DOCSLIB.ORG

Data from Expressed Sequence Tags from the Organs and Embryos Of

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Data from Expressed Sequence Tags from the Organs and Embryos Of Umemiya‑Shirafuji et al. BMC Res Notes (2021) 14:326 https://doi.org/10.1186/s13104‑021‑05740‑3 BMC Research Notes DATA NOTE Open Access Data from expressed sequence tags from the organs and embryos of parthenogenetic Haemaphysalis longicornis Rika Umemiya‑Shirafuji1* , Jinlin Zhou1,2, Min Liao1, Badgar Battsetseg1,3, Damdinsuren Boldbaatar1,4, Takeshi Hatta1,5,6, Thasaneeya Kuboki1,7, Takeshi Sakaguchi1, Huey Shy Chee1, Takeharu Miyoshi5, Xiaohong Huang5, Naotoshi Tsuji5,6, Xuenan Xuan1 and Kozo Fujisaki1 Abstract Objectives: Haemaphysalis longicornis is the most important tick species in Japan and has a wide range of vector capacity. Due to its veterinary and medical importance, this tick species has been used as a model for tick/vector biological studies. To identify the key molecules associated with physiological processes during blood feeding and embryogenesis, full‑length cDNA libraries were constructed using the fat body, hemocytes‑containing hemolymph, midgut, ovary and salivary glands of fed females and embryos of the laboratory colony of parthenogenetic H. longi- cornis. The sequences of cDNA from the salivary glands had been already released. However, the related information is still poor, and the other expressed sequence tags have not yet been deposited. Data description: A total of 39,113 expressed sequence tags were obtained and deposited at the DNA DataBank of Japan. There were 7745 sequences from embryos, 7385 from the fat body, 8303 from the hemolymph including hemocytes, 7385 from the midgut, and 8295 from the ovary. The data, including expressed sequence tags from the salivary glands was summarized into Microsoft Excel fles. Sharing this data resource with the tick research community will be valuable for the identifcation of novel genes and advance the progress of tick research. Keywords: Tick, Haemaphysalis longicornis, Embryo, Fat body, Hemolymph, Midgut, Ovary, Salivary glands, Expressed sequence tags, Full‑length cDNA library Objective vaccines or therapeutic agents against T. orientalis infec- Haemaphysalis longicornis is an important tick species, tion available at present in Japan. H. longicornis also and is a vector for various pathogens afecting humans occurs in Australia, New Zealand, New Caledonia, the and animals in Asia and Oceania. In the veterinary feld, Fiji Islands, Korea, China and Russia [1]. Although the the tick species is a major pest of cattle, because it can tick species was not detected outside of quarantine until spread Teileria orientalis, a protozoan parasite, which 2017, a heavy infestation of H. longicornis was recently causes piroplasmosis and produces economic losses reported in the United States [2]. H. longicornis is a vec- to livestock industry producers. Tere are no anti-tick tor of not only bovine piroplasmosis, but also canine babesiosis caused by Babesia parasites, and rickettsiosis and viral diseases in humans. Troughout its distribu- *Correspondence: [email protected] 1 National Research Center for Protozoan Diseases, Obihiro University tion, H. longicornis is an increasing threat to livestock of Agriculture and Veterinary Medicine, Inada‑Cho, Obihiro, Hokkaido animals and humans. 080‑8555, Japan Haemaphysalis longicornis has been used as a model Full list of author information is available at the end of the article for tick/vector studies. As a development platform for © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http:// creat iveco mmons. org/ licen ses/ by/4. 0/. The Creative Commons Public Domain Dedication waiver (http:// creat iveco mmons. org/ publi cdoma in/ zero/1. 0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Umemiya‑Shirafuji et al. BMC Res Notes (2021) 14:326 Page 2 of 4 novel control strategies, including anti-tick vaccines, hemocytes, midgut, and salivary glands were pooled for bio-acaricides and anti-protozoal drugs against ticks each organ. Te ovary samples were collected from both and tick-borne diseases, we have constructed full-length partially-engorged (four to fve-day-fed) and engorged cDNA libraries using laboratory-reared parthenogenetic female ticks, and pooled. Eggs laid at the third to fourth H. longicornis. Te expressed sequence tags (ESTs) in day after the onset of oviposition were collected and these libraries have made it possible to identify cDNA incubated at 28 °C for seven to eight days to develop. Te sequences which may be used to elucidate molecular samples were homogenized using a pestle in TRI reagent processes such as blood digestion, oxidative stress, apop- (Sigma-Aldrich, MO, USA). Total RNA extraction was tosis, reproduction, and survival [3–8]. Currently, only performed using TRI reagent, according to the manu- 8471 EST sequences of the salivary glands are available facturer’s protocol. cDNA was synthesized from 5 μg of in public databases [9]; information regarding the other total RNA using the G-Capping method [11], and ligated sequences has not been shared yet. Tis situation means into the plasmid vector pGCAP1. Te resulting plasmids that the extension and improvement of tick research is were transformed into Escherichia coli DH12S (Termo limited. Te data should be shared worldwide, because of Fisher Scientifc, MA, USA). A total of 10,000 recom- its veterinary and medical importance. binant transformants from the library were randomly selected for plasmid DNA purifcation and sequencing. Data description Te nucleotide sequences were determined using an Te full-length cDNA library was made using the vector- automated sequencer (ABI PRISM 310 Genetic Analyzer; capping method [11]. Te construction of each cDNA Termo Fisher Scientifc) and then analyzed for identity library has previously been reported [4, 5]. Te parthe- using the BLASTX program (National Center for Bio- nogenetic tick H. longicornis (Okayama strain) was main- technology Information (NCBI); https:// blast. ncbi. nlm. tained at the National Research Center for Protozoan nih. gov/ Blast. cgi). Te ESTs were constructed by random Diseases, Obihiro University of Agriculture and Veteri- partial sequencing of the 5’-terminal of the cDNA clones nary Medicine, and was fed on the ears of Japanese white from each cDNA library. rabbits (Japan SLC, Shizuoka, Japan) using the cotton A total of 39,113 ESTs obtained were deposited in bag method [10]. Female ticks which had been fed from the DNA DataBank of Japan (DDBJ) [12]. Te depos- three to four days (corresponding to the rapid feeding ited sequences contained 7745 ESTs from embryos stage) were dissected in cold phosphate-bufered saline (Table 1, Data fle 12) [13], 7385 from the fat body (137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM (Table 1, Data fle 7) [14], 8303 from the hemolymph KH2PO4, pH 7.4), and the fat body, hemolymph including including hemocytes (Table 1, Data fle 8) [15], 7385 Table 1 Overview of data fles/data sets Label Name of data fle/data set File types Data repository and identifer (DOI or accession number) (fle extension) Data fle 1 ESTs_Hl_Fat Body MS Excel fle (.xlsx) Obihiro University Archives of Knowledge (http:// doi. org/ 10. 24556/ 00004 700) [18] Data fle 2 ESTs_Hl_Hemolymph MS Excel fle (.xlsx) Obihiro University Archives of Knowledge (http:// doi. org/ 10. 24556/ 00004 701) [19] Data fle 3 ESTs_Hl_Midgut MS Excel fle (.xlsx) Obihiro University Archives of Knowledge (http:// doi. org/ 10. 24556/ 00004 702) [20] Data fle 4 ESTs_Hl_Ovary MS Excel fle (.xlsx) Obihiro University Archives of Knowledge (http:// doi. org/ 10. 24556/ 00004 703) [21] Data fle 5 ESTs_Hl_Salivary glands MS Excel fle (.xlsx) Obihiro University Archives of Knowledge (http:// doi. org/ 10. 24556/ 00004 704) [22] Data fle 6 ESTs_Hl_Embryo MS Excel fle (.xlsx) Obihiro University Archives of Knowledge (http:// doi. org/ 10. 24556/ 00004 705) [23] Data fle 7 Hl FB full‑length cDNA library FASTA DDBJ/ENA/GenBank (Accession numbers: HY961648‑HY969032) https:// ident ifers. org/ ncbi/ insdc: HY961 648 [14] Data fle 8 Hl HE full‑length cDNA library FASTA DDBJ/ENA/GenBank (Accession numbers: HY969033‑HY977335) https:// ident ifers. org/ ncbi/ insdc: HY969 033 [15] Data fle 9 Hl MG full‑length cDNA library FASTA DDBJ/ENA/GenBank (Accession numbers: HY977336‑HY984720) https:// ident ifers. org/ ncbi/ insdc: HY977 336 [16] Data fle 10 Hl OV full‑length cDNA library FASTA DDBJ/ENA/GenBank (Accession numbers: HY984721‑HY993015) https:// ident ifers. org/ ncbi/ insdc: HY984 721 [17] Data fle 11 Hl Sg full‑length cDNA library FASTA DDBJ/ENA/GenBank (Accession numbers: DC574924‑DC583394) https:// ident ifers. org/ ncbi/ insdc: DC574 924 [9] Data fle 12 Hl EM full‑length cDNA library FASTA DDBJ/ENA/GenBank (Accession numbers: HY953903‑HY961647) https:// ident ifers. org/ ncbi/ insdc: HY953 903 [13] Umemiya‑Shirafuji et al. BMC Res Notes (2021) 14:326 Page 3 of 4 from the midgut (Table 1, Data fle 9) [16], and 8295 Abbreviations BLAST: Basic Local Alignment Search Tool; DDBJ: DNA DataBank of Japan; ENA: from the ovary (Table 1, Data fle 10) [17]. Sample European Nucleotide Archive; EST: Expressed sequence tag; NCBI: National information was deposited in the DDBJ BioSample Center for Biotechnology Information. database (Table 1, Data fles 7–10 and 12) [13–17].
Load more

Recommended publications
  • Genbank Dennis A
    D48–D53 Nucleic Acids Research, 2012, Vol. 40, Database issue Published online 5 December 2011 doi:10.1093/nar/gkr1202 GenBank Dennis A. Benson, Ilene Karsch-Mizrachi, Karen Clark, David J. Lipman, James Ostell and Eric W. Sayers* National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA Received September 30, 2011; Revised November 14, 2011; Accepted November 17, 2011 ABSTRACT sequence (GSS), whole-genome shotgun (WGS) and Õ other high-throughput data from sequencing centers. GenBank is a comprehensive database that The US Office of Patents and Trademarks also contributes contains publicly available nucleotide sequences sequences from issued patents. GenBank participates with for more than 250 000 formally described species. the EMBL Nucleotide Sequence Database (EMBL-Bank), Downloaded from These sequences are obtained primarily through part of the European Nucleotide Archive (ENA) (2), and submissions from individual laboratories and batch the DNA Data Bank of Japan (DDBJ) (3) as a partner submissions from large-scale sequencing projects, in the International Nucleotide Sequence Database including whole-genome shotgun (WGS) and envir- Collaboration (INSDC). The INSDC partners exchange onmental sampling projects. Most submissions data daily to ensure that a uniform and comprehensive http://nar.oxfordjournals.org/ are made using the web-based BankIt or standalone collection of sequence information is available worldwide. Sequin programs, and accession numbers are NCBI makes the GenBank data available at no cost over the Internet, through FTP and a wide range of web-based assigned by GenBank staff upon receipt. Daily data retrieval and analysis services (4).
    [Show full text]
  • Rapid Evolution and Selection Inferred from the Transcriptomes of Sympatric Crater Lake Cichlid Fishes
    Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes K. R. ELMER, S. FAN, H. M. GUNTER, J. C. JONES, S. BOEKHOFF, S. KURAKU and A. MEYER Lehrstuhl fUr Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitiitstrasse 10, 78457 Konstanz, Germany Abstract Crater lakes provide a natural laboratory to study speciation of cichlid fishes by ecological divergence. Up to now, there has been a dearth of transcriptomic and genomic information that would aid in understanding the molecular basis of the phenotypic differentiation between young species. We used next-generation sequencing (Roche 454 massively parallel pyrosequencing) to characterize the diversity of expressed sequence tags between ecologically divergent, endemic and sympatric species of cichlid fishes from crater lake Apoyo, Nicaragua: benthic Amphilophus astorquii and limnetic Amphilophus zaliosus. We obtained 24174 A. astorquii and 21382 A. zaliosus high­ quality expressed sequence tag contigs, of which 13 106 pairs are orthologous between species. Based on the ratio of non synonymous to synonymous substitutions, we identified six sequences exhibiting signals of strong diversifying selection (KalKs > 1). These included genes involved in biosynthesis, metabolic processes and development. This transcriptome sequence variation may be reflective of natural selection acting on the genomes of these young, sympatric sister species. Based on Ks ratios and p-distances between 3'-untranslated regions (UTRs) calibrated to previously published species divergence times, we estimated a neutral transcriptome-wide substitutional mutation rate of ~1.25 x 10-6 per site per year. We conclude that next-generation sequencing technologies allow us to infer natural selection acting to diversify the genomes of young species, such as crater lake cichlids, with much greater scope than previously possible.
    [Show full text]
  • Genomic Approaches to Research in Lung Cancer Edward Gabrielson the Johns Hopkins University School of Medicine, Baltimore, USA
    http://respiratory-research.com/content/1/1/036 Review Genomic approaches to research in lung cancer Edward Gabrielson The Johns Hopkins University School of Medicine, Baltimore, USA Received: 21 April 2000 Respir Res 2000, 1:36–39 Revisions requested: 11 May 2000 The electronic version of this article can be found online at Revisions received: 1 June 2000 http://respiratory-research.com/content/1/1/036 Accepted: 1 June 2000 Published: 23 June 2000 © Current Science Ltd (Print ISSN 1465-9921; Online ISSN 1465-993X) Abstract The medical research community is experiencing a marked increase in the amount of information available on genomic sequences and genes expressed by humans and other organisms. This information offers great opportunities for improving our understanding of complex diseases such as lung cancer. In particular, we should expect to witness a rapid increase in the rate of discovery of genes involved in lung cancer pathogenesis and we should be able to develop reliable molecular criteria for classifying lung cancers and predicting biological properties of individual tumors. Achieving these goals will require collaboration by scientists with specialized expertise in medicine, molecular biology, and decision-based statistical analysis. Keywords: cDNA arrays, genomics, lung cancer Introduction those diseases. Knowing the polymorphisms that make Genomics – the discipline that characterizes the struc- each of us unique individuals could be the key in the future tural and functional anatomy of the genome – has to predicting individual risks for developing disease and attracted continuously increased interest and invest- individual responses to pharmacological agents. However, ment over the past decade. The complete sequencing the full impact of genomics on medical research is still of the human genome is expected within a few years; unknown.
    [Show full text]
  • Comparative Transcriptomes and Development of Expressed Sequence Tag-Simple Sequence Repeat Markers for Two Closely Related Oak Species
    Journal of Systematics JSE and Evolution doi: 10.1111/jse.12469 Research Article Comparative transcriptomes and development of expressed sequence tag-simple sequence repeat markers for two closely related oak species Jing-Jing Sun1, Tao Zhou2, Rui-Ting Zhang1, Yun Jia1, Yue-Mei Zhao3, Jia Yang1, and Gui-Fang Zhao1* 1Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China 2School of Pharmary, Xi’an Jiaotong University, Xi’an 710061, China 3College of Biopharmaceutical and Food Engineering, Shangluo University, Shangluo 726000, Shaanxi, China *Author for correspondence. E-mail: [email protected]. Tel.: 86-29-88305264. Fax: 86-29-88303572. Received 1 December 2017; Accepted 7 October 2018; Article first published online11 xx November Month 2018 2018 Abstract Quercus species comprise the major genera in the family Fagaceae and they are widely distributed in the Northern Hemisphere. Many Quercus species, including several endemics, are distributed in China. Genetic resources have been established for the important genera but few transcriptomes are available for Quercus species in China. In this study, we used Illumina paired-end sequencing to obtain the transcriptomes of two oak species, Q. liaotungensis Koidz. and Q. mongolica Fisch. ex Turcz. Approximately 24 million reads were generated and then a total of 103 618 unigenes were obtained after assembly for both species. Comparative transcriptome analyses of both species identified a total of 12 981 orthologous contigs. The Ka/Ks estimation and enrichment analysis indicated that 1179 (9.08%) orthologs showed rapid evolution, and most of these orthologs were related to functions comprising “DNA repair”, “response to cold”, and “response to drought”.
    [Show full text]
  • Characterization of an EST Database for the Perennial Weed Leafy Spurge: an Important Resource for Weed Biology Research James V
    Weed Science 2007 55:193–203 Characterization of an EST Database for the Perennial Weed Leafy Spurge: An Important Resource for Weed Biology Research James V. Anderson, David P. Horvath, Wun S. Chao, Michael E. Foley, Alvaro G. Hernandez, Jyothi Thimmapuram, Lie Liu, George L. Gong, Mark Band, Ryan Kim, and Mark A. Mikel* Genomics programs in the weed science community have not developed as rapidly as that of other crop, horticultural, forestry, and model plant systems. Development of genomic resources for selected model weeds are expected to enhance our understanding of weed biology, just as they have in other plant systems. In this report, we describe the development, characteristics, and information gained from an expressed sequence tag (EST) database for the perennial weed leafy spurge. ESTs were obtained using a normalized cDNA library prepared from a comprehensive collection of tissues. During the EST characterization process, redundancy was minimized by periodic subtractions of the normalized cDNA library. A sequencing success rate of 88% yielded 45,314 ESTs with an average read length of 671 nucleotides. Using bioinformatic analysis, the leafy spurge EST database was assembled into 23,472 unique sequences representing 19,015 unigenes (10,293 clusters and 8,722 singletons). Blast similarity searches to the GenBank nonredundant protein database identified 18,186 total matches, of which 14,205 were nonredundant. These data indicate that 77.4% of the 23,472 unique sequences and 74.7% of the 19,015 unigenes are similar to other known proteins. Further bioinformatics analysis indicated that 2,950, or 15.5%, of the unigenes have previously not been identified suggesting that some may be novel to leafy spurge.
    [Show full text]
  • Navigating the Human Transcriptome
    Commentary Navigating the human transcriptome Robert L. Strausberg*† and Gregory J. Riggins‡ Cancer Genomics Office, National Cancer Institute, Bethesda, MD 20892; and ‡Departments of Pathology and Genetics, Duke University Medical Center, Durham, NC 27710 he potential coding capacity of the hu- mouse ESTs. Each project has produced Research (FAPESP͞LICR)-Human Can- Tman genome is currently a topic of great cDNA libraries based on the use primers for cer Genome Project (13). The power of interest. The number of genes predicted first-strand synthesis that are anchored at ORESTES is that a high proportion of the from the recent human-genome analysis the 3Ј transcript end [the poly(A) sequence]. sequence tags are in the coding regions of was at the lower end of previous estimates, Sometimes, the resulting cDNA molecules transcripts (see Fig. 1). In the ORESTES which had ranged between about 30,000 and represent the entire transcript. More often, approach, low-stringency PCR conditions 120,000 (1, 2). Whereas estimates of gene they are incomplete, either because of are used to produce cDNA libraries from number are likely to increase based on ad- mRNA degradation or incomplete enzy- which a relatively small number of individ- ditional experimental evidence and im- matic processing during conversion of ual clones are sequenced. Several thousand proved gene-finding algorithms, it is clear mRNA to cDNA. Thus, for a given tran- ORESTES libraries have been produced, that gene number is only one mechanism for script, there might be several different forms each with different primers, such that each creating the genetic diversity required to of cDNA in the library.
    [Show full text]
  • Patentability of Expressed Sequence Tags Joshua Kim
    Hastings Communications and Entertainment Law Journal Volume 29 | Number 3 Article 3 1-1-2007 Fisher of Genes: Patentability of Expressed Sequence Tags Joshua Kim Follow this and additional works at: https://repository.uchastings.edu/ hastings_comm_ent_law_journal Part of the Communications Law Commons, Entertainment, Arts, and Sports Law Commons, and the Intellectual Property Law Commons Recommended Citation Joshua Kim, Fisher of Genes: Patentability of Expressed Sequence Tags, 29 Hastings Comm. & Ent. L.J. 401 (2007). Available at: https://repository.uchastings.edu/hastings_comm_ent_law_journal/vol29/iss3/3 This Note is brought to you for free and open access by the Law Journals at UC Hastings Scholarship Repository. It has been accepted for inclusion in Hastings Communications and Entertainment Law Journal by an authorized editor of UC Hastings Scholarship Repository. For more information, please contact [email protected]. Fisher of Genes: Patentability of Expressed Sequence Tags by JOSHUA KIM* I. Introduction .................................................................................................. 40 1 II. ESTs: Significance in Biotechnology ...................................................... 402 III. History of Patent Status of ESTs .............................................................. 404 IV . In re F isher .............................................................................................. 406 V . F isher A nalysis .......................................................................................
    [Show full text]
  • In Silico Gene Expression Analysis–An Overview
    Molecular Cancer BioMed Central Review Open Access In silico gene expression analysis – an overview David Murray1, Peter Doran1, Padraic MacMathuna2 and Alan C Moss*3 Address: 1General Clinical Research Unit, UCD School of Medicine and Medical Sciences, Mater Misericordiae University Hospital, Dublin 7, Ireland, 2Gastrointestinal Unit, Mater Misericordiae University Hospital, Dublin 7, Ireland and 3Division of Gastroenterology, Beth Israel Deaconess Medical Center, 330 Brookline Ave, Boston, MA 02215, USA Email: David Murray - [email protected]; Peter Doran - [email protected]; Padraic MacMathuna - [email protected]; Alan C Moss* - [email protected] * Corresponding author Published: 7 August 2007 Received: 27 June 2007 Accepted: 7 August 2007 Molecular Cancer 2007, 6:50 doi:10.1186/1476-4598-6-50 This article is available from: http://www.molecular-cancer.com/content/6/1/50 © 2007 Murray et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Efforts aimed at deciphering the molecular basis of complex disease are underpinned by the availability of high throughput strategies for the identification of biomolecules that drive the disease process. The completion of the human genome-sequencing project, coupled to major technological developments, has afforded investigators myriad opportunities for multidimensional analysis of biological systems. Nowhere has this research explosion been more evident than in the field of transcriptomics. Affordable access and availability to the technology that supports such investigations has led to a significant increase in the amount of data generated.
    [Show full text]
  • Training Modules Documentation Release 1
    training_modules Documentation Release 1 Marc B Rossello Sep 24, 2021 ENA Data Submission 1 General Guide on ENA Data Submission3 2 How to Register a Study 29 3 How to Register Samples 35 4 Preparing Files for Submission 47 5 How to Submit Raw Reads 83 6 How to Submit Assemblies 103 7 How to Submit Targeted Sequences 145 8 How to Submit Other Analyses 161 9 General Guide on ENA Data Retrieval 183 10 Updating Metadata Objects 223 11 Updating Assemblies 231 12 Updating Annotated Sequences 233 13 Data Release Policies 235 14 Common Run Submission Errors 237 15 Common Sample Submission Errors 243 16 Tips for Sample Taxonomy 245 17 Requesting New Taxon IDs 249 18 Metagenome Submission Queries 255 19 Locus Tag Prefixes 261 20 Archive Generated FASTQ Files 263 i 21 Third Party Tools 269 22 Introductory Webinar 271 ii training_modules Documentation, Release 1 Welcome to the guidelines for submission and retrieval for the European Nucleotide Archive. Please use the links to find instructions specific to your needs. If you’re completely new to ENA, you can see an introductory webinar at the bottom of the page. ENA Data Submission 1 training_modules Documentation, Release 1 2 ENA Data Submission CHAPTER 1 General Guide on ENA Data Submission Welcome to the general guide for the European Nucleotide Archive submission. Please take a moment to view this introduction and consider the options available to you before you begin your submission. ENA allows submissions via three routes, each of which is appropriate for a different set of submission types.
    [Show full text]
  • Searching Expressed Sequence Tag Databases: Discovery and Confirmation of a Common Polymorphism in the Thymidylate Synthase Gene1
    Vol. 9, 1381–1385, December 2000 Cancer Epidemiology, Biomarkers & Prevention 1381 Short Communication Searching Expressed Sequence Tag Databases: Discovery and Confirmation of a Common Polymorphism in the Thymidylate Synthase Gene1 Cornelia M. Ulrich,2 Jeannette Bigler, Introduction Christine M. Velicer, Elizabeth A. Greene, As part of the human genome project, terabytes of sequence Federico M. Farin, and John D. Potter information are stored in public databases. ESTs3 comprise Cancer Prevention Research Program [C. M. U., J. B., C. M. V., J. D. P.] and much of the available data; they are partial cDNA sequences Biocomputing Shared Resource [E. A. G.], Fred Hutchinson Cancer Research that have been generated from many different tissues. ESTs Center, Seattle, Washington 98109, and Department of Epidemiology reflect some or all of the transcribed sequence of a gene, which [C. M. U., C. M. V., J. D. P.] and Department of Environmental Health, Center Ј Ј for Ecogenetics and Environmental Health [F. M. F.], University of includes the coding sequence as well as 5 - and 3 -UTRs. Washington, Seattle, Washington 98195 Currently, the EST database for humans contains more than one million entries and is publicly available.4 As demonstrated by others (1–4), this resource is a rich source for identifying genetic variations. Whereas most of these researchers used a Abstract broad search pattern, it is possible to direct screening of ESTs Databases of expressed sequence tags (EST) can be used to specific proteins of physiological interest. On the basis of to screen rapidly for potential polymorphisms in findings linking folate availability to carcinogenesis, our inter- candidate proteins.
    [Show full text]
  • Transcriptomics in the RNA-Seq Era
    Available online at www.sciencedirect.com Transcriptomics in the RNA-seq era Paul A McGettigan The transcriptomics field has developed rapidly with the generated by these technologies has generated problems advent of next-generation sequencing technologies. RNA-seq both of data management and storage as well as posing has now displaced microarrays as the preferred method for novel analytical problems. gene expression profiling.The comprehensive nature of the data generated has been a boon in terms of transcript Although the transcriptome can encompass many species identification but analysis challenges remain. Key among of RNA (miRNA, snoRNA, etc.) this review will focus these problems is the development of suitable expression mainly on mRNAs, specifically mammalian mRNAs. metrics for expression level comparisons and methods for Readers can find good reviews of the advances that have identification of differentially expressed genes (and exons). been made in nonmammalian and noneukaryotic tran- Several approaches have been developed but as yet no scriptomics in other locations [4,5]. consensus exists on the best pipeline to use.De novo transcriptome approaches are increasingly viable for In contemporary multidisciplinary projects global tran- organisms lacking a sequenced genome. The reduction in scription profiling is frequently the first ‘omics technology starting RNA required has enabled the development of to be applied. It generates information about which genes new applications such as single cell transcriptomics.The are expressed, at what level and can also provide infor- emerging picture of mammalian transcription is complex mation about different transcript isoforms used. A pre- with further refinement expected with the integration of liminary analysis via microarray or RNA-seq can indicate epigenomic data generated by projects such as the appropriateness or usefulness of other ‘omics tech- ENCODE.
    [Show full text]
  • The European Nucleotide Archive
    D28–D31 Nucleic Acids Research, 2011, Vol. 39, Database issue Published online 23 October 2010 doi:10.1093/nar/gkq967 The European Nucleotide Archive Rasko Leinonen*, Ruth Akhtar, Ewan Birney, Lawrence Bower, Ana Cerdeno-Ta´ rraga, Ying Cheng, Iain Cleland, Nadeem Faruque, Neil Goodgame, Richard Gibson, Gemma Hoad, Mikyung Jang, Nima Pakseresht, Sheila Plaister, Rajesh Radhakrishnan, Kethi Reddy, Siamak Sobhany, Petra Ten Hoopen, Robert Vaughan, Vadim Zalunin and Guy Cochrane European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Received September 15, 2010; Accepted October 3, 2010 ABSTRACT archived nucleotide data. All primary data in the INSDC belongs to the submitters and can only be The European Nucleotide Archive (ENA; http://www updated with submitter consent. For full policy details .ebi.ac.uk/ena) is Europe’s primary nucleotide- please refer to: http://www.insdc.org/policy.html. sequence repository. The ENA consists of three main databases: the Sequence Read Archive (SRA), the Trace Archive and EMBL-Bank. The ob- CONTENT jective of ENA is to support and promote the use of In October 2010, the ENA contained 500 billion raw and nucleotide sequencing as an experimental research assembled sequences consisting of 50 trillion base pairs. platform by providing data submission, archive, In the last 3 years, the next-generation sequence reads search and download services. In this article, we stored in the Sequence Read Archive (SRA) have outline these services and describe major changes become the largest and fastest growing source of new and improvements introduced during 2010. These data accounting now for 95% of all base pairs made available by ENA.
    [Show full text]