IP Library › Granted Patent US 12,716,092
Granted Patent B2
US 12,716,092 · App. 18/320,097 · Granted Aug 25, 2026

Method of identifying circular RNA

View Patent ↗
Loading inventors, assignments & file history…
Monitor This Case
Get email alerts when status or documents change.
Order Certified Copies
Most orders are placed with the USPTO same day — all within 24 business hours.
Order via The Patent Place →
Pre-filled with this patent's details
Quick Facts
Patent No.
US 12,716,092
App. No.
18/320,097
Granted
Aug 25, 2026
Kind
B2
Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jun 21, 2023
From: COSTA, JUSTIN
To: 10X GENOMICS, INC.
Reel/Frame 064021/0702 →
Continuity (2)
Provisional Application 63343922 · May 19, 2022
Related Publication 20230374580A1 · Nov 23, 2023
References Cited (384)
US 4318846A · Khanna et al. · 1982 [cited by applicant]
US 4683195A · Mullis et al. · 1987 [cited by applicant]
US 4683202A · Mullis · 1987 [cited by applicant]
US 4757141A · Fung et al. · 1988 [cited by applicant]
US 4800159A · Mullis et al. · 1989 [cited by applicant]
US 4849336A · Miyoshi et al. · 1989 [cited by applicant]
US 4965188A · Mullis et al. · 1990 [cited by applicant]
US 5066580A · Lee · 1991 [cited by applicant]
US 5091519A · Cruickshank · 1992 [cited by applicant]
US 5151507A · Hobbs et al. · 1992 [cited by applicant]
US 5188934A · Menchen et al. · 1993 [cited by applicant]
US 5192782A · Djuric et al. · 1993 [cited by applicant]
US 5198537A · Huber et al. · 1993 [cited by applicant]
US 5344757A · Holtke et al. · 1994 [cited by applicant]
US 5354657A · Holtke et al. · 1994 [cited by applicant]
US 5366860A · Bergot et al. · 1994 [cited by applicant]
US 5512462A · Cheng · 1996 [cited by applicant]
US 5599675A · Brenner · 1997 [cited by applicant]
US 5635352A · Urdea et al. · 1997 [cited by applicant]
US 5688648A · Mathies et al. · 1997 [cited by applicant]
US 5695940A · Drmanac et al. · 1997 [cited by applicant]
US 5702888A · Holtke et al. · 1997 [cited by applicant]
US 5750341A · Macevicz · 1998 [cited by applicant]
US 5800996A · Lee et al. · 1998 [cited by applicant]
US 5847162A · Lee et al. · 1998 [cited by applicant]
US 5990479A · Weiss et al. · 1999 [cited by applicant]
US 6054274A · Sampson et al. · 2000 [cited by applicant]
US 6172218B1 · Brenner · 2001 [cited by applicant]
US 6207392B1 · Weiss et al. · 2001 [cited by applicant]
US 6251303B1 · Bawendi et al. · 2001 [cited by applicant]
US 6291187B1 · Kingsmore et al. · 2001 [cited by applicant]
US 6306597B1 · Macevicz · 2001 [cited by applicant]
US 6319426B1 · Bawendi et al. · 2001 [cited by applicant]
US 6322901B1 · Bawendi et al. · 2001 [cited by applicant]
US 6323009B1 · Lasken et al. · 2001 [cited by applicant]
US 6344329B1 · Lizardi et al. · 2002 [cited by applicant]
US 6368801B1 · Faruqi · 2002 [cited by applicant]
US 6391937B1 · Beuhler et al. · 2002 [cited by applicant]
US 6423551B1 · Weiss et al. · 2002 [cited by applicant]
US 6426513B1 · Bawendi et al. · 2002 [cited by applicant]
US 6444143B2 · Bawendi et al. · 2002 [cited by applicant]
US 6534266B1 · Singer · 2003 [cited by applicant]
US 6576291B2 · Bawendi et al. · 2003 [cited by applicant]
US 6828109B2 · Kaplan · 2004 [cited by applicant]
US 6969488B2 · Bridgham et al. · 2005 [cited by applicant]
US 7057026B2 · Barnes et al. · 2006 [cited by applicant]
US 7255994B2 · Lao · 2007 [cited by applicant]
US 7345159B2 · Ju et al. · 2008 [cited by applicant]
US 7473767B2 · Dimitrov · 2009 [cited by applicant]
US 7534991B2 · Miller et al. · 2009 [cited by applicant]
US 7544794B1 · Benner · 2009 [cited by applicant]
US 7555155B2 · Levenson et al. · 2009 [cited by applicant]
US 7566537B2 · Balasubramanian et al. · 2009 [cited by applicant]
US 7632641B2 · Dirks et al. · 2009 [cited by applicant]
US 7655898B2 · Miller · 2010 [cited by applicant]
US 7721721B1 · Kronengold et al. · 2010 [cited by applicant]
US 7893227B2 · Wu et al. · 2011 [cited by applicant]
US 7910304B2 · Drmanac · 2011 [cited by applicant]
US 7941279B2 · Hwang et al. · 2011 [cited by applicant]
US 7989166B2 · Koch et al. · 2011 [cited by applicant]
US 8124751B2 · Pierce et al. · 2012 [cited by applicant]
US 8199999B2 · Hoyt et al. · 2012 [cited by applicant]
US 8268554B2 · Schallmeiner · 2012 [cited by applicant]
US 8330087B2 · Domenicali · 2012 [cited by applicant]
US 8415102B2 · Geiss et al. · 2013 [cited by applicant]
US 8431691B2 · McKernan et al. · 2013 [cited by applicant]
US 8460865B2 · Chee et al. · 2013 [cited by applicant]
US 8462981B2 · Determan et al. · 2013 [cited by applicant]
US 8481258B2 · Church et al. · 2013 [cited by applicant]
US 8519115B2 · Webster et al. · 2013 [cited by applicant]
US 8551710B2 · Bernitz et al. · 2013 [cited by applicant]
US 8632975B2 · Vander Horn et al. · 2014 [cited by applicant]
US 8658361B2 · Wu et al. · 2014 [cited by applicant]
US 8771950B2 · Church et al. · 2014 [cited by applicant]
US 8986926B2 · Ferree et al. · 2015 [cited by applicant]
US 9201063B2 · Sood et al. · 2015 [cited by applicant]
US 9217178B2 · Fedurco et al. · 2015 [cited by applicant]
US 9273349B2 · Nguyen et al. · 2016 [cited by applicant]
US 9371563B2 · Geiss et al. · 2016 [cited by applicant]
US 9371598B2 · Chee · 2016 [cited by applicant]
US 9376717B2 · Gao et al. · 2016 [cited by applicant]
US 9512422B2 · Barnard et al. · 2016 [cited by applicant]
US 9541504B2 · Hoyt · 2017 [cited by applicant]
US 9551032B2 · Landegren et al. · 2017 [cited by applicant]
US 9624538B2 · Church et al. · 2017 [cited by applicant]
US 9650406B2 · Zhou et al. · 2017 [cited by applicant]
US 9714446B2 · Webster et al. · 2017 [cited by applicant]
US 9714937B2 · Dunaway · 2017 [cited by applicant]
US 9727810B2 · Fodor et al. · 2017 [cited by applicant]
US 9778155B2 · Gradinaru et al. · 2017 [cited by applicant]
US 9783841B2 · Nolan et al. · 2017 [cited by applicant]
US 9889422B2 · Smith et al. · 2018 [cited by applicant]
US 9909167B2 · Samusik et al. · 2018 [cited by applicant]
US 10032064B2 · Hoyt · 2018 [cited by applicant]
US 10059990B2 · Boyden et al. · 2018 [cited by applicant]
US 10126242B2 · Miller et al. · 2018 [cited by applicant]
US 10138509B2 · Church et al. · 2018 [cited by applicant]
US 10179932B2 · Church et al. · 2019 [cited by applicant]
US 10227639B2 · Levner et al. · 2019 [cited by applicant]
US 10246700B2 · Dunaway et al. · 2019 [cited by applicant]
US 10266888B2 · Daugharthy et al. · 2019 [cited by applicant]
US 10267808B2 · Cai · 2019 [cited by applicant]
US 10309879B2 · Chen et al. · 2019 [cited by applicant]
US 10317321B2 · Tillberg et al. · 2019 [cited by applicant]
US 10364457B2 · Wassie et al. · 2019 [cited by applicant]
US 10370698B2 · Nolan et al. · 2019 [cited by applicant]
US 10415080B2 · Dunaway et al. · 2019 [cited by applicant]
US 10457980B2 · Cai et al. · 2019 [cited by applicant]
US 10465235B2 · Gullberg et al. · 2019 [cited by applicant]
US 10494662B2 · Church et al. · 2019 [cited by applicant]
US 10495554B2 · Deisseroth et al. · 2019 [cited by applicant]
US 10501777B2 · Beechem et al. · 2019 [cited by applicant]
US 10501791B2 · Church et al. · 2019 [cited by applicant]
US 10510435B2 · Cai et al. · 2019 [cited by applicant]
US 10526649B2 · Chen et al. · 2020 [cited by applicant]
US 10545075B2 · Deisseroth et al. · 2020 [cited by applicant]
US 10580128B2 · Miller · 2020 [cited by applicant]
US 10640816B2 · Beechem et al. · 2020 [cited by applicant]
US 10640826B2 · Church et al. · 2020 [cited by applicant]
US 10669569B2 · Gullberg et al. · 2020 [cited by applicant]
US 10746981B2 · Tomer et al. · 2020 [cited by applicant]
US 10774372B2 · Chee et al. · 2020 [cited by applicant]
US 10774374B2 · Frisén et al. · 2020 [cited by applicant]
US 10794802B2 · Gradinaru et al. · 2020 [cited by applicant]
US 10802262B2 · Tomer et al. · 2020 [cited by applicant]
US 10815519B2 · Husain et al. · 2020 [cited by applicant]
US 10829814B2 · Fan et al. · 2020 [cited by applicant]
US 10844426B2 · Daugharthy et al. · 2020 [cited by applicant]
US 10858698B2 · Church et al. · 2020 [cited by applicant]
US 10872679B2 · Cai et al. · 2020 [cited by applicant]
US 10964001B2 · Miller · 2021 [cited by applicant]
US 11174281B1 · Graham et al. · 2021 [cited by applicant]
US 11287422B2 · Previte et al. · 2022 [cited by applicant]
US 11434525B2 · Glezer · 2022 [cited by applicant]
US 11459603B2 · Tyagi et al. · 2022 [cited by applicant]
US 11499185B2 · Vijayan et al. · 2022 [cited by applicant]
US 11643679B2 · Glezer et al. · 2023 [cited by applicant]
US 11999999B2 · Ju et al. · 2024 [cited by applicant]
US 20020045045A1 · Adams et al. · 2002 [cited by applicant]
US 20030017264A1 · Treadway et al. · 2003 [cited by applicant]
US 20050100900A1 · Kawashima et al. · 2005 [cited by applicant]
US 20060188901A1 · Barnes et al. · 2006 [cited by applicant]
US 20060234261A1 · Pierce et al. · 2006 [cited by applicant]
US 20060240439A1 · Smith et al. · 2006 [cited by applicant]
US 20060281109A1 · Ost et al. · 2006 [cited by applicant]
US 20070166705A1 · Milton et al. · 2007 [cited by applicant]
US 20090118128A1 · Liu et al. · 2009 [cited by applicant]
US 20100055733A1 · Lutolf et al. · 2010 [cited by applicant]
US 20110059865A1 · Smith et al. · 2011 [cited by applicant]
US 20110223585A1 · Gullberg et al. · 2011 [cited by applicant]
US 20120270305A1 · Reed et al. · 2012 [cited by applicant]
US 20130079232A1 · Kain et al. · 2013 [cited by applicant]
US 20130260372A1 · Buermann et al. · 2013 [cited by applicant]
US 20130288249A1 · Gullberg et al. · 2013 [cited by applicant]
US 20130323729A1 · Landegren et al. · 2013 [cited by applicant]
US 20160024555A1 · Church et al. · 2016 [cited by applicant]
US 20160108458A1 · Frei et al. · 2016 [cited by applicant]
US 20160305856A1 · Boyden et al. · 2016 [cited by applicant]
US 20160369329A1 · Cai et al. · 2016 [cited by applicant]
US 20160376642A1 · Landegren et al. · 2016 [cited by applicant]
US 20170009278A1 · Söderberg et al. · 2017 [cited by applicant]
US 20170081489A1 · Rodriques et al. · 2017 [cited by applicant]
US 20170101672A1 · Luo et al. · 2017 [cited by applicant]
US 20170219465A1 · Desseroth et al. · 2017 [cited by applicant]
US 20170220733A1 · Zhuang et al. · 2017 [cited by applicant]
US 20170253918A1 · Kohman · 2017 [cited by applicant]
US 20180052081A1 · Kohman · 2018 [cited by applicant]
US 20180080876A1 · Rockel et al. · 2018 [cited by applicant]
US 20180208967A1 · Larman et al. · 2018 [cited by applicant]
US 20180237864A1 · Imler et al. · 2018 [cited by applicant]
US 20180251833A1 · Daugharthy et al. · 2018 [cited by applicant]
US 20180320226A1 · Church et al. · 2018 [cited by applicant]
US 20190017106A1 · Frisen et al. · 2019 [cited by applicant]
US 20190032128A1 · Chen et al. · 2019 [cited by applicant]
US 20190055594A1 · Samusik et al. · 2019 [cited by applicant]
US 20190106733A1 · Kishi et al. · 2019 [cited by applicant]
US 20190112599A1 · Church et al. · 2019 [cited by applicant]
US 20190119735A1 · Deisseroth et al. · 2019 [cited by applicant]
US 20190155835A1 · Daugharthy et al. · 2019 [cited by applicant]
US 20190161796A1 · Hauling et al. · 2019 [cited by applicant]
US 20190177718A1 · Church et al. · 2019 [cited by applicant]
US 20190194709A1 · Church et al. · 2019 [cited by applicant]
US 20190218608A1 · Daugharthy et al. · 2019 [cited by applicant]
US 20190249248A1 · Beechem et al. · 2019 [cited by applicant]
US 20190264270A1 · Zhuang et al. · 2019 [cited by applicant]
US 20190271028A1 · Khafizov et al. · 2019 [cited by applicant]
US 20190276881A1 · Zhuang et al. · 2019 [cited by applicant]
US 20190339203A1 · Miller et al. · 2019 [cited by applicant]
US 20190376956A1 · Bobrow et al. · 2019 [cited by applicant]
US 20200010891A1 · Beechem et al. · 2020 [cited by applicant]
US 20200071751A1 · Daugharthy et al. · 2020 [cited by applicant]
US 20200123597A1 · Daniel · 2020 [cited by applicant]
US 20200140920A1 · Pierce et al. · 2020 [cited by applicant]
US 20200224243A1 · Desai et al. · 2020 [cited by applicant]
US 20200224244A1 · Nilsson et al. · 2020 [cited by applicant]
US 20200239946A1 · Dewal · 2020 [cited by applicant]
US 20200354774A1 · Church et al. · 2020 [cited by applicant]
US 20200354782A1 · Dewal · 2020 [cited by applicant]
US 20200362398A1 · Kishi et al. · 2020 [cited by applicant]
US 20200393343A1 · Kennedy-Darling et al. · 2020 [cited by applicant]
US 20200399689A1 · Luo et al. · 2020 [cited by applicant]
US 20210017587A1 · Cai et al. · 2021 [cited by applicant]
US 20210115504A1 · Cai et al. · 2021 [cited by applicant]
US 20210164039A1 · Wang et al. · 2021 [cited by applicant]
US 20210222234A1 · Carlson · 2021 [cited by applicant]
US 20210238662A1 · Bava et al. · 2021 [cited by applicant]
US 20210238674A1 · Bava · 2021 [cited by applicant]
US 20210254140A1 · Stahl et al. · 2021 [cited by applicant]
US 20210262018A1 · Bava et al. · 2021 [cited by applicant]
US 20210277460A1 · Bava · 2021 [cited by applicant]
US 20210340621A1 · Daugharthy et al. · 2021 [cited by applicant]
US 20210388423A1 · Bava et al. · 2021 [cited by applicant]
US 20210388424A1 · Bava · 2021 [cited by applicant]
US 20220026433A1 · Guo et al. · 2022 [cited by applicant]
US 20220049302A1 · Daugharthy et al. · 2022 [cited by applicant]
US 20220049303A1 · Busby et al. · 2022 [cited by applicant]
US 20220064697A1 · Zhuang et al. · 2022 [cited by applicant]
US 20220083832A1 · Shah · 2022 [cited by applicant]
US 20220084628A1 · Shah · 2022 [cited by applicant]
US 20220084629A1 · Shah · 2022 [cited by applicant]
US 20220128565A1 · Miller et al. · 2022 [cited by applicant]
US 20220136049A1 · Bava et al. · 2022 [cited by applicant]
US 20220186300A1 · Bava · 2022 [cited by applicant]
US 20220195498A1 · Kuhnemund et al. · 2022 [cited by applicant]
US 20220213529A1 · Kuhnemund et al. · 2022 [cited by applicant]
US 20220228200A1 · Bava · 2022 [cited by applicant]
US 20220235403A1 · Costa · 2022 [cited by applicant]
US 20220282306A1 · Bava et al. · 2022 [cited by applicant]
US 20220282316A1 · Bava · 2022 [cited by applicant]
US 20220282319A1 · Verheyen · 2022 [cited by applicant]
US 20220372570A1 · Costa · 2022 [cited by applicant]
US 20220380838A1 · Kuhnemund et al. · 2022 [cited by applicant]
US 20220403458A1 · Bava · 2022 [cited by applicant]
US 20230002808A1 · Mignardi · 2023 [cited by applicant]
US 20230012607A1 · Kuhnemund et al. · 2023 [cited by applicant]
US 20230013775A1 · Chen et al. · 2023 [cited by applicant]
US 20230015226A1 · Chen et al. · 2023 [cited by applicant]
US 20230026886A1 · Chen · 2023 [cited by applicant]
US 20230031305A1 · Hernandez Neuta et al. · 2023 [cited by applicant]
US 20230031996A1 · Hernandez Neuta et al. · 2023 [cited by applicant]
US 20230035685A1 · Hernandez Neuta et al. · 2023 [cited by applicant]
US 20230037182A1 · Bava et al. · 2023 [cited by applicant]
US 20230039148A1 · Verheyen · 2023 [cited by applicant]
US 20230041485A1 · Hernandez Neuta et al. · 2023 [cited by applicant]
US 20230044650A1 · Dockter · 2023 [cited by applicant]
US 20230057571A1 · Costa et al. · 2023 [cited by applicant]
US 20230061542A1 · Kuhnemund · 2023 [cited by applicant]
US 20230084407A1 · Hernandez Neuta et al. · 2023 [cited by applicant]
US 20230159997A1 · Belhocine et al. · 2023 [cited by applicant]
US 20230160794A1 · Dockter et al. · 2023 [cited by applicant]
US 20230183787A1 · Bava et al. · 2023 [cited by applicant]
US 20230242974A1 · Costa et al. · 2023 [cited by applicant]
US 20230279465A1 · He et al. · 2023 [cited by applicant]
US 20230279475A1 · Kuhnemund et al. · 2023 [cited by applicant]
US 20230279480A1 · Kuhnemund · 2023 [cited by applicant]
US 20230287478A1 · Bava · 2023 [cited by applicant]
US 20230314327A1 · Hoffman · 2023 [cited by applicant]
US 20230314328A1 · Costa · 2023 [cited by applicant]
US 20230323427A1 · Schnall-Levin · 2023 [cited by applicant]
US 20230323430A1 · Shastry · 2023 [cited by applicant]
US 20230323437A1 · Chen et al. · 2023 [cited by applicant]
US 20230374573A1 · Qian et al. · 2023 [cited by applicant]
US 20230374580A1 · Costa · 2023 [cited by applicant]
US 20230416821A1 · Bava et al. · 2023 [cited by applicant]
US 20240002902A1 · Jakobsen et al. · 2024 [cited by applicant]
US 20240026426A1 · Bava · 2024 [cited by applicant]
US 20240026427A1 · Kuhnemund et al. · 2024 [cited by applicant]
US 20240026439A1 · Sasaki · 2024 [cited by applicant]
US 20240026448A1 · Costa · 2024 [cited by applicant]
US 20240035070A1 · Christopherson · 2024 [cited by applicant]
US 20240035071A1 · Delaney et al. · 2024 [cited by applicant]
US 20240035072A1 · Christopherson · 2024 [cited by applicant]
US 20240043910A1 · Shastry · 2024 [cited by applicant]
US 20240043914A1 · Chen et al. · 2024 [cited by applicant]
US 20240060119A1 · Bava · 2024 [cited by applicant]
US 20240084373A1 · Shastry · 2024 [cited by applicant]
US 20240084378A1 · Marks et al. · 2024 [cited by applicant]
US 20240101978A1 · Boghospor et al. · 2024 [cited by applicant]
US 20240132938A1 · Kuhnemund · 2024 [cited by applicant]
US 20240141418A1 · Mielinis · 2024 [cited by applicant]
US 20240150816A1 · Feng et al. · 2024 [cited by applicant]
US 20240158852A1 · Belhocine et al. · 2024 [cited by applicant]
US 20240167081A1 · Bava et al. · 2024 [cited by applicant]
US 20240175082A1 · Costa · 2024 [cited by applicant]
US 20240175083A1 · Bava et al. · 2024 [cited by applicant]
US 20240191297A1 · Christopherson et al. · 2024 [cited by applicant]
US 20240209330A1 · Shastry et al. · 2024 [cited by applicant]
US 20240218424A1 · Costa et al. · 2024 [cited by applicant]
US 20240218437A1 · Belhocine et al. · 2024 [cited by applicant]
US 20240263219A1 · Kuhnemund · 2024 [cited by applicant]
US 20240263220A1 · Olofsson · 2024 [cited by applicant]
US 20240264155A1 · Costa · 2024 [cited by applicant]
IN 201931015071A · 2020 [cited by examiner]
WO WO2017143155 · 2017 [cited by applicant]
WO WO2019199579 · 2019 [cited by applicant]
WO WO2020076976 · 2020 [cited by applicant]
WO WO2020076979 · 2020 [cited by applicant]
WO WO2020096687 · 2020 [cited by applicant]
WO WO2020099640 · 2020 [cited by applicant]
WO WO2020117914 · 2020 [cited by applicant]
WO WO2020123316 · 2020 [cited by applicant]
WO WO2020123742 · 2020 [cited by applicant]
WO WO2020142490 · 2020 [cited by applicant]
WO WO2020240025 · 2020 [cited by applicant]
WO WO2020254519 · 2020 [cited by applicant]
WO WO2021123282 · 2021 [cited by applicant]
WO WO2021123286 · 2021 [cited by applicant]
WO WO2021138676 · 2021 [cited by applicant]
WO WO2021155063 · 2021 [cited by applicant]
WO WO2021168326 · 2021 [cited by applicant]
WO WO2023108139 · 2023 [cited by applicant]
WO WO2023141476 · 2023 [cited by applicant]
WO WO2023172915 · 2023 [cited by applicant]
WO WO2023192302 · 2023 [cited by applicant]
WO WO2024148300 · 2024 [cited by applicant]
Zaghlool, A., Ameur, A., Wu, C. et al. Expression profiling and in situ screening of circular RNAs in human tissues. Sci Rep 8, 16953 (2018). https://doi.org/10.1038/s41598-018-35001-6 (Year: 2018). [cited by examiner]
Baner et al., “Signal amplification of padlock probes by rolling circle replication,” Nucleic Acids Res. (1998) 26(22):5073-5078. [cited by applicant]
Bibikova et al., “Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays,” Am J Pathol. Nov. 2004; 165(5):1799-807. [cited by applicant]
Bolognesi et al., “Multiplex Staining by Sequential Immunostaining and Antibody Removal on Routine Tissue Sections,” J. Histochem. Cytochem. (2017); 65(8):431-444. [cited by applicant]
Capodieci et al., “Gene expression profiling in single cells within tissue,” Nat Methods. (2005) 2(9): 663-5. [cited by applicant]
Chen et al., “Nanoscale imaging of RNA with expansion microscopy,” Nat Methods. (2016) 13:679-684. [cited by applicant]
Chen et al., “RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells,” Science. (2015) 348(6233): aaa6090. 16 pgs. [cited by applicant]
Chen et al., “Expansion Microscopy,” Science (2015) 347(6221):543-548. [cited by applicant]
Choi et al., “Programmable in situ amplification for multiplexed imaging of mRNA expression,” Nat Biotechnol. (2010) 28(11): 1208-1212. [cited by applicant]
Conze et al., “Single molecule analysis of combinatorial splicing,” Nucleic Acids Res. (2010) 38(16): e163. [cited by applicant]
Dean et al., “Rapid Amplification Of Plasmid And Phage DNA Using Phi29 DNA Polymerase And Multiply-Primed Rolling Circle Amplification,” Genome Research (2001) 11:1095-1099. [cited by applicant]
Dirks et al., “Triggered amplification by hybridization chain reaction,” Proc Natl Acad Sci U S A. (2004) 101(43): 15275-15278. [cited by applicant]
Eng et al., “Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH,” Nature. (2019) 568(7751): 235-239. [cited by applicant]
Faruqi et al., “High-throughput genotyping of single nucleotide polymorphisms with rolling circle amplification,” BMC Genomics. (2001) 2:4. [cited by applicant]
Femino et al., “Visualization of single RNA transcripts in situ,” Science. (1998) 280(5363): 585-90. [cited by applicant]
Forcucci et al., “All-plastic miniature fluorescence microscope for point-of-care readout of bead-based bioassays,” J Biomed Opt. (2015) 20(10): 105010. [cited by applicant]
Gavrilovic et al., “Automated classification of multicolored rolling circle products in dual-channel wide-field fluorescence microscopy,” Cytometry A. (2011) 79(7): 518-27. [cited by applicant]
Geiss et al., “Direct multiplexed measurement of gene expression with color-coded probe pairs,” Nat Biotechnol. (2008) 26(3): 317-25. [cited by applicant]
Glass et al., “SIMPLE: a sequential immunoperoxidase labeling and erasing method,” J Histochem Cytochem. (2009) 57(10); 899-905. [cited by applicant]
Goh, J.J.L. et al. (Jul. 2020, e-pub. Jun. 15, 2020). “Highly Specific Multiplexed RNA Imaging In Tissues With Split-FISH,” Nat Methods 17(7):689-693. doi: 10.1038/s41592-020-0858-0. Epub Jun. 15, 2020. [cited by applicant]
Goransson et al., “A single molecule array for digital targeted molecular analyses,” Nucleic Acids Res. 2009 37(1): e7. doi: 10.1093/nar/gkn921. [cited by applicant]
Gunderson et al. “Decoding randomly ordered DNA arrays.” Genomne research 14.5 (2004): 870-877. [cited by applicant]
Gyllborg et al., “Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue,” Nucleic Acids Res. (2020) 48(19): e112. [cited by applicant]
Han et al., “Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules,” Nat Biotechnol. (2001) 19(7): 631-5. [cited by applicant]
Henegariu et al., “Custom fluorescent-nucleotide synthesis as an alternative method for nucleic acid labeling,” Nature Biotechnol. (2000) 18:345. [cited by applicant]
Itzkovitz et al., “Single-molecule transcript counting of stem-cell markers in the mouse intestine,” Nat Cell Biol. (2011) 14(1): 106-14. [cited by applicant]
Itzkovitz et al., “Validating Transcripts with Probes and Imaging Technology,” Nat Methods. (2011) 8(4 Suppl): S12-S19. [cited by applicant]
Jamur et al., “Permeabilization of cell membranes,” Method Mol. Biol. (2010) 588: 63-66 (abstract only). [cited by applicant]
Korlach et al. “Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures.” [cited by applicant]
Lagunavicius et al., “Novel application of Phi29 DNA polymerase: RNA detection and analysis in vitro and in situ by target RNA-primed RCA,” RNA. (2009) 15(5):765-71. [cited by applicant]
Lakowicz et al., “Silver particles enhance emission of fluorescent DNA oligomers,” Bio Techniques (2003) 34(1); 62-66. [cited by applicant]
Larsson et al. “In situ detection and genotyping of individual mRNA molecules,” Nat Methods. (2010) 7(5):395-397. [cited by applicant]
Lee et al. “Highly Multiplexed Subcellular RNA Sequencing In Situ”, Science (2014) 343(6177):1360-1363. [cited by applicant]
Levene et al. “Zero-mode waveguides for single-molecule analysis at high concentrations.” [cited by applicant]
Levsky et al., “Fluorescence in situ hybridization: past, present and future,” J Cell Sci. (2003) 116(Pt 14): 2833-8. [cited by applicant]
Levsky et al., “Single-cell gene expression profiling,” Science. (2002) 297(5582): 836-40. [cited by applicant]
Lin et al., “Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method,” Nat Commun. (2015) 6:8390. [cited by applicant]
Liu et al. Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses. Nucleic Acids Res. (2021) 49(10): e58, 15 pages. doi: 10.1093/nar/gkab120. [cited by applicant]
Liu et al., “Direct detection of circRNA in real samples using reverse transcription—rolling circle amplification,” Anal Chim Acta. (2020) 1101:169-175. [cited by applicant]
Lizardi et al., “Mutation detection and single-molecule counting using isothermal rolling-circle amplification,” Nat Genet. (1998) 19(3): 225-232. [cited by applicant]
Lundquist et al. “Parallel confocal detection of single molecules in real time.” Optics letters 33.9 (2008): 1026-1028. [cited by applicant]
Maierhorfer et al., “Multicolor deconvolution microscopy of thick biological specimens,” Am J Pathol. (2003) 162(2): 373-9. [cited by applicant]
McGinn et al., “New technologies for DNA analysis—a review of the READNA Project,” N Biotechnol. (2016) 33(3): 311-30. doi: 10.1016/j.nbt.2015.10.003. [cited by applicant]
Meade et al. “Multiplexed DNA detection using spectrally encoded porous SiO2 photonic crystal particles,” Anal Chem. (2009) 81(7): 2618-25. [cited by applicant]
Mitra et al., “Fluorescent in situ sequencing on polymerase colonies,” Anal. Biochem. (2003) 320, 55-65. [cited by applicant]
Mohsen et al., “The Discovery of Rolling Circle Amplification and Rolling Circle Transcription,” Acc Chem Res. (2016) 49(11): 2540-2550. [cited by applicant]
Nallur et al., “Signal amplification by rolling circle amplification on DNA microarrays,” Nucleic Acids Res. (2001) 29(23): e118. [cited by applicant]
Niu et al., “Fluorescence detection for DNA using hybridization chain reaction with enzyme-amplification,” Chem C+A277ommun (Camb). (2010) 46(18): 3089-91. [cited by applicant]
Payne et al. “In situ genome sequencing resolves DNA sequence and structure in intact biological samples,” Science. (2021) 371(6532): eaay3446. doi: 10.1126/science.aay3446. Epub Dec. 31, 2020. [cited by applicant]
Pirici et al., “Antibody elution method for multiple immunohistochemistry on primary antibodies raised in the same species and of the same subtype,” J Histochem Cytochem. (2009) 57(6); 567-75. [cited by applicant]
Raj et al., “Imaging individual mRNA molecules using multiple singly labeled probes,” Nat Methods. (2008) 5(10): 877-879. [cited by applicant]
Rajeswari et al., “Multiple pathogen biomarker detection using an encoded bead array in droplet PCR,” J Microbiol Methods. (2017) 139: 22-28. [cited by applicant]
Rouhanifard et al. “ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification,” Nat Biotechnol. (2018) 17 pages. doi: 10.1038/nbt.4286. [cited by applicant]
Schweitzer et al. “Immunoassays with rolling circle DNA amplification: A versatile platform for ultrasensitive antigen detection,” Proc. Natl Acad. Sci. USA (2000) 97:10113-119. [cited by applicant]
Schweitzer et al., “Multiplexed protein profiling on microarrays by rolling-circle amplification,” Nature Biotech. (2002) 20:359-365. [cited by applicant]
Shendure et al, “Accurate multiplex polony sequencing of an evolved bacterial genome,” Science (2005) 309(5741); 1728-1732. [cited by applicant]
Song et al., “Hybridization chain reaction-based aptameric system for the highly selective and sensitive detection of protein,” Analyst. (2012) 137(6):1396-1401. [cited by applicant]
Sun et al., “Composite organic-inorganic nanoparticles as Raman labels for tissue analysis,” Nano Lett. (2007) 7(2): 351-6. [cited by applicant]
Takei et al., (Feb. 2021, e-pub Jan. 27, 2021). “Integrated Spatial Genomics Reveals Global Architecture Of Single Nuclei,” Nature 590(7845):344-350, 53 pages. doi: 10.1038/s41586-020-03126-2. [cited by applicant]
Wählby et al., “Sequential immunofluorescence staining and image analysis for detection of large numbers of antigens in individual cell nuclei,” Cytometry. (2002) 47(1): 32-41. [cited by applicant]
Weibrecht et al., “Simultaneous visualization of both signaling cascade activity and end-point gene expression in single cells,” PLoS One. (2011) 6(5): e20148. [cited by applicant]
Wetmur, “DNA Probes: Applications of the Principles of Nucleic Acid Hybridization,” Critical Reviews in Biochemistry and Molecular Biology, (1991) 26(91); 227-259. [cited by applicant]
Wilson et al., “Encoded microcarriers for high-throughput multiplexed detection,” Angew Chem Int Ed Engl. (2006) 18;45(37): 6104-17. [cited by applicant]
Wu, C. et al. “RollFISh Achieves Robust Quantification Of Single-Molecule RNA Biomarkers In Paraffin-Embedded Tumor Tissue Samples,” Commun Biol. (2018) 1:(209):1-8. doi: 10.1038/s42003-018-0218-0. [cited by applicant]
Xia et al. “Multiplexed detection of RNA using MERFISH and branched DNA amplification.” Scientific reports 9.1 (2019): 1-13. [cited by applicant]
Zhao et al., “Advances of multiplex and high throughput biomolecular detection technologies based on encoding microparticles,” Sci China Chem. (2011) 54(8):1185. [cited by applicant]
Chemeris et al., “Real-time hybridization chain reaction,” Dokl Biochem Biophys. (2008) 419: 53-55. [cited by applicant]
Chen et al., “Efficient in situ barcode sequencing using padlock probe-based BaristaSeq,” Nucleic Acids Res. (2018) 46(4): e22. [cited by applicant]
Sun et al., “Integrating barcoded neuroanatomy with spatial transcriptional profiling enables identification of gene correlates of projections,” Nat Neurosci. (2021) 24(6):873-885. [cited by applicant]