Raley, Yuliya Kriga, Sujatha Gowda, Carissa Grose, Matthew Drew, Veronica Roberts, Kwong Tai Cheng, Sandra Burkett, Steffen Oeser, Robert Stephens, Daniel Soppet, Xiongfeng Chen, Parimal Kumar, Oksana German, Tatyana Smirnova, Christopher Hautman, Jyoti Shetty, Bao Tran, Yongmei Zhao, Dominic Esposito
BACKGROUND: Trichoplusia ni derived cell lines are commonly used to enable recombinant protein expression via baculovirus infection to generate materials approved for clinical use and in clinical trials. In order to develop systems biology and genome engineering tools to improve protein expression in this host, we performed de novo genome assembly of the Trichoplusia ni -derived cell line Tni-FNL. METHODS: By integration of PacBio single-molecule sequencing, Bionano optical mapping, and 10X Genomics linked-reads data, we have produced a draft genome assembly of Tni-FNL...
January 23, 2019: Genes
https://read.qxmd.com/read/30624602/a-critical-comparison-of-technologies-for-a-plant-genome-sequencing-project
#4
Pirita Paajanen, George Kettleborough, Elena López-Girona, Michael Giolai, Darren Heavens, David Baker, Ashleigh Lister, Fiorella Cugliandolo, Gail Wilde, Ingo Hein, Iain Macaulay, Glenn J Bryan, Matthew D Clark
Background: A high quality genome sequence of any model organism is an essential starting point for genetic and other studies. Older clone based methods are slow and expensive, whereas faster, cheaper short read only assemblies can be incomplete and highly fragmented, which minimises their usefulness. The last few years have seen the introduction of many new technologies for genome assembly. These new technologies and associated new algorithms are typically benchmarked on microbial genomes or, if they scale appropriately, on larger (e...
January 9, 2019: GigaScience
https://read.qxmd.com/read/30620341/the-sequence-and-de-novo-assembly-of-hog-deer-genome
#5
Wei Wang, Hui-Juan Yan, Shi-Yi Chen, Zhen-Zhen Li, Jun Yi, Li-Li Niu, Jia-Po Deng, Wei-Gang Chen, Yang Pu, Xianbo Jia, Yu Qu, Ang Chen, Yan Zhong, Xin-Ming Yu, Shuai Pang, Wan-Long Huang, Yue Han, Guang-Jian Liu, Jian-Qiu Yu
Hog deer (Axis porcinus) is a small deer species in family Cervidae and has been undergoing a serious and global decline during the past decades. Chengdu Zoo currently holds a captive population of hog deer with sufficient genetic diversity in China. We sequenced and de novo assembled its genome sequence in the present study. A total of six different insert-size libraries were sequenced and generated 395 Gb of clean data in total. With aid of the linked reads of 10X Genomics, genome sequence was assembled to 2...
January 8, 2019: Scientific Data
https://read.qxmd.com/read/30581450/evaluation-and-recommendations-for-routine-genotyping-using-skim-whole-genome-re-sequencing-in-canola
#6
M Michelle Malmberg, Denise M Barbulescu, Michelle C Drayton, Maiko Shinozuka, Preeti Thakur, Yvonne O Ogaji, German C Spangenberg, Hans D Daetwyler, Noel O I Cogan
Whole genome sequencing offers genome wide, unbiased markers, and inexpensive library preparation. With the cost of sequencing decreasing rapidly, many plant genomes of modest size are amenable to skim whole genome resequencing (skim WGR). The use of skim WGR in diverse sample sets without the use of imputation was evaluated in silico in 149 canola samples representative of global diversity. Fastq files with an average of 10x coverage of the reference genome were used to generate skim samples representing 0...
2018: Frontiers in Plant Science
https://read.qxmd.com/read/30576740/vasc-dimension-reduction-and-visualization-of-single-cell-rna-seq-data-by-deep-variational-autoencoder
#7
Dongfang Wang, Jin Gu
Single-cell RNA sequencing (scRNA-seq) is a powerful technique to analyze the transcriptomic heterogeneities at the single cell level. It is an important step for studying cell sub-populations and lineages, with an effective low-dimensional representation and visualization of the original scRNA-Seq data. At the single cell level, the transcriptional fluctuations are much larger than the average of a cell population, and the low amount of RNA transcripts will increase the rate of technical dropout events. Therefore, scRNA-seq data are much noisier than traditional bulk RNA-seq data...
December 18, 2018: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30523036/minerva-an-alignment-and-reference-free-approach-to-deconvolve-linked-reads-for-metagenomics
#8
David Danko, Dmitry Meleshko, Daniela Bezdan, Christopher Mason, Iman Hajirasouliha
Emerging Linked-Read technologies (aka Read-Cloud or barcoded short-reads) have revived interest in short-read technology as a viable way to understand large-scale structure in genomes and metagenomes. Linked-Read technologies, such as the 10x Chromium system, use a microfluidic system and a specialized set of 3' barcodes (aka UIDs) to tag short DNA reads sourced from the same long fragment of DNA; subsequently, the tagged reads are sequenced on standard short read platforms. This approach results in interesting compromises...
December 6, 2018: Genome Research
https://read.qxmd.com/read/30510133/advantages-of-single-nucleus-over-single-cell-rna-sequencing-of-adult-kidney-rare-cell-types-and-novel-cell-states-revealed-in-fibrosis
#9
Haojia Wu, Yuhei Kirita, Erinn L Donnelly, Benjamin D Humphreys
BACKGROUND: A challenge for single-cell genomic studies in kidney and other solid tissues is generating a high-quality single-cell suspension that contains rare or difficult-to-dissociate cell types and is free of both RNA degradation and artifactual transcriptional stress responses. METHODS: We compared single-cell RNA sequencing (scRNA-seq) using the DropSeq platform with single-nucleus RNA sequencing (snRNA-seq) using sNuc-DropSeq, DroNc-seq, and 10X Chromium platforms on adult mouse kidney...
January 2019: Journal of the American Society of Nephrology: JASN
https://read.qxmd.com/read/30472192/comparative-analysis-of-droplet-based-ultra-high-throughput-single-cell-rna-seq-systems
#10
Xiannian Zhang, Tianqi Li, Feng Liu, Yaqi Chen, Jiacheng Yao, Zeyao Li, Yanyi Huang, Jianbin Wang
Since its establishment in 2009, single-cell RNA sequencing (RNA-seq) has been a major driver behind progress in biomedical research. In developmental biology and stem cell studies, the ability to profile single cells confers particular benefits. Although most studies still focus on individual tissues or organs, the recent development of ultra-high-throughput single-cell RNA-seq has demonstrated potential power in characterizing more complex systems or even the entire body. However, although multiple ultra-high-throughput single-cell RNA-seq systems have attracted attention, no systematic comparison of these systems has been performed...
January 3, 2019: Molecular Cell
https://read.qxmd.com/read/30367597/tigmint-correcting-assembly-errors-using-linked-reads-from-large-molecules
#11
Shaun D Jackman, Lauren Coombe, Justin Chu, Rene L Warren, Benjamin P Vandervalk, Sarah Yeo, Zhuyi Xue, Hamid Mohamadi, Joerg Bohlmann, Steven J M Jones, Inanc Birol
BACKGROUND: Genome sequencing yields the sequence of many short snippets of DNA (reads) from a genome. Genome assembly attempts to reconstruct the original genome from which these reads were derived. This task is difficult due to gaps and errors in the sequencing data, repetitive sequence in the underlying genome, and heterozygosity. As a result, assembly errors are common. In the absence of a reference genome, these misassemblies may be identified by comparing the sequencing data to the assembly and looking for discrepancies between the two...
October 26, 2018: BMC Bioinformatics
https://read.qxmd.com/read/30355765/highly-continuous-genome-assembly-of-eurasian-perch-perca-fluviatilis-using-linked-read-sequencing
#12
Mikhail Yu Ozerov, Freed Ahmad, Riho Gross, Lilian Pukk, Siim Kahar, Veljo Kisand, Anti Vasemägi
The Eurasian perch ( Perca fluviatilis ) is the most common fish of the Percidae family and is widely distributed across Eurasia. Perch is a popular target for professional and recreational fisheries, and a promising freshwater aquaculture species in Europe. However, despite its high ecological, economical and societal importance, the available genomic resources for P. fluviatilis are rather limited. In this work, we report de novo assembly and annotation of the whole genome sequence of perch. The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a draft perch genome ~1...
October 24, 2018: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30346553/cost-effective-assembly-of-the-african-wild-dog-lycaon-pictus-genome-using-linked-reads
#13
Ellie E Armstrong, Ryan W Taylor, Stefan Prost, Peter Blinston, Esther van der Meer, Hillary Madzikanda, Olivia Mufute, Roseline Mandisodza-Chikerema, John Stuelpnagel, Claudio Sillero-Zubiri, Dmitri Petrov
Background: A high-quality reference genome assembly is a valuable tool for the study of non-model organisms. Genomic techniques can provide important insights about past population sizes, local adaptation, and aid in the development of breeding management plans. This information is important for fields like conservation genetics, where endangered species require critical and immediate attention. However, funding for genomic-based methods can be sparse for conservation projects, as costs for general species management can consume budgets...
October 22, 2018: GigaScience
https://read.qxmd.com/read/30275930/new-chromosome-counts-and-genome-size-estimates-for-28-species-of-taraxacum-sect-taraxacum
#14
Petra Macháčková, Ľuboš Majeský, Michal Hroneš, Eva Hřibová, Bohumil Trávníček, Radim J Vašut
The species-rich and widespread genus Taraxacum F. H. Wiggers, 1780 (Asteraceae subfamily Cichorioideae) is one of the most taxonomically complex plant genera in the world, mainly due to its combination of different sexual and asexual reproduction strategies. Polyploidy is usually confined to apomictic microspecies, varying from 3x to 6x (rarely 10x). In this study, we focused on Taraxacum sect. Taraxacum (= T.sect.Ruderalia; T.officinale group), i.e., the largest group within the genus. We counted chromosome numbers and measured the DNA content for species sampled in Central Europe, mainly in Czechia...
2018: Comparative Cytogenetics
https://read.qxmd.com/read/30247488/a-universal-snp-and-small-indel-variant-caller-using-deep-neural-networks
#15
Ryan Poplin, Pi-Chuan Chang, David Alexander, Scott Schwartz, Thomas Colthurst, Alexander Ku, Dan Newburger, Jojo Dijamco, Nam Nguyen, Pegah T Afshar, Sam S Gross, Lizzie Dorfman, Cory Y McLean, Mark A DePristo
Despite rapid advances in sequencing technologies, accurately calling genetic variants present in an individual genome from billions of short, errorful sequence reads remains challenging. Here we show that a deep convolutional neural network can call genetic variation in aligned next-generation sequencing read data by learning statistical relationships between images of read pileups around putative variant and true genotype calls. The approach, called DeepVariant, outperforms existing state-of-the-art tools...
November 2018: Nature Biotechnology
https://read.qxmd.com/read/30228881/comparison-of-clustering-tools-in-r-for-medium-sized-10x-genomics-single-cell-rna-sequencing-data
#16
Saskia Freytag, Luyi Tian, Ingrid Lönnstedt, Milica Ng, Melanie Bahlo
Background: The commercially available 10x Genomics protocol to generate droplet-based single-cell RNA-seq (scRNA-seq) data is enjoying growing popularity among researchers. Fundamental to the analysis of such scRNA-seq data is the ability to cluster similar or same cells into non-overlapping groups. Many competing methods have been proposed for this task, but there is currently little guidance with regards to which method to use. Methods: Here we use one gold standard 10x Genomics dataset, generated from the mixture of three cell lines, as well as three silver standard 10x Genomics datasets generated from peripheral blood mononuclear cells to examine not only the accuracy but also robustness of a dozen methods...
2018: F1000Research
https://read.qxmd.com/read/30138581/statistical-binning-for-barcoded-reads-improves-downstream-analyses
#17
Ariya Shajii, Ibrahim Numanagić, Christopher Whelan, Bonnie Berger
Sequencing technologies are capturing longer-range genomic information at lower error rates, enabling alignment to genomic regions that are inaccessible with short reads. However, many methods are unable to align reads to much of the genome, recognized as important in disease, and thus report erroneous results in downstream analyses. We introduce EMA, a novel two-tiered statistical binning model for barcoded read alignment, that first probabilistically maps reads to potentially multiple "read clouds" and then within clouds by newly exploiting the non-uniform read densities characteristic of barcoded read sequencing...
August 22, 2018: Cell Systems
https://read.qxmd.com/read/30124856/draft-genome-of-glyptosternon-maculatum-an-endemic-fish-from-tibet-plateau
#18
Haiping Liu, Qiyong Liu, Zhiqiang Chen, Yanchao Liu, Chaowei Zhou, Qiqi Liang, Caixia Ma, Jianshe Zhou, Yingzi Pan, Meiqun Chen, Wangjiu, Wenkai Jiang, Shijun Xiao, Zhenbo Mou
Background: Mechanisms for high-altitude adaption have attracted widespread interest among evolutionary biologists. Several genome-wide studies have been carried out for endemic vertebrates in Tibet, including mammals, birds, and amphibians. However, little information is available about the adaptive evolution of highland fishes. Glyptosternon maculatum (Regan 1905), also known as Regan or barkley and endemic to the Tibetan Plateau, belongs to the Sisoridae family, order Siluriformes (catfishes)...
September 1, 2018: GigaScience
https://read.qxmd.com/read/30061114/single-cell-rna-seq-analysis-identifies-markers-of-resistance-to-targeted-braf-inhibitors-in-melanoma-cell-populations
#19
Yu-Jui Ho, Naishitha Anaparthy, David Molik, Grinu Mathew, Toby Aicher, Ami Patel, James Hicks, Molly Gale Hammell
Single-cell RNA-seq's (scRNA-seq) unprecedented cellular resolution at a genome-wide scale enables us to address questions about cellular heterogeneity that are inaccessible using methods that average over bulk tissue extracts. However, scRNA-seq data sets also present additional challenges such as high transcript dropout rates, stochastic transcription events, and complex population substructures. Here, we present a <u>s</u>ingle-cell RNA-seq <u>a</u>nalysis and <u>k</u>lustering <u>e</u>valuation (SAKE), a robust method for scRNA-seq analysis that provides quantitative statistical metrics at each step of the analysis pipeline...
September 2018: Genome Research
https://read.qxmd.com/read/29991676/detection-and-removal-of-barcode-swapping-in-single-cell-rna-seq-data
#20
Jonathan A Griffiths, Arianne C Richard, Karsten Bach, Aaron T L Lun, John C Marioni
Barcode swapping results in the mislabelling of sequencing reads between multiplexed samples on patterned flow-cell Illumina sequencing machines. This may compromise the validity of numerous genomic assays; however, the severity and consequences of barcode swapping remain poorly understood. We have used two statistical approaches to robustly quantify the fraction of swapped reads in two plate-based single-cell RNA-sequencing datasets. We found that approximately 2.5% of reads were mislabelled between samples on the HiSeq 4000, which is lower than previous reports...
July 10, 2018: Nature Communications
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