{"id":"https://openalex.org/W3080085336","doi":null,"title":"Whole transcriptome profiling of germinal center B-lymphocytes using a universal, integrated workflow of FACS cell sorting and TempO-Seq\u00ae assay","display_name":"Whole transcriptome profiling of germinal center B-lymphocytes using a universal, integrated workflow of FACS cell sorting and TempO-Seq\u00ae assay","publication_year":2020,"publication_date":"2020-08-01","ids":{"openalex":"https://openalex.org/W3080085336","mag":"3080085336"},"language":"en","primary_location":{"id":"pmh:oai:pubmedcentral.nih.gov:7424633","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7424633","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 Biomol Tech","raw_type":"Text"},"volume":null,"type":"article","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7424633","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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":[],"countries":[],"is_corresponding":false,"raw_author_name":"Seligmann, Bruce","raw_affiliation_strings":["1 BioSpyder"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 BioSpyder","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071470602","display_name":"Klaus Pechhold","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pechhold, Klaus","raw_affiliation_strings":["2 BioSpyder Technologies, Inc"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 BioSpyder Technologies, Inc","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087748905","display_name":"Carol E. Schrader","orcid":"https://orcid.org/0000-0001-8920-6803","observed_orcids":["https://orcid.org/0000-0001-8920-6803"]},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Schrader, Carol","raw_affiliation_strings":["3 U Mass Medical School"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 U Mass Medical School","institution_ids":["https://openalex.org/I166722992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058055761","display_name":"Megha Raghunathan","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Raghunathan, Megha","raw_affiliation_strings":["BioSpyder Technologies, Inc"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioSpyder Technologies, Inc","institution_ids":[]}]},{"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":[],"countries":[],"is_corresponding":false,"raw_author_name":"Babic, Milos","raw_affiliation_strings":["BioSpyder Technologies, Inc"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioSpyder Technologies, Inc","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038255436","display_name":"Travis John Williams","orcid":"https://orcid.org/0000-0003-3021-5005","observed_orcids":["https://orcid.org/0000-0003-3021-5005"]},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Williams, Travis","raw_affiliation_strings":["U Mass Medical School"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"U Mass Medical School","institution_ids":["https://openalex.org/I166722992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.07599203,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.8759999871253967,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.8759999871253967,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.066600002348423,"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/T10885","display_name":"Gene expression and cancer classification","score":0.02459999918937683,"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/germinal-center-b-cells","display_name":"germinal center B cells","score":0.9459999799728394},{"id":"https://openalex.org/keywords/tempo-seq","display_name":"TempO-Seq","score":0.8230000138282776},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"gene expression profiling","score":0.6729999780654907},{"id":"https://openalex.org/keywords/peyer-s-patches","display_name":"Peyer's patches","score":0.8069999814033508},{"id":"https://openalex.org/keywords/facs-sorting","display_name":"FACS cell sorting","score":0.8360000252723694},{"id":"https://openalex.org/keywords/intracellular-staining","display_name":"intracellular staining","score":0.781000018119812},{"id":"https://openalex.org/keywords/b220","display_name":"B220","score":0.6269999742507935},{"id":"https://openalex.org/keywords/fas","display_name":"Fas","score":0.9760000109672546},{"id":"https://openalex.org/keywords/bcl6","display_name":"BCL6","score":0.8730000257492065},{"id":"https://openalex.org/keywords/cxcr4","display_name":"CXCR4","score":0.984000027179718},{"id":"https://openalex.org/keywords/class-switch-recombination","display_name":"class switch recombination","score":0.8489999771118164},{"id":"https://openalex.org/keywords/ki-67","display_name":"Ki-67","score":0.9129999876022339},{"id":"https://openalex.org/keywords/somatic-hypermutation","display_name":"somatic hypermutation","score":0.9729999899864197},{"id":"https://openalex.org/keywords/affinity-maturation","display_name":"affinity maturation","score":0.9459999799728394},{"id":"https://openalex.org/keywords/mice","display_name":"mice","score":0.35100001096725464}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6687796711921692},{"id":"https://openalex.org/C153911025","wikidata":"https://www.wikidata.org/wiki/Q7202","display_name":"Molecular biology","level":1,"score":0.6592003703117371},{"id":"https://openalex.org/C96926380","wikidata":"https://www.wikidata.org/wiki/Q1737968","display_name":"Germinal center","level":4,"score":0.4996964931488037},{"id":"https://openalex.org/C112190416","wikidata":"https://www.wikidata.org/wiki/Q2124450","display_name":"RNA extraction","level":4,"score":0.4885803163051605},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4852621257305145},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.41023749113082886},{"id":"https://openalex.org/C2778453870","wikidata":"https://www.wikidata.org/wiki/Q188930","display_name":"B cell","level":3,"score":0.3980039954185486},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.33176112174987793},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.31722795963287354},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.162153422832489}],"mesh":[],"locations_count":1,"locations":[{"id":"pmh:oai:pubmedcentral.nih.gov:7424633","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7424633","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 Biomol Tech","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:7424633","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7424633","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 Biomol Tech","raw_type":"Text"},"sustainable_development_goals":[{"score":0.504800021648407,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"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/W2899754599","https://openalex.org/W4389229066","https://openalex.org/W4405855320","https://openalex.org/W2143299729","https://openalex.org/W7148862054","https://openalex.org/W2619508573","https://openalex.org/W4200418942","https://openalex.org/W4408989569","https://openalex.org/W2097663766","https://openalex.org/W4256070538"],"abstract_inverted_index":{"Next":[0],"Generation":[1],"Sequencing":[2],"(NGS)":[3],"workflows":[4],"for":[5,68,223],"transcriptionally":[6],"profiling":[7,115],"cells":[8,98,110],"involved":[9],"in":[10,17,161],"complex":[11],"tissue":[12],"functions":[13],"have":[14],"been":[15],"limited":[16],"identifying":[18],"and":[19,26,34,58,82,99,126,129,173,190,213,252,254],"isolating":[20],"rare":[21],"cells,":[22],"preparing":[23],"suitable":[24],"samples,":[25],"sequencing":[27],"assays.":[28],"TempO-Seq\u00ae":[29],"provides":[30],"a":[31],"robust,":[32],"quantitative,":[33],"specific":[35],"gene":[36,116],"expression":[37,117,192,200],"platform":[38],"that":[39,79,232],"does":[40],"not":[41,53],"require":[42,56],"RNA":[43,191],"extraction":[44],"or":[45,55],"reverse":[46],"transcription.":[47],"It":[48],"targets":[49],"short":[50],"RNA-sequences,":[51],"is":[52,59],"biased,":[54],"polyadenylation,":[57],"compatible":[60],"with":[61,86,170,204],"fixed":[62],"cell":[63,76,162,225],"samples.":[64],"Assays":[65],"are":[66],"available":[67],"human,":[69],"rat,":[70],"mouse.":[71],"We":[72,101,197,248],"implemented":[73],"an":[74,153],"integrated":[75],"suspension":[77],"workflow":[78],"combines":[80],"surface":[81,123],"intracellular":[83],"(ic)":[84],"staining":[85],"WT":[87],"TempO-Seq":[88],"assay":[89,151],"(\u223c27,000":[90],"mouse":[91,106],"genes)":[92],"followed":[93],"by":[94,182],"FACS-purification":[95],"of":[96,104,118,134,147,184,201,215,235],"selected":[97,185],"sequencing.":[100],"assayed":[102],"suspensions":[103],"individual":[105],"Peyer":[107],"Patch":[108],"(PP)":[109],"(6-8":[111],"PP,":[112],"\u223c3x106":[113],"cells/mouse),":[114],"GC":[119,131,165,206,237],"B-cells.":[120],"After":[121],"sequential":[122],"labeling,":[124],"fixation":[125],"permeabilization,":[127],"ic-staining,":[128],"TempO-Seq,":[130],"B-cells":[132,166,238],"(\u223c2-3%":[133],"total":[135],"cells)":[136],"were":[137],"FACS-purified":[138],"based":[139],"on":[140],"B220+CD95+GL7+":[141],"staining,":[142],"then":[143],"sequencing-ready":[144],"libraries":[145],"prepared":[146],"100-cell":[148],"aliquots/sample.":[149],"The":[150],"has":[152],"excellent":[154],"replicate":[155],"repeatability":[156,171],"(R2=0.94":[157],"detecting":[158],">11,000":[159],"genes":[160,176,202],"lines).":[163],"Sorted,":[164],"appeared":[167],"more":[168],"heterogeneous,":[169],"R2=0.73-0.78":[172],"7,000-8,000":[174],"different":[175],"measured.":[177],"Data":[178],"integrity":[179],"was":[180],"demonstrated":[181],"concordance":[183],"protein":[186],"markers":[187],"(B220,":[188],"CD95)":[189],"(B-cell":[193],"lineage":[194],"genes,":[195],"Fas).":[196],"confirmed":[198],"selective":[199],"associated":[203],"the":[205,216,224],"including":[207],"BCL6,":[208],"CXCR4,":[209],"immunoglobulin":[210],"class-switched":[211],"isotypes,":[212],"downregulation":[214],"GL7":[217],"repressor":[218],"CMP-Neu5Ac":[219],"hydroxylase.":[220],"Using":[221],"ic-staining":[222],"cycle":[226],"progression":[227],"biomarker":[228],"Ki67,":[229],"we":[230],"found":[231],"only":[233],"40-45%":[234],"PP":[236],"stained":[239],"positive,":[240],"presumably":[241],"undergoing":[242],"affinity":[243],"maturation":[244],"through":[245],"somatic":[246],"hypermutation.":[247],"measured":[249],"differential":[250],"profiles":[251],"these":[253],"other":[255],"data":[256],"will":[257],"be":[258],"presented.":[259]},"counts_by_year":[],"updated_date":"2026-10-27T15:51:10.671819","created_date":"2020-09-01T00:00:00"}