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Fine mapping of RNA isoform diversity using an innovative targeted long-read RNA sequencing protocol with novel dedicated bioinformatics pipeline
Aucouturier, Camille, Soirat, Nicolas, Castéra, Laurent, Bertrand, Denis, Atkinson, Alexandre, Lavolé, Thibaut, Goardon, Nicolas, Quesnelle, Céline, Levilly, Julien, Barbachou, Sosthène, Legros, Angelina, Caron, Olivier, Crivelli, Louise, Denizeau, Philippe, Berthet, Pascaline, Ricou, Agathe, Boulouard, Flavie, Vaur, Dominique, Krieger, Sophie, Leman, Raphael
Published in BMC genomics (30.09.2024)
Published in BMC genomics (30.09.2024)
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TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing
Wang, Feng, Xu, Yang, Wang, Robert, Zhang, Beatrice, Smith, Noah, Notaro, Amber, Gaerlan, Samantha, Kutschera, Eric, Kadash-Edmondson, Kathryn E., Xing, Yi, Lin, Lan
Published in Nature communications (08.08.2023)
Published in Nature communications (08.08.2023)
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Targeted long–read RNA sequencing reveals the complexity of CLN3 transcription and the consequences of the most common 1–kb deletion in patients with juvenile CLN3 disease
Minnis, Christopher J, Zhang, Hao-Yu, Gustavsson, Emil, Lee, Jasmaine, Anderson, Claire, Gardner, Emily, Schulz, Angela, Nickel, Miriam, Arno, Gavin, Jurkute, Neringa, Webster, Andrew R, Gammaldi, Nicola, Santorelli, Filippo M, Gissen, Paul, Mills, Phillipa, Ryten, Mina, Mole, Sara E
Published in bioRxiv (24.04.2025)
Published in bioRxiv (24.04.2025)
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High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing
Lagarde, Julien, Uszczynska-Ratajczak, Barbara, Carbonell, Silvia, Pérez-Lluch, Sílvia, Abad, Amaya, Davis, Carrie, Gingeras, Thomas R, Frankish, Adam, Harrow, Jennifer, Guigo, Roderic, Johnson, Rory
Published in Nature genetics (01.12.2017)
Published in Nature genetics (01.12.2017)
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Targeted, High-Resolution RNA Sequencing of Non-coding Genomic Regions Associated With Neuropsychiatric Functions
Hardwick, Simon A., Bassett, Maya, Kaczorowski, Dominik, Blackburn, James, Barton, Kirston, Bartonicek, Nenad, Carswell, Shaun L., Tilgner, Hagen U., Loy, Clement, Halliday, Glenda, Mercer, Tim R., Smith, Martin A., Mattick, John S.
Published in Frontiers in genetics (12.04.2019)
Published in Frontiers in genetics (12.04.2019)
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Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer
Byrne, Ashley, Le, Daniel, Sereti, Kostianna, Menon, Hari, Vaidya, Samir, Patel, Neha, Lund, Jessica, Xavier-Magalhães, Ana, Shi, Minyi, Liang, Yuxin, Sterne-Weiler, Timothy, Modrusan, Zora, Stephenson, William
Published in Nature communications (12.08.2024)
Published in Nature communications (12.08.2024)
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CHOP Researchers Develop Versatile and Low-Cost Technology for Targeted Long-read RNA Sequencing
Published in PR Newswire
(15.08.2023)
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Promoter Deletion Leading to Allele Specific Expression in a Genetically Unsolved Case of Primary Ciliary Dyskinesia
Beaman, M. Makenzie, Yin, Weining, Smith, Amanda J., Sears, Patrick R., Leigh, Margaret W., Ferkol, Thomas W., Kearney, Brendan, Olivier, Kenneth N., Kimple, Adam J., Clarke, Shannon, Huggins, Erin, Nading, Erica, Jung, Seung‐Hye, Iyengar, Apoorva K., Zou, Xue, Dang, Hong, Barrera, Alejandro, Majoros, William H., Rehder, Catherine W., Reddy, Timothy E., Ostrowski, Lawrence E., Allen, Andrew S., Knowles, Michael R., Zariwala, Maimoona A., Crawford, Gregory E.
Published in American journal of medical genetics. Part A (01.02.2025)
Published in American journal of medical genetics. Part A (01.02.2025)
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Utility analyses of AVITI sequencing chemistry
Liu, Silvia, Obert, Caroline, Yu, Yan-Ping, Zhao, Junhua, Ren, Bao-Guo, Liu, Jia-Jun, Wiseman, Kelly, Krajacich, Benjamin J., Wang, Wenjia, Metcalfe, Kyle, Smith, Mat, Ben-Yehezkel, Tuval, Luo, Jian-Hua
Published in BMC genomics (10.08.2024)
Published in BMC genomics (10.08.2024)
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Targeted long-read sequencing reveals clonally expanded HBV-associated chromosomal translocations in patients with chronic hepatitis B
van Buuren, Nicholas, Ramirez, Ricardo, Soulette, Cameron, Suri, Vithika, Han, Dong, May, Lindsey, Turner, Scott, Parvangada, P.C., Martin, Ross, Chan, Henry L.Y., Marcellin, Patrick, Buti, Maria, Bui, Nam, Bhardwaj, Neeru, Gaggar, Anuj, Li, Li, Mo, Hongmei, Feierbach, Becket
Published in JHEP reports (01.04.2022)
Published in JHEP reports (01.04.2022)
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Defining the transcriptome of PIK3CA-altered cells in a human capillary malformation using single cell long-read sequencing
Wedemeyer, Michelle A., Ding, Tianli, Garfinkle, Elizabeth A. R., Westfall, Jesse J., Navarro, Jaye B., Hernandez Gonzalez, Maria Elena, Varga, Elizabeth A., Witman, Patricia, Mardis, Elaine R., Cottrell, Catherine E., Miller, Anthony R., Miller, Katherine E.
Published in Scientific reports (25.10.2024)
Published in Scientific reports (25.10.2024)
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Long-read technologies identify a hidden LINE-1/ERV1 insertion in IQCB1 as causative variant for Senior-Løken syndrome
de Bruijn, Suzanne E., Ingeborgh van den Born, L., Derks, Ronny, Haer-Wigman, Lonneke, O’Gorman, Luke, Cremers, Frans P. M., van Beek, Ronald, Hoischen, Alexander, Roosing, Susanne, Neveling, Kornelia
Published in Npj genomic medicine (22.04.2025)
Published in Npj genomic medicine (22.04.2025)
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CHOP Researchers Develop Versatile and Low-Cost Technology for Targeted Long-read RNA Sequencing
Published in PR newswire
(15.08.2023)
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Newspaper Article
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Targeted Long-Read Sequencing Reveals Comprehensive Architecture, Burden, and Transcriptional Signatures from Hepatitis B Virus-Associated Integrations and Translocations in Hepatocellular Carcinoma Cell Lines
Ramirez, Ricardo, van Buuren, Nicholas, Gamelin, Lindsay, Soulette, Cameron, May, Lindsey, Han, Dong, Yu, Mei, Choy, Regina, Cheng, Guofeng, Bhardwaj, Neeru, Chiu, Joy, Muench, Robert C., Delaney, William E., Mo, Hongmei, Feierbach, Becket, Li, Li
Published in Journal of virology (09.09.2021)
Published in Journal of virology (09.09.2021)
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Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems
Alon, Shahar, Goodwin, Daniel R., Sinha, Anubhav, Wassie, Asmamaw T., Chen, Fei, Daugharthy, Evan R., Bando, Yosuke, Kajita, Atsushi, Xue, Andrew G., Marrett, Karl, Prior, Robert, Cui, Yi, Payne, Andrew C., Yao, Chun-Chen, Suk, Ho-Jun, Wang, Ru, Yu, Chih-Chieh (Jay), Tillberg, Paul, Reginato, Paul, Pak, Nikita, Liu, Songlei, Punthambaker, Sukanya, Iyer, Eswar P. R., Kohman, Richie E., Miller, Jeremy A., Lein, Ed S., Lako, Ana, Cullen, Nicole, Rodig, Scott, Helvie, Karla, Abravanel, Daniel L., Wagle, Nikhil, Johnson, Bruce E., Klughammer, Johanna, Slyper, Michal, Waldman, Julia, Jané-Valbuena, Judit, Rozenblatt-Rosen, Orit, Regev, Aviv, Church, George M., Marblestone, Adam H., Boyden, Edward S., Ali, H. R., Al Sa’d, M., Alon, S., Aparicio, S., Battistoni, G., Balasubramanian, S., Becker, R., Bodenmiller, B., Boyden, E. S., Bressan, D., Bruna, A., Burger, Marcel, Caldas, C., Callari, M., Cannell, I. G., Casbolt, H., Chornay, N., Cui, Y., Dariush, A., Dinh, K., Emenari, A., Eyal-Lubling, Y., Fan, J., Fatemi, A., Fisher, E., González-Solares, E. A., González-Fernández, C., Goodwin, D., Greenwood, W., Grimaldi, F., Hannon, G. J., Harris, O., Harris, S., Jauset, C., Joyce, J. A., Karagiannis, E. D., Kovačević, T., Kuett, L., Kunes, R., Küpcü Yoldaş, A., Lai, D., Laks, E., Lee, H., Lee, M., Lerda, G., Li, Y., McPherson, A., Millar, N., Mulvey, C. M., Nugent, F., O'Flanagan, C. H., Paez-Ribes, M., Pearsall, I., Qosaj, F., Roth, A. J., Rueda, O. M., Ruiz, T., Sawicka, K.
Published in Science (American Association for the Advancement of Science) (29.01.2021)
Published in Science (American Association for the Advancement of Science) (29.01.2021)
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capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements
Li, Xuemei, Lu, Keying, Chen, Xiao, Tu, Kailing, Xie, Dan
Published in Communications biology (23.09.2023)
Published in Communications biology (23.09.2023)
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Coordination of alternative splicing and alternative polyadenylation revealed by targeted long read sequencing
Zhang, Zhiping, Bae, Bongmin, Cuddleston, Winston H., Miura, Pedro
Published in Nature communications (07.09.2023)
Published in Nature communications (07.09.2023)
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