• Login
    View Item 
    •   Home
    • Research
    • Articles
    • View Item
    •   Home
    • Research
    • Articles
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Browse

    All of KAUSTCommunitiesIssue DateSubmit DateThis CollectionIssue DateSubmit Date

    My Account

    Login

    Quick Links

    Open Access PolicyORCID LibguidePlumX LibguideSubmit an Item

    Statistics

    Display statistics

    A cross strain Plasmodium falciparum microarray optimized for the transcriptome analysis of Plasmodium falciparum patient derived isolates

    • CSV
    • RefMan
    • EndNote
    • BibTex
    • RefWorks
    Thumbnail
    Name:
    1-s2.0-S2213596016300939-main.pdf
    Size:
    1.094Mb
    Format:
    PDF
    Description:
    Main article
    Download
    Thumbnail
    Name:
    mmc1.pdf
    Size:
    772.7Kb
    Format:
    PDF
    Description:
    Supplemental files
    Download
    Thumbnail
    Name:
    mmc2.xlsx
    Size:
    2.014Mb
    Format:
    Microsoft Excel 2007
    Description:
    Supplemental files
    Download
    Thumbnail
    Name:
    mmc3.xlsx
    Size:
    350.2Kb
    Format:
    Microsoft Excel 2007
    Description:
    Supplemental files
    Download
    Thumbnail
    Name:
    mmc4.xlsx
    Size:
    33.93Kb
    Format:
    Microsoft Excel 2007
    Description:
    Supplemental files
    Download
    Thumbnail
    Name:
    mmc5.xlsx
    Size:
    29.13Kb
    Format:
    Microsoft Excel 2007
    Description:
    Supplemental files
    Download
    Thumbnail
    Name:
    mmc6.xlsx
    Size:
    22.44Kb
    Format:
    Microsoft Excel 2007
    Description:
    Supplemental files
    Download
    Thumbnail
    Name:
    mmc7.xlsx
    Size:
    24.30Kb
    Format:
    Microsoft Excel 2007
    Description:
    Supplemental files
    Download
    Thumbnail
    Name:
    mmc8.xlsx
    Size:
    15.93Kb
    Format:
    Microsoft Excel 2007
    Description:
    Supplemental files
    Download
    Thumbnail
    Name:
    mmc9.xlsx
    Size:
    407.3Kb
    Format:
    Microsoft Excel 2007
    Description:
    Supplemental files
    Download
    View more filesView fewer files
    Type
    Article
    Authors
    Subudhi, Amit
    Boopathi, P.A.
    Middha, Sheetal
    Acharya, Jyoti
    Rao, Sudha Narayana
    Mugasimangalam, Raja C.
    Sirohi, Paramendra
    Kochar, Sanjay K.
    Kochar, Dhanpat K.
    Das, Ashis
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Pathogen Genomics Group
    Date
    2016-07-21
    Online Publication Date
    2016-07-21
    Print Publication Date
    2016-09
    Permanent link to this record
    http://hdl.handle.net/10754/618192
    
    Metadata
    Show full item record
    Abstract
    Malarial parasite P. falciparum, an apicomplexan protozoan has a 23.3 MB nuclear genome and encodes ~ 5600 transcripts. The genetic diversity of the parasite within and across geographical zones is a challenge to gene expression studies which are essential for understanding of disease process, outcome and developing markers for diagnostics and prognostics. Here, we describe the strategy involved in designing a custom P. falciparum 15K array using the Agilent platform and Genotypic's Right Design methodology to study the transcriptome of Indian field isolates for which genome sequence information is limited. The array contains probes representing genome sequences of two distinct geographical isolates (i.e. 3D7 and HB3) and sub-telomeric var gene sequences of a third isolate (IT4) known to adhere in culture condition. Probes in the array have been selected based on their efficiency to detect transcripts through a 244K array experimentation. Array performance for the 15K array, was evaluated and validated using RNA materials from P. falciparum clinical isolates. A large percentage (91%) of the represented transcripts was detected from Indian P. falciparum patient isolates. Replicated probes and multiple probes representing the same gene showed perfect correlation between them suggesting good probe performance. Additional transcripts could be detected due to inclusion of unique probes representing HB3 strain transcripts. Variant surface antigen (VSA) transcripts were detected by optimized probes representing the VSA genes of three geographically distinct strains. The 15K cross strain P. falciparum array has shown good efficiency in detecting transcripts from P. falciparum parasite samples isolated from patients. The low parasite loads and presence of host RNA makes arrays a preferred platform for gene expression studies over RNA-Seq.
    Citation
    A cross strain Plasmodium falciparum microarray optimized for the transcriptome analysis of Plasmodium falciparum patient derived isolates 2016, 9:118 Genomics Data
    Sponsors
    We thank all the patients and technical workers for their participation in and support of this project. A.K.S. acknowledges Senior Research Fellowship from the Council of Scientific and Industrial Research (CSIR), New Delhi, India and Project Assistantship from Department of Biotechnology (DBT), New Delhi, India. P.A.B. acknowledges Basic Scientific Research fellowship from University Grant Commission, New Delhi, India and Project Assistantship from Department of Biotechnology (DBT), New Delhi, India. A.K.D., S.K.K. and D.K.K. acknowledges Department of Biotechnology (DBT), New Delhi, India for the financial support through the grant BT/PR7520/BRB/10/481/2006 and Birla Institute of Technology and Science, Pilani, India and S.P. Medical College, Bikaner, India for providing the required infrastructural facilities during this study. We thank the PlasmoDB team for making available the whole genome expression data for P. falciparum. We also thank Genotypic Technology Pvt. Ltd., Bangalore, India for the microarray hybridization service provided by them. We acknowledge National Institute of Allergy and Infectious Disease (NIAID), National Institute of Health (NIH) funded Genome Sequencing Center for Infectious Diseases at the Broad Institute for making available the HB3 genome sequence and annotation.
    Publisher
    Elsevier BV
    Journal
    Genomics Data
    DOI
    10.1016/j.gdata.2016.07.006
    Additional Links
    http://linkinghub.elsevier.com/retrieve/pii/S2213596016300939
    ae974a485f413a2113503eed53cd6c53
    10.1016/j.gdata.2016.07.006
    Scopus Count
    Collections
    Articles; Biological and Environmental Sciences and Engineering (BESE) Division

    entitlement

     
    DSpace software copyright © 2002-2021  DuraSpace
    Quick Guide | Contact Us | KAUST University Library
    Open Repository is a service hosted by 
    Atmire NV
     

    Export search results

    The export option will allow you to export the current search results of the entered query to a file. Different formats are available for download. To export the items, click on the button corresponding with the preferred download format.

    By default, clicking on the export buttons will result in a download of the allowed maximum amount of items. For anonymous users the allowed maximum amount is 50 search results.

    To select a subset of the search results, click "Selective Export" button and make a selection of the items you want to export. The amount of items that can be exported at once is similarly restricted as the full export.

    After making a selection, click one of the export format buttons. The amount of items that will be exported is indicated in the bubble next to export format.