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W Miachel Hanson, Zhe Chen, Laurie K Jackson, Meriem Attaf, Andrew K Sewell, Jennifer M Heemstra, John D Phillips
Next-generation sequencing (NGS) has proven to be an exceptionally powerful tool for studying genetic variation and differences in gene expression profiles between cell populations. However, these population-wide studies are limited by their inability to detect variation between individual cells within a population, inspiring the development of single-cell techniques such as Drop-seq, which add a unique barcode to the mRNA from each cell prior to sequencing. Current Drop-seq technology enables capture, amplification, and barcoding of the entire mRNA transcriptome of individual cells...
September 7, 2016: Journal of the American Chemical Society
Xiao Huo, Sheng'en Hu, Chengchen Zhao, Yong Zhang
MOTIVATION: Drop-seq has recently emerged as a powerful technology to analyze gene expression from thousands of individual cells simultaneously. Currently, Drop-seq technology requires refinement and quality control (QC) steps are critical for such data analysis. There is a strong need for a convenient and comprehensive approach to obtain dedicated QC and to determine the relationships between cells for ultra-high-dimensional datasets. RESULTS: We developed Dr.seq, a QC and analysis pipeline for Drop-seq data...
July 15, 2016: Bioinformatics
Anthony Hickey, Caroline Esnault, Anasuya Majumdar, Atreyi Ghatak Chatterjee, James R Iben, Philip G McQueen, Andrew X Yang, Takeshi Mizuguchi, Shiv I S Grewal, Henry L Levin
Transposable elements (TEs) constitute a substantial fraction of the eukaryotic genome and, as a result, have a complex relationship with their host that is both adversarial and dependent. To minimize damage to cellular genes, TEs possess mechanisms that target integration to sequences of low importance. However, the retrotransposon Tf1 of Schizosaccharomyces pombe integrates with a surprising bias for promoter sequences of stress-response genes. The clustering of integration in specific promoters suggests that Tf1 possesses a targeting mechanism that is important for evolutionary adaptation to changes in environment...
November 2015: Genetics
Hongzheng Sun, Ting Peng, Yafan Zhao, Yanxiu Du, Jing Zhang, Junzhou Li, Zeyu Xin, Quanzhi Zhao
Poor grain filling of inferior grains located on lower secondary panicle branch causes great drop in rice yield and quality. Dynamic gene expression patterns between superior and inferior grains were examined from the view of the whole transcriptome by using RNA-Seq method. In total, 19,442 genes were detected during rice grain development. Genes involved in starch synthesis, grain storage and grain development were interrogated in particular in superior and inferior grains. Of the genes involved in sucrose to starch transformation process, most were expressed at lower level in inferior grains at early filling stage compared to that of superior grains...
2015: PloS One
Jae-Woong Min, Woo Jin Kim, Jeong A Han, Yu-Jin Jung, Kyu-Tae Kim, Woong-Yang Park, Hae-Ock Lee, Sun Shim Choi
Single-cell sequencing, which is used to detect clinically important tumor subpopulations, is necessary for understanding tumor heterogeneity. Here, we analyzed transcriptomic data obtained from 34 single cells from human lung adenocarcinoma (LADC) patient-derived xenografts (PDXs). To focus on the intrinsic transcriptomic signatures of these tumors, we filtered out genes that displayed extensive expression changes following xenografting and cell culture. Then, we performed clustering analysis using co-regulated gene modules rather than individual genes to minimize read drop-out errors associated with single-cell sequencing...
2015: PloS One
Zixia Huang, Aurore Gallot, Nga T Lao, Sébastien J Puechmaille, Nicole M Foley, David Jebb, Michaël Bekaert, Emma C Teeling
The acquisition of tissue samples from wild populations is a constant challenge in conservation biology, especially for endangered species and protected species where nonlethal sampling is the only option. Whole blood has been suggested as a nonlethal sample type that contains a high percentage of bodywide and genomewide transcripts and therefore can be used to assess the transcriptional status of an individual, and to infer a high percentage of the genome. However, only limited quantities of blood can be nonlethally sampled from small species and it is not known if enough genetic material is contained in only a few drops of blood, which represents the upper limit of sample collection for some small species...
January 2016: Molecular Ecology Resources
Assaf Rotem, Oren Ram, Noam Shoresh, Ralph A Sperling, Michael Schnall-Levin, Huidan Zhang, Anindita Basu, Bradley E Bernstein, David A Weitz
The importance of single-cell level data is increasingly appreciated, and significant advances in this direction have been made in recent years. Common to these technologies is the need to physically segregate individual cells into containers, such as wells or chambers of a micro-fluidics chip. High-throughput Single-Cell Labeling (Hi-SCL) in drops is a novel method that uses drop-based libraries of oligonucleotide barcodes to index individual cells in a population. The use of drops as containers, and a microfluidics platform to manipulate them en-masse, yields a highly scalable methodological framework...
2015: PloS One
Evan Z Macosko, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, Allison R Bialas, Nolan Kamitaki, Emily M Martersteck, John J Trombetta, David A Weitz, Joshua R Sanes, Alex K Shalek, Aviv Regev, Steven A McCarroll
Cells, the basic units of biological structure and function, vary broadly in type and state. Single-cell genomics can characterize cell identity and function, but limitations of ease and scale have prevented its broad application. Here we describe Drop-seq, a strategy for quickly profiling thousands of individual cells by separating them into nanoliter-sized aqueous droplets, associating a different barcode with each cell's RNAs, and sequencing them all together. Drop-seq analyzes mRNA transcripts from thousands of individual cells simultaneously while remembering transcripts' cell of origin...
May 21, 2015: Cell
Vita Maria Cristiana Moliterni, Roberta Paris, Chiara Onofri, Luigi Orrù, Luigi Cattivelli, Daniela Pacifico, Carla Avanzato, Alberto Ferrarini, Massimo Delledonne, Giuseppe Mandolino
Major metabolic pathways and genes affected by low-temperature treatment were identified and a thorough picture of the early transcriptional changes in sugar beet plantlets upon cold stress was given. Sugar beet (Beta vulgaris L.) is an important source of sugar and bioethanol production in temperate areas worldwide. In these areas, plantlet survival and sucrose yield of mature plants can be seriously limited by low temperatures, especially when plantlets are exposed to freezing temperatures (below 0 °C) at the early developmental stages...
July 2015: Planta
Jeffery Li, Travers Ching, Sijia Huang, Lana X Garmire
BACKGROUND: Epigenetic alterations are known to correlate with changes in gene expression among various diseases including cancers. However, quantitative models that accurately predict the up or down regulation of gene expression are currently lacking. METHODS: A new machine learning-based method of gene expression prediction is developed in the context of lung cancer. This method uses the Illumina Infinium HumanMethylation450K Beadchip CpG methylation array data from paired lung cancer and adjacent normal tissues in The Cancer Genome Atlas (TCGA) and histone modification marker CHIP-Seq data from the ENCODE project, to predict the differential expression of RNA-Seq data in TCGA lung cancers...
2015: BMC Bioinformatics
Shanrong Zhao, Baohong Zhang
BACKGROUND: RNA-Seq has become increasingly popular in transcriptome profiling. One aspect of transcriptome research is to quantify the expression levels of genomic elements, such as genes, their transcripts and exons. Acquiring a transcriptome expression profile requires genomic elements to be defined in the context of the genome. Multiple human genome annotation databases exist, including RefGene (RefSeq Gene), Ensembl, and the UCSC annotation database. The impact of the choice of an annotation on estimating gene expression remains insufficiently investigated...
2015: BMC Genomics
Ayalew Mentewab, Kinnari Matheson, Morayo Adebiyi, Shanice Robinson, Brianna Elston
Plants are exposed to antibiotics produced by soil microorganisms, but little is known about their responses at the transcriptional level. Likewise, few endogenous mechanisms of antibiotic resistance have been reported. The Arabidopsis thaliana ATP Binding Cassette (ABC) transporter AtWBC19 (ABCG19) is known to confer kanamycin resistance, but the exact mechanism of resistance is not well understood. Here we examined the transcriptomes of control seedlings and wbc19 mutant seedlings using RNA-seq analysis. Exposure to kanamycin indicated changes in the organization of the photosynthetic apparatus, metabolic fluxes and metal uptake...
2014: PloS One
Guohui Huang, Tong Li, Xinyue Li, Dongmei Tan, Zhongyu Jiang, Yun Wei, Juncai Li, Aide Wang
The fruit of Pyrus ussuriensis is typically climacteric. During ripening, the fruits produce a large amount of ethylene, and their firmness drops rapidly. Although the molecular basis of climacteric fruit ripening has been studied in depth, some aspects remain unclear. Here, we compared the transcriptomes of pre- and post-climacteric fruits of Chinese pear (P. ussuriensis c.v. Nanguo) using RNA-seq. In total, 3,279 unigenes were differentially expressed between the pre- and post-climacteric fruits. Differentially expressed genes (DEGs) were subjected to Gene Ontology analysis, and 31 categories were significantly enriched in the groups 'biological process', 'molecular function' and 'cellular component'...
2014: PloS One
Jihoon Kim, Eric Levy, Alex Ferbrache, Petra Stepanowsky, Claudiu Farcas, Shuang Wang, Stefan Brunner, Tyler Bath, Yuan Wu, Lucila Ohno-Machado
SUMMARY: MAGI is a web service for fast MicroRNA-Seq data analysis in a graphics processing unit (GPU) infrastructure. Using just a browser, users have access to results as web reports in just a few hours->600% end-to-end performance improvement over state of the art. MAGI's salient features are (i) transfer of large input files in native FASTA with Qualities (FASTQ) format through drag-and-drop operations, (ii) rapid prediction of microRNA target genes leveraging parallel computing with GPU devices, (iii) all-in-one analytics with novel feature extraction, statistical test for differential expression and diagnostic plot generation for quality control and (iv) interactive visualization and exploration of results in web reports that are readily available for publication...
October 2014: Bioinformatics
Jing Qin, Yaohua Hu, Feng Xu, Hari Krishna Yalamanchili, Junwen Wang
Inferring gene regulatory networks from gene expression data at whole genome level is still an arduous challenge, especially in higher organisms where the number of genes is large but the number of experimental samples is small. It is reported that the accuracy of current methods at genome scale significantly drops from Escherichia coli to Saccharomyces cerevisiae due to the increase in number of genes. This limits the applicability of current methods to more complex genomes, like human and mouse. Least absolute shrinkage and selection operator (LASSO) is widely used for gene regulatory network inference from gene expression profiles...
June 1, 2014: Methods: a Companion to Methods in Enzymology
Bryan A Bailey, Rachel L Melnick, Mary D Strem, Jayne Crozier, Jonathan Shao, Richard Sicher, Wilberth Phillips-Mora, Shahin S Ali, Dapeng Zhang, Lyndel Meinhardt
Frosty pod rot (FPR) of Theobroma cacao (cacao) is caused by the hemibiotrophic fungus Moniliophthora roreri. Cacao clones tolerant to FPR are being planted throughout Central America. To determine whether M. roreri shows a differential molecular response during successful infections of tolerant clones, we collected field-infected pods at all stages of symptomatology for two highly susceptible clones (Pound-7 and CATIE-1000) and three tolerant clones (UF-273, CATIE-R7 and CATIE-R4). Metabolite analysis was carried out on clones Pound-7, CATIE-1000, CATIE-R7 and CATIE-R4...
September 2014: Molecular Plant Pathology
Steven R Head, H Kiyomi Komori, Sarah A LaMere, Thomas Whisenant, Filip Van Nieuwerburgh, Daniel R Salomon, Phillip Ordoukhanian
High-throughput sequencing, also known as next-generation sequencing (NGS), has revolutionized genomic research. In recent years, NGS technology has steadily improved, with costs dropping and the number and range of sequencing applications increasing exponentially. Here, we examine the critical role of sequencing library quality and consider important challenges when preparing NGS libraries from DNA and RNA sources. Factors such as the quantity and physical characteristics of the RNA or DNA source material as well as the desired application (i...
2014: BioTechniques
Matthew E Johnson, Sandra Deliard, Fengchang Zhu, Qianghua Xia, Andrew D Wells, Kurt D Hankenson, Struan F A Grant
Genome-wide association studies (GWAS) have demonstrated that genetic variation at the MADS box transcription enhancer factor 2, polypeptide C (MEF2C) locus is robustly associated with bone mineral density, primarily at the femoral neck. MEF2C is a transcription factor known to operate via the Wnt signaling pathway. Our hypothesis was that MEF2C regulates the expression of a set of molecular pathways critical to skeletal function. Drawing on our laboratory and bioinformatic experience with ChIP-seq, we analyzed ChIP-seq data for MEF2C available via the ENCODE project to gain insight in to its global genomic binding pattern...
April 2014: Calcified Tissue International
Qu Zhang, Jun Zhang, Hong Jin, Sitong Sheng
BACKGROUND: The accumulation of somatic mutations in genes and molecular pathways is a major factor in the evolution of oral squamous cell carcinoma (OSCC), which sparks studies to identify somatic mutations with clinical potentials. Recently, massively parallel sequencing technique has started to revolutionize biomedical studies, due to the rapid increase in its throughput and drop in cost. Hence sequencing of whole transcriptome (RNA-Seq) becomes a superior approach in cancer studies, which enables the detection of somatic mutations and accurate measurement of gene expression simultaneously...
2013: BMC Medical Genomics
Ching Yong Yick, Aeilko H Zwinderman, Peter W Kunst, Katrien Grünberg, Thais Mauad, Kees Fluiter, Elisabeth H Bel, René Lutter, Frank Baas, Peter J Sterk
RATIONALE: Glucocorticoids are the mainstay of asthma therapy. However, it is unclear whether the benefits of glucocorticoids in asthma are merely based on antiinflammatory properties. Glucocorticoids may also alter gene expression of airway smooth muscle (ASM). We hypothesized that the gene expression profile of the ASM layer in endobronchial biopsies of patients with asthma is altered by oral glucocorticoid therapy as compared with placebo. OBJECTIVES: First, we investigated the change in ASM transcriptomic profile in endobronchial biopsies after 14 days of oral glucocorticoid therapy...
May 15, 2013: American Journal of Respiratory and Critical Care Medicine
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