{"id":"https://openalex.org/W4249734632","doi":"https://doi.org/10.1158/1538-7445.sabcs18-5241","title":"Abstract 5241: Whole transcriptome TempO-Seq profiling of focal areas of H&E stained FFPE: Differentiation of normal colon and cancer phenotypes between donors","display_name":"Abstract 5241: Whole transcriptome TempO-Seq profiling of focal areas of H&E stained FFPE: Differentiation of normal colon and cancer phenotypes between donors","publication_year":2019,"publication_date":"2019-07-01","ids":{"openalex":"https://openalex.org/W4249734632","doi":"https://doi.org/10.1158/1538-7445.sabcs18-5241"},"language":"en","primary_location":{"id":"doi:10.1158/1538-7445.sabcs18-5241","doi":"https://doi.org/10.1158/1538-7445.sabcs18-5241","is_oa":false,"landing_page_url":"https://doi.org/10.1158/1538-7445.sabcs18-5241","pdf_url":null,"source":{"id":"https://openalex.org/S4306520151","display_name":"Molecular and Cellular Biology / Genetics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Molecular and Cellular Biology / Genetics","raw_type":"proceedings-article"},"volume":null,"type":"conference-abstract","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004350870","display_name":"Christy L. Trejo","orcid":"https://orcid.org/0000-0001-5535-3725","observed_orcids":["https://orcid.org/0000-0001-5535-3725"]},"institutions":[{"id":"https://openalex.org/I4210145439","display_name":"Biospyder (United States)","ror":"https://ror.org/05076r819","country_code":"US","type":"company","lineage":["https://openalex.org/I4210145439"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christy Trejo","raw_affiliation_strings":["BioSpyder Technologies, Inc., Carlsbad, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioSpyder Technologies, Inc., Carlsbad, CA","institution_ids":["https://openalex.org/I4210145439"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067028641","display_name":"Elliot Imler","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210145439","display_name":"Biospyder (United States)","ror":"https://ror.org/05076r819","country_code":"US","type":"company","lineage":["https://openalex.org/I4210145439"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elliot Imler","raw_affiliation_strings":["BioSpyder Technologies, Inc., Carlsbad, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioSpyder Technologies, Inc., Carlsbad, CA","institution_ids":["https://openalex.org/I4210145439"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051157653","display_name":"Milo\u0161 Babi\u0107","orcid":"https://orcid.org/0000-0002-4040-0370","observed_orcids":["https://orcid.org/0000-0002-4040-0370"]},"institutions":[{"id":"https://openalex.org/I4210145439","display_name":"Biospyder (United States)","ror":"https://ror.org/05076r819","country_code":"US","type":"company","lineage":["https://openalex.org/I4210145439"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Milos Babic","raw_affiliation_strings":["BioSpyder Technologies, Inc., Carlsbad, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioSpyder Technologies, Inc., Carlsbad, CA","institution_ids":["https://openalex.org/I4210145439"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001459712","display_name":"Peter J. Shepard","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210145439","display_name":"Biospyder (United States)","ror":"https://ror.org/05076r819","country_code":"US","type":"company","lineage":["https://openalex.org/I4210145439"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter Shepard","raw_affiliation_strings":["BioSpyder Technologies, Inc., Carlsbad, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioSpyder Technologies, Inc., Carlsbad, CA","institution_ids":["https://openalex.org/I4210145439"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080916822","display_name":"Raymond B. Nagle","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Raymond Nagle","raw_affiliation_strings":["University of Arizona, Tucson, AZ"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Arizona, Tucson, AZ","institution_ids":["https://openalex.org/I138006243"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024499105","display_name":"Joanne M. Yeakley","orcid":"https://orcid.org/0000-0002-8500-0442","observed_orcids":["https://orcid.org/0000-0002-8500-0442"]},"institutions":[{"id":"https://openalex.org/I4210145439","display_name":"Biospyder (United States)","ror":"https://ror.org/05076r819","country_code":"US","type":"company","lineage":["https://openalex.org/I4210145439"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joanne Yeakley","raw_affiliation_strings":["BioSpyder Technologies, Inc., Carlsbad, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioSpyder Technologies, Inc., Carlsbad, CA","institution_ids":["https://openalex.org/I4210145439"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002573031","display_name":"Bruce E. Seligmann","orcid":"https://orcid.org/0000-0002-1342-801X","observed_orcids":["https://orcid.org/0000-0002-1342-801X"]},"institutions":[{"id":"https://openalex.org/I4210145439","display_name":"Biospyder (United States)","ror":"https://ror.org/05076r819","country_code":"US","type":"company","lineage":["https://openalex.org/I4210145439"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bruce Seligmann","raw_affiliation_strings":["BioSpyder Technologies, Inc., Carlsbad, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioSpyder Technologies, Inc., Carlsbad, CA","institution_ids":["https://openalex.org/I4210145439"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"5241","last_page":"5241"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.6230000257492065,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.6230000257492065,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.27730000019073486,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.03959999978542328,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/tempo-seq","display_name":"TempO-Seq","score":0.9800000190734863},{"id":"https://openalex.org/keywords/whole-transcriptome-profiling","display_name":"whole transcriptome profiling","score":0.8500000238418579},{"id":"https://openalex.org/keywords/formalin-fixed-paraffin-embedded-tissue","display_name":"formalin-fixed paraffin-embedded tissue","score":0.7210000157356262},{"id":"https://openalex.org/keywords/archived-tissue","display_name":"archival tissue","score":0.6110000014305115},{"id":"https://openalex.org/keywords/colorectal-cancer","display_name":"colorectal cancer","score":0.9210000038146973},{"id":"https://openalex.org/keywords/h-e-stained-tissue","display_name":"H&E-stained tissue","score":0.6100000143051147},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"gene expression profiling","score":0.5899999737739563},{"id":"https://openalex.org/keywords/donor-variability","display_name":"donor variability","score":0.5699999928474426},{"id":"https://openalex.org/keywords/cancer-subtyping","display_name":"cancer subtyping","score":0.49900001287460327},{"id":"https://openalex.org/keywords/fixation-duration","display_name":"fixation duration","score":0.5350000262260437},{"id":"https://openalex.org/keywords/tissue-age","display_name":"tissue age","score":0.5440000295639038},{"id":"https://openalex.org/keywords/sample-size-reduction","display_name":"sample size reduction","score":0.4269999861717224},{"id":"https://openalex.org/keywords/principal-component-analysis","display_name":"principal component analysis","score":0.621999979019165}],"concepts":[{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.7323247194290161},{"id":"https://openalex.org/C112190416","wikidata":"https://www.wikidata.org/wiki/Q2124450","display_name":"RNA extraction","level":4,"score":0.5864467620849609},{"id":"https://openalex.org/C555283112","wikidata":"https://www.wikidata.org/wiki/Q1637543","display_name":"Carcinogenesis","level":3,"score":0.5698283314704895},{"id":"https://openalex.org/C526805850","wikidata":"https://www.wikidata.org/wiki/Q188874","display_name":"Colorectal cancer","level":3,"score":0.534119188785553},{"id":"https://openalex.org/C153911025","wikidata":"https://www.wikidata.org/wiki/Q7202","display_name":"Molecular biology","level":1,"score":0.5292726755142212},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5225776433944702},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.48642754554748535},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.48624148964881897},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.44251322746276855},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4175604581832886},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.36678972840309143},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3048626184463501},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.24102362990379333},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19431957602500916}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1158/1538-7445.sabcs18-5241","doi":"https://doi.org/10.1158/1538-7445.sabcs18-5241","is_oa":false,"landing_page_url":"https://doi.org/10.1158/1538-7445.sabcs18-5241","pdf_url":null,"source":{"id":"https://openalex.org/S4306520151","display_name":"Molecular and Cellular Biology / Genetics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Molecular and Cellular Biology / Genetics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.9391000270843506}],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2887543465","https://openalex.org/W2949097641","https://openalex.org/W2135973238","https://openalex.org/W7161990228","https://openalex.org/W2490153962","https://openalex.org/W2954812520","https://openalex.org/W4417405441","https://openalex.org/W2326964154","https://openalex.org/W4362592928","https://openalex.org/W7139195038"],"abstract_inverted_index":{"Profiling":[0],"gene":[1],"expression":[2,177,295],"from":[3,15,116,159,170,194,202,213,294],"small":[4,112],"amounts":[5],"of":[6,13,27,30,47,66,71,84,105,128,176,207,221,262,274,316,319,324,335],"FFPE":[7,51,93,267],"using":[8,92,265],"methods":[9],"that":[10,95,208],"require":[11],"extraction":[12],"RNA":[14],"the":[16,31,55,63,69,82,85,106,160,167,171,203,217,225,250,272,336],"tissue,":[17,119],"such":[18],"as":[19,111,113],"RNA-seq,":[20],"have":[21],"been":[22],"problematic.":[23],"We":[24,269],"report":[25],"use":[26,253],"a":[28,75,103,174],"modification":[29],"whole":[32,254],"transcriptome":[33,255,313],"TempO-Seq\u00ae":[34],"assay":[35,109,145],"(Yeakley":[36],"et":[37],"al,":[38],"PLOSone,":[39],"2017;":[40],"DOI:10.1371/journal.pone.0178302)":[41],"to":[42,74,98,108,123,239,252,258,278,284],"profile":[43,126,193,206],"2":[44,76,114],"mm2":[45,77,115],"areas":[46,110,127,318],"5":[48],"\u03bcm":[49],"thick":[50],"sections":[52],"by":[53],"scraping":[54],"tissue":[56,192,205,219,227],"and":[57,68,125,134,139,163,283,327],"assaying":[58],"lysates":[59],"directly":[60,243],"without":[61],"extracting":[62],"RNA.":[64],"Duration":[65],"fixation":[67],"amount":[70],"sample":[72],"down":[73],"area":[78],"do":[79],"not":[80,198],"impact":[81],"performance":[83],"assay.":[86],"Good":[87],"results":[88,248],"can":[89],"be":[90,242],"achieved":[91],"blocks":[94],"are":[96,270],"up":[97],"30":[99],"years":[100],"old.":[101],"As":[102],"consequence":[104],"ability":[107,251],"H&E":[117,320],"stained":[118,321],"we":[120],"were":[121,229],"able":[122],"scrape":[124],"colorectal":[129],"cancer":[130,191,226,264,328],"vs":[131],"adjacent":[132],"normal":[133,168,204,218,325],"obtain":[135],"replicates":[136,155],"within":[137,216],"donors,":[138],"then":[140],"compare":[141],"between":[142,153,245,330],"donors.":[143],"The":[144,190],"shows":[146],"excellent":[147],"reproducibility,":[148],"with":[149],"R2":[150],">":[151],"0.95":[152],"biological":[154],"(separate":[156],"samples":[157],"taken":[158],"same":[161],"patient":[162,196],"lysed/processed":[164],"separately).":[165],"While":[166],"tissues":[169],"patients":[172,275],"exhibited":[173],"range":[175],"variability,":[178],"they":[179],"all":[180,214,222],"clustered":[181],"very":[182],"tightly":[183],"when":[184],"analyzed":[185],"via":[186],"principal":[187],"component":[188],"analysis.":[189],"each":[195],"was":[197],"only":[199],"substantially":[200,211],"different":[201,212],"patient,":[209],"but":[210],"profiles":[215,228],"cluster":[220],"patients.":[223,246],"Furthermore,":[224],"separated":[230],"into":[231],"distinct":[232],"subgroups.":[233],"Changes":[234],"in":[235],"regulatory":[236],"pathways":[237],"leading":[238],"oncogenesis":[240],"could":[241],"distinguished":[244],"These":[247],"demonstrate":[249],"TempO-Seq":[256,314],"profiling":[257,315],"investigate":[259,279],"molecular":[260],"subtypes":[261],"colon":[263,326],"archival":[266],"samples.":[268],"expanding":[271],"cohort":[273],"being":[276],"profiled":[277],"these":[280],"signatures":[281,287],"further,":[282],"draw":[285],"out":[286],"which":[288],"allow":[289],"direct":[290],"subtype":[291],"classification":[292],"purely":[293],"data.Citation":[296],"Format:":[297],"Christy":[298],"Trejo,":[299],"Elliot":[300],"Imler,":[301],"Milos":[302],"Babic,":[303],"Peter":[304],"Shepard,":[305],"Raymond":[306],"Nagle,":[307],"Joanne":[308],"Yeakley,":[309],"Bruce":[310],"Seligmann.":[311],"Whole":[312],"focal":[317],"FFPE:":[322],"Differentiation":[323],"phenotypes":[329],"donors":[331],"[abstract].":[332],"In:":[333],"Proceedings":[334],"American":[337],"Association":[338],"for":[339],"Cancer":[340,354],"Research":[341],"Annual":[342],"Meeting":[343],"2019;":[344],"2019":[345],"Mar":[346],"29-Apr":[347],"3;":[348],"Atlanta,":[349],"GA.":[350],"Philadelphia":[351],"(PA):":[352],"AACR;":[353],"Res":[355],"2019;79(13":[356],"Suppl):Abstract":[357],"nr":[358],"5241.":[359]},"counts_by_year":[],"updated_date":"2026-10-30T12:39:25.321706","created_date":"2022-05-12T00:00:00"}
