{"id":"https://openalex.org/W2030748346","doi":"https://doi.org/10.3791/51961","title":"An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus","display_name":"An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus","publication_year":2014,"publication_date":"2014-11-30","ids":{"openalex":"https://openalex.org/W2030748346","doi":"https://doi.org/10.3791/51961","mag":"2030748346","pmid":"https://pubmed.ncbi.nlm.nih.gov/25490084","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/4354392"},"language":"en","primary_location":{"id":"doi:10.3791/51961","doi":"https://doi.org/10.3791/51961","is_oa":true,"landing_page_url":"https://doi.org/10.3791/51961","pdf_url":"https://www.jove.com/pdf/51961/an-experimental-bioinformatics-protocol-for-rna-seq-analyses","source":{"id":"https://openalex.org/S199738284","display_name":"Journal of Visualized Experiments","issn_l":"1940-087X","issn":["1940-087X","2834-8400"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-d","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320416","host_organization_name":"MyJOVE","host_organization_lineage":["https://openalex.org/P4310320416"],"host_organization_lineage_names":["MyJOVE"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Visualized Experiments","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://www.jove.com/pdf/51961/an-experimental-bioinformatics-protocol-for-rna-seq-analyses","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077698266","display_name":"Monica F. Poelchau","orcid":"https://orcid.org/0000-0002-4584-6056","observed_orcids":["https://orcid.org/0000-0002-4584-6056"]},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Monica F. Poelchau","raw_affiliation_strings":["Department of Biology, Georgetown University; mpoelchau@gmail.com","Department of Biology, Georgetown University;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Georgetown University; mpoelchau@gmail.com","institution_ids":["https://openalex.org/I184565670"]},{"raw_affiliation_string":"Department of Biology, Georgetown University;","institution_ids":["https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011726094","display_name":"Xin Huang","orcid":"https://orcid.org/0000-0003-2466-4373","observed_orcids":["https://orcid.org/0000-0003-2466-4373"]},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xin Huang","raw_affiliation_strings":["Department of Biology, Georgetown University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Georgetown University","institution_ids":["https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076173338","display_name":"Allison C. Goff","orcid":"https://orcid.org/0000-0002-1557-618X","observed_orcids":["https://orcid.org/0000-0002-1557-618X"]},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Allison Goff","raw_affiliation_strings":["Department of Biology, Georgetown University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Georgetown University","institution_ids":["https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042129713","display_name":"Julie A. Reynolds","orcid":"https://orcid.org/0000-0002-6749-4514","observed_orcids":["https://orcid.org/0000-0002-6749-4514"]},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Julie Reynolds","raw_affiliation_strings":["Insect Physiology Lab, EEOB, The Ohio State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Insect Physiology Lab, EEOB, The Ohio State University","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069323728","display_name":"Peter Armbruster","orcid":"https://orcid.org/0000-0002-8183-3842","observed_orcids":["https://orcid.org/0000-0002-8183-3842"]},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter Armbruster","raw_affiliation_strings":["Department of Biology, Georgetown University; paa9@georgetown.edu","Department of Biology, Georgetown University;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Georgetown University; paa9@georgetown.edu","institution_ids":["https://openalex.org/I184565670"]},{"raw_affiliation_string":"Department of Biology, Georgetown University;","institution_ids":["https://openalex.org/I184565670"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.1548,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.77721435,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":null,"issue":"93","first_page":"e51961","last_page":"e51961"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11056","display_name":"Physiological and biochemical adaptations","score":0.6401000022888184,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11056","display_name":"Physiological and biochemical adaptations","score":0.6401000022888184,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10166","display_name":"Mosquito-borne diseases and control","score":0.26420000195503235,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10423","display_name":"Neurobiology and Insect Physiology Research","score":0.019200000911951065,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/photoperiodic-diapause","display_name":"photoperiodic diapause","score":0.9990000128746033},{"id":"https://openalex.org/keywords/aedes-albopictus","display_name":"Aedes albopictus","score":0.9990000128746033},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"gene expression profiling","score":0.7689999938011169},{"id":"https://openalex.org/keywords/differentially-expressed-genes","display_name":"differentially expressed genes","score":0.8740000128746033},{"id":"https://openalex.org/keywords/diapause-induction","display_name":"diapause induction","score":0.7829999923706055},{"id":"https://openalex.org/keywords/mosquito-rearing","display_name":"mosquito rearing","score":0.7490000128746033},{"id":"https://openalex.org/keywords/rna-extraction","display_name":"RNA extraction","score":0.5879999995231628},{"id":"https://openalex.org/keywords/life-history-traits","display_name":"life-history traits","score":0.6129999756813049},{"id":"https://openalex.org/keywords/developmental-arrest","display_name":"developmental arrest","score":0.6200000047683716},{"id":"https://openalex.org/keywords/seasonal-adaptation","display_name":"seasonal adaptation","score":0.4569999873638153}],"concepts":[{"id":"https://openalex.org/C86670359","wikidata":"https://www.wikidata.org/wiki/Q913288","display_name":"Diapause","level":3,"score":0.974656343460083},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8821418285369873},{"id":"https://openalex.org/C2776853612","wikidata":"https://www.wikidata.org/wiki/Q477918","display_name":"Aedes albopictus","level":4,"score":0.8376863598823547},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5287715196609497},{"id":"https://openalex.org/C139807058","wikidata":"https://www.wikidata.org/wiki/Q352374","display_name":"Adaptation (eye)","level":2,"score":0.4360440969467163},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.42540496587753296},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4239999055862427},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.4214155673980713},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.39314156770706177},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3583776354789734},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3182380795478821},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.28635749220848083},{"id":"https://openalex.org/C173758957","wikidata":"https://www.wikidata.org/wiki/Q129270","display_name":"Larva","level":2,"score":0.2721722722053528},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.05347427725791931},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C2777775583","wikidata":"https://www.wikidata.org/wiki/Q1148004","display_name":"Aedes aegypti","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000330","descriptor_name":"Aedes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000330","descriptor_name":"Aedes","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017440","descriptor_name":"Photoperiod","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064666","descriptor_name":"Diapause, Insect","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.3791/51961","doi":"https://doi.org/10.3791/51961","is_oa":true,"landing_page_url":"https://doi.org/10.3791/51961","pdf_url":"https://www.jove.com/pdf/51961/an-experimental-bioinformatics-protocol-for-rna-seq-analyses","source":{"id":"https://openalex.org/S199738284","display_name":"Journal of Visualized Experiments","issn_l":"1940-087X","issn":["1940-087X","2834-8400"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-d","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320416","host_organization_name":"MyJOVE","host_organization_lineage":["https://openalex.org/P4310320416"],"host_organization_lineage_names":["MyJOVE"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Visualized Experiments","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:4048351","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4354392","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:4354392","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4354392","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Vis Exp","raw_type":"Text"},{"id":"pmid:25490084","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25490084","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of visualized experiments : JoVE","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.3791/51961","doi":"https://doi.org/10.3791/51961","is_oa":true,"landing_page_url":"https://doi.org/10.3791/51961","pdf_url":"https://www.jove.com/pdf/51961/an-experimental-bioinformatics-protocol-for-rna-seq-analyses","source":{"id":"https://openalex.org/S199738284","display_name":"Journal of Visualized Experiments","issn_l":"1940-087X","issn":["1940-087X","2834-8400"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-d","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320416","host_organization_name":"MyJOVE","host_organization_lineage":["https://openalex.org/P4310320416"],"host_organization_lineage_names":["MyJOVE"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Visualized Experiments","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G7100817091","display_name":"Massively parallel sequencing of the diapause transcriptome in Aedes albopictus","funder_award_id":"R21AI081041","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320310223","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2030748346.pdf","grobid_xml":"https://content.openalex.org/works/W2030748346.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W92308610","https://openalex.org/W94939360","https://openalex.org/W232841441","https://openalex.org/W1762192569","https://openalex.org/W1885614507","https://openalex.org/W1912338927","https://openalex.org/W1912438529","https://openalex.org/W1991099782","https://openalex.org/W1999574084","https://openalex.org/W2000401496","https://openalex.org/W2005223063","https://openalex.org/W2008687577","https://openalex.org/W2011430831","https://openalex.org/W2017348556","https://openalex.org/W2023473182","https://openalex.org/W2034963028","https://openalex.org/W2045952588","https://openalex.org/W2078782861","https://openalex.org/W2089071639","https://openalex.org/W2089653176","https://openalex.org/W2090950329","https://openalex.org/W2097205777","https://openalex.org/W2102532874","https://openalex.org/W2114104545","https://openalex.org/W2116978877","https://openalex.org/W2122016967","https://openalex.org/W2126419817","https://openalex.org/W2128864789","https://openalex.org/W2130373635","https://openalex.org/W2136482257","https://openalex.org/W2136879569","https://openalex.org/W2142619120","https://openalex.org/W2143621972","https://openalex.org/W2145335031","https://openalex.org/W2146710315","https://openalex.org/W2150115852","https://openalex.org/W2150812798","https://openalex.org/W2151241855","https://openalex.org/W2176275638","https://openalex.org/W2178689966","https://openalex.org/W2250982082","https://openalex.org/W2354210172","https://openalex.org/W2504851667","https://openalex.org/W4206263975","https://openalex.org/W4233619870"],"related_works":["https://openalex.org/W2000401496","https://openalex.org/W2010871937","https://openalex.org/W2123735157","https://openalex.org/W2150115852","https://openalex.org/W2501543983","https://openalex.org/W7096868311","https://openalex.org/W1912438529","https://openalex.org/W7100911886","https://openalex.org/W2078782861","https://openalex.org/W2552228354"],"abstract_inverted_index":{"Photoperiodic":[0],"diapause":[1,60,96,104,177],"is":[2,50],"an":[3,51],"important":[4,35,180],"adaptation":[5],"that":[6,139],"allows":[7],"individuals":[8],"to":[9,62,94,101,120,145,159,171],"escape":[10],"harsh":[11],"seasonal":[12],"environments":[13],"via":[14,31],"a":[15,78,106,129],"series":[16],"of":[17,41,59,65,131,176],"physiological":[18],"changes,":[19],"most":[20],"notably":[21],"developmental":[22],"arrest":[23],"and":[24,70,97,108,111],"reduced":[25],"metabolism.":[26],"Global":[27],"gene":[28],"expression":[29],"profiling":[30],"RNA-Seq":[32,122],"can":[33,142,167],"provide":[34],"insights":[36],"into":[37],"the":[38,56,71,152,173],"transcriptional":[39,57,85,153,174],"mechanisms":[40],"photoperiodic":[42,160],"diapause.":[43],"The":[44,135],"Asian":[45],"tiger":[46],"mosquito,":[47],"Aedes":[48],"albopictus,":[49],"outstanding":[52],"organism":[53],"for":[54,82,114],"studying":[55],"bases":[58,175],"due":[61,158],"its":[63],"ease":[64],"rearing,":[66],"easily":[67],"induced":[68],"diapause,":[69],"genomic":[72],"resources":[73],"available.":[74],"This":[75],"manuscript":[76],"presents":[77],"general":[79],"experimental":[80],"workflow":[81,119,166],"identifying":[83],"diapause-induced":[84],"differences":[86],"in":[87,105,128,155,184],"A.":[88,156],"albopictus.":[89],"Rearing":[90],"techniques,":[91],"conditions":[92],"necessary":[93],"induce":[95],"non-diapause":[98],"development,":[99],"methods":[100],"estimate":[102],"percent":[103],"population,":[107],"RNA":[109],"extraction":[110],"integrity":[112],"assessment":[113],"mosquitoes":[115],"are":[116],"documented.":[117],"A":[118],"process":[121],"data":[123],"from":[124],"Illumina":[125],"sequencers":[126],"culminates":[127],"list":[130],"differentially":[132,149],"expressed":[133],"genes.":[134],"representative":[136],"results":[137],"demonstrate":[138],"this":[140,165],"protocol":[141],"be":[143,168],"used":[144],"effectively":[146],"identify":[147],"genes":[148],"regulated":[150],"at":[151],"level":[154],"albopictus":[157],"differences.":[161],"With":[162],"modest":[163],"adjustments,":[164],"readily":[169],"adapted":[170],"study":[172],"or":[178],"other":[179,185],"life":[181],"history":[182],"traits":[183],"mosquitoes.":[186]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}