Profiling of Differentially Expressed Genes Using Suppression Subtractive Hybridization in an Equine Model of Chronic Asthma
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{"title"=>"Profiling of Differentially Expressed Genes Using Suppression Subtractive Hybridization in an Equine Model of Chronic Asthma", "type"=>"journal", "authors"=>[{"first_name"=>"Jean-Pierre", "last_name"=>"Lavoie"}, {"first_name"=>"Josiane", "last_name"=>"Lefebvre-Lavoie"}, {"first_name"=>"Mathilde", "last_name"=>"Leclere"}, {"first_name"=>"Anouk", "last_name"=>"Lavoie-Lamoureux"}, {"first_name"=>"Annie", "last_name"=>"Chamberland"}, {"first_name"=>"Catherine", "last_name"=>"Laprise"}, {"first_name"=>"Jacques", "last_name"=>"Lussier"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"1932-6203", "doi"=>"10.1371/journal.pone.0029440", "pmid"=>"22235296"}, "id"=>"bc16dd74-7b1d-35ea-93fc-41963c53d3a7", "abstract"=>"Gene expression analyses are used to investigate signaling pathways involved in diseases. In asthma, they have been primarily derived from the analysis of bronchial biopsies harvested from mild to moderate asthmatic subjects and controls. Due to ethical considerations, there is currently limited information on the transcriptome profile of the peripheral lung tissues in asthma.", "link"=>"http://www.mendeley.com/research/profiling-differentially-expressed-genes-using-suppression-subtractive-hybridization-equine-model-ch-2", "reader_count"=>16, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Librarian"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>5, "Other"=>2, "Student > Master"=>1, "Student > Bachelor"=>1, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Librarian"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>5, "Other"=>2, "Student > Master"=>1, "Student > Bachelor"=>1, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>4, "Medicine and Dentistry"=>2, "Agricultural and Biological Sciences"=>4, "Veterinary Science and Veterinary Medicine"=>3, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>2}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>3}}, "reader_count_by_country"=>{"United States"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/696584"], "description"=>"<p>Schematic representation of the different steps described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029440#s2\" target=\"_blank\">Material and Methods</a> (A), the sample pooling (n corresponds to the number of samples) (B), and the different hybridization steps performed with the SSH technique (C).</p>", "links"=>[], "tags"=>["genetics and genomics", "immunology", "molecular biology", "respiratory medicine"], "article_id"=>366990, "categories"=>["Medicine", "Molecular Biology", "Genetics", "Immunology"], "users"=>["Jean-Pierre Lavoie", "Josiane Lefebvre-Lavoie", "Mathilde Leclere", "Anouk Lavoie-Lamoureux", "Annie Chamberland", "Catherine Laprise", "Jacques Lussier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029440.g001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Methodology_for_SSH_/366990", "title"=>"Methodology for SSH.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-03 01:56:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/696751"], "description"=>"<p>Representative differential screening results of macroarrays of the SH-Ctls library. Four identical membranes were dot-blotted with PCR products obtained by SSH. The membranes were then hybridized with four different probes: SH-Ctls subtracted cDNAs (A), SH unsubtracted cDNAs (B), Ctls-SH subtracted cDNAs (C) and Ctls unsubtracted cDNAs. The arrow in the top left corner indicates the positive control (<i>LCN2</i>). The arrow head indicates an example of differentially expressed genes in SH compare with Ctls.</p>", "links"=>[], "tags"=>["hybridization"], "article_id"=>367161, "categories"=>["Medicine", "Molecular Biology", "Genetics", "Immunology"], "users"=>["Jean-Pierre Lavoie", "Josiane Lefebvre-Lavoie", "Mathilde Leclere", "Anouk Lavoie-Lamoureux", "Annie Chamberland", "Catherine Laprise", "Jacques Lussier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029440.g003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differential_hybridization_screening_/367161", "title"=>"Differential hybridization screening.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-03 01:59:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/696842"], "description"=>"<p>Analysis of mRNA expression using qPCR of six genes found up-regulated with SSH. <i>LCN2</i> (A), <i>COL1A2</i> (B), <i>PP3CB</i> (C), <i>PTGDR</i> (D), <i>LTA4H</i> (E) and <i>IGF1</i> (F) were studied in six horses with heaves (black bars) and six control horses (white bars). When compared to baseline, the six genes were significantly increased in heaves-affected horses after the allergen challenge (p<0.05). <i>PTDGR</i> was also increased in control horses when compared to heaves-affected horses at baseline.</p>", "links"=>[], "tags"=>["genetics and genomics", "immunology", "molecular biology", "respiratory medicine"], "article_id"=>367247, "categories"=>["Medicine", "Molecular Biology", "Genetics", "Immunology"], "users"=>["Jean-Pierre Lavoie", "Josiane Lefebvre-Lavoie", "Mathilde Leclere", "Anouk Lavoie-Lamoureux", "Annie Chamberland", "Catherine Laprise", "Jacques Lussier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029440.g004", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_expression_analysis_/367247", "title"=>"Gene expression analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-03 02:00:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/355121", "https://ndownloader.figshare.com/files/355172"], "description"=>"<div><h3>Background</h3><p>Gene expression analyses are used to investigate signaling pathways involved in diseases. In asthma, they have been primarily derived from the analysis of bronchial biopsies harvested from mild to moderate asthmatic subjects and controls. Due to ethical considerations, there is currently limited information on the transcriptome profile of the peripheral lung tissues in asthma.</p> <h3>Objective</h3><p>To identify genes contributing to chronic inflammation and remodeling in the peripheral lung tissue of horses with heaves, a naturally occurring asthma-like condition.</p> <h3>Methods</h3><p>Eleven adult horses (6 heaves-affected and 5 controls) were studied while horses with heaves were in clinical remission (Pasture), and during disease exacerbation induced by a 30-day natural antigen challenge during stabling (Challenge). Large peripheral lung biopsies were obtained by thoracoscopy at both time points. Using suppression subtractive hybridization (SSH), lung cDNAs of controls (Pasture and Challenge) and asymptomatic heaves-affected horses (Pasture) were subtracted from cDNAs of horses with heaves in clinical exacerbation (Challenge). The differential expression of selected genes of interest was confirmed using quantitative PCR assay.</p> <h3>Results</h3><p>Horses with heaves, but not controls, developed airway obstruction when challenged. Nine hundred and fifty cDNA clones isolated from the subtracted library were screened by dot blot array and 224 of those showing the most marked expression differences were sequenced. The gene expression pattern was confirmed by quantitative PCR in 15 of 22 selected genes. Novel genes and genes with an already defined function in asthma were identified in the subtracted cDNA library. Genes of particular interest associated with asthmatic airway inflammation and remodeling included those related to PPP3CB/NFAT, RhoA, and LTB4/GPR44 signaling pathways.</p> <h3>Conclusions</h3><p>Pathways representing new possible targets for anti-inflammatory and anti-remodeling therapies for asthma were identified. The findings of genes previously associated with asthma validate this equine model for gene expression studies.</p> </div>", "links"=>[], "tags"=>["profiling", "differentially", "expressed", "genes", "suppression", "subtractive", "hybridization", "equine", "asthma"], "article_id"=>130177, "categories"=>["Medicine", "Molecular Biology", "Genetics", "Immunology"], "users"=>["Jean-Pierre Lavoie", "Josiane Lefebvre-Lavoie", "Mathilde Leclere", "Anouk Lavoie-Lamoureux", "Annie Chamberland", "Catherine Laprise", "Jacques Lussier"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0029440.s001", "https://dx.doi.org/10.1371/journal.pone.0029440.s002"], "stats"=>{"downloads"=>2, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Profiling_of_Differentially_Expressed_Genes_Using_Suppression_Subtractive_Hybridization_in_an_Equine_Model_of_Chronic_Asthma/130177", "title"=>"Profiling of Differentially Expressed Genes Using Suppression Subtractive Hybridization in an Equine Model of Chronic Asthma", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-01-03 00:02:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/696689"], "description"=>"<p>A: Reduction of <i>GAPDH</i> cDNA following subtraction in the SH-Ctls sample. PCR was performed on SH-Ctls subtracted and SH unsubtracted samples. <i>GAPDH</i> PCR products (760 pb) were detectable 10 cycles earlier in the unsubtracted sample (18 cycles) than in the subtracted sample (28 cycles). B: Enrichment of <i>LCN2</i> cDNA following subtraction in the SH-Ctls sample. PCR was performed on SH-Ctls and Ctls-SH subtracted samples as well as SH and Ctls unsubtracted samples. <i>LCN2</i> PCR products (210 pb) were detected after 20 cycles for both SH unsubtracted and SH-Ctls subtracted samples, the difference in the intensity of the 2 bands indicate the enrichment compare to Ctls unsubtracted and Ctls-SH subtracted samples.</p>", "links"=>[], "tags"=>["subtraction"], "article_id"=>367095, "categories"=>["Medicine", "Molecular Biology", "Genetics", "Immunology"], "users"=>["Jean-Pierre Lavoie", "Josiane Lefebvre-Lavoie", "Mathilde Leclere", "Anouk Lavoie-Lamoureux", "Annie Chamberland", "Catherine Laprise", "Jacques Lussier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029440.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evaluation_of_subtraction_efficiency_/367095", "title"=>"Evaluation of subtraction efficiency.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-03 01:58:15"}

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Relative Metric

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