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45 results on '"Bayraktar, Omer Ali"'

1. Human skeletal muscle aging atlas

Author

Kedlian, Veronika R., Wang, Yaning, Liu, Tianliang, Chen, Xiaoping, Bolt, Liam, Tudor, Catherine, Shen, Zhuojian, Fasouli, Eirini S., Prigmore, Elena, Kleshchevnikov, Vitalii, Pett, Jan Patrick, Li, Tong, Lawrence, John E. G., Perera, Shani, Prete, Martin, Huang, Ni, Guo, Qin, Zeng, Xinrui, Yang, Lu, Polański, Krzysztof, Chipampe, Nana-Jane, Dabrowska, Monika, Li, Xiaobo, Bayraktar, Omer Ali, Patel, Minal, Kumasaka, Natsuhiko, Mahbubani, Krishnaa T., Xiang, Andy Peng, Meyer, Kerstin B., Saeb-Parsy, Kourosh, Teichmann, Sarah A., and Zhang, Hongbo

Published
2024
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2. Spatial multiomics map of trophoblast development in early pregnancy

Author

Arutyunyan, Anna, Roberts, Kenny, Troulé, Kevin, Wong, Frederick C. K., Sheridan, Megan A., Kats, Ilia, Garcia-Alonso, Luz, Velten, Britta, Hoo, Regina, Ruiz-Morales, Elias R., Sancho-Serra, Carmen, Shilts, Jarrod, Handfield, Louis-Francois, Marconato, Luca, Tuck, Elizabeth, Gardner, Lucy, Mazzeo, Cecilia Icoresi, Li, Qian, Kelava, Iva, Wright, Gavin J., Prigmore, Elena, Teichmann, Sarah A., Bayraktar, Omer Ali, Moffett, Ashley, Stegle, Oliver, Turco, Margherita Y., and Vento-Tormo, Roser

Published
2023
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4. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche

Author

Madissoon, Elo, Oliver, Amanda J., Kleshchevnikov, Vitalii, Wilbrey-Clark, Anna, Polanski, Krzysztof, Richoz, Nathan, Ribeiro Orsi, Ana, Mamanova, Lira, Bolt, Liam, Elmentaite, Rasa, Pett, J. Patrick, Huang, Ni, Xu, Chuan, He, Peng, Dabrowska, Monika, Pritchard, Sophie, Tuck, Liz, Prigmore, Elena, Perera, Shani, Knights, Andrew, Oszlanczi, Agnes, Hunter, Adam, Vieira, Sara F., Patel, Minal, Lindeboom, Rik G. H., Campos, Lia S., Matsuo, Kazuhiko, Nakayama, Takashi, Yoshida, Masahiro, Worlock, Kaylee B., Nikolić, Marko Z., Georgakopoulos, Nikitas, Mahbubani, Krishnaa T., Saeb-Parsy, Kourosh, Bayraktar, Omer Ali, Clatworthy, Menna R., Stegle, Oliver, Kumasaka, Natsuhiko, Teichmann, Sarah A., and Meyer, Kerstin B.

Published
2023
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5. Spatial genomics maps the structure, nature and evolution of cancer clones

Author

Lomakin, Artem, Svedlund, Jessica, Strell, Carina, Gataric, Milana, Shmatko, Artem, Rukhovich, Gleb, Park, Jun Sung, Ju, Young Seok, Dentro, Stefan, Kleshchevnikov, Vitalii, Vaskivskyi, Vasyl, Li, Tong, Bayraktar, Omer Ali, Pinder, Sarah, Richardson, Andrea L., Santagata, Sandro, Campbell, Peter J., Russnes, Hege, Gerstung, Moritz, Nilsson, Mats, and Yates, Lucy R.

Published
2022
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6. Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map

Author

Bayraktar, Omer Ali, Bartels, Theresa, Holmqvist, Staffan, Kleshchevnikov, Vitalii, Martirosyan, Araks, Polioudakis, Damon, Ben Haim, Lucile, Young, Adam MH, Batiuk, Mykhailo Y, Prakash, Kirti, Brown, Alexander, Roberts, Kenny, Paredes, Mercedes F, Kawaguchi, Riki, Stockley, John H, Sabeur, Khalida, Chang, Sandra M, Huang, Eric, Hutchinson, Peter, Ullian, Erik M, Hemberg, Martin, Coppola, Giovanni, Holt, Matthew G, Geschwind, Daniel H, and Rowitch, David H

Subjects
Biomedical and Clinical Sciences, Neurosciences, Genetics, Biotechnology, Brain Disorders, Human Genome, 1.1 Normal biological development and functioning, Underpinning research, Neurological, Animals, Astrocytes, Brain Mapping, Cerebral Cortex, Humans, Mice, Neurons, Transcriptome, Psychology, Cognitive Sciences, Neurology & Neurosurgery, Biological psychology
Abstract

Although the cerebral cortex is organized into six excitatory neuronal layers, it is unclear whether glial cells show distinct layering. In the present study, we developed a high-content pipeline, the large-area spatial transcriptomic (LaST) map, which can quantify single-cell gene expression in situ. Screening 46 candidate genes for astrocyte diversity across the mouse cortex, we identified superficial, mid and deep astrocyte identities in gradient layer patterns that were distinct from those of neurons. Astrocyte layer features, established in the early postnatal cortex, mostly persisted in adult mouse and human cortex. Single-cell RNA sequencing and spatial reconstruction analysis further confirmed the presence of astrocyte layers in the adult cortex. Satb2 and Reeler mutations that shifted neuronal post-mitotic development were sufficient to alter glial layering, indicating an instructive role for neuronal cues. Finally, astrocyte layer patterns diverged between mouse cortical regions. These findings indicate that excitatory neurons and astrocytes are organized into distinct lineage-associated laminae.

Published
2020

7. Single-cell roadmap of human gonadal development

Author

Garcia-Alonso, Luz, Lorenzi, Valentina, Mazzeo, Cecilia Icoresi, Alves-Lopes, João Pedro, Roberts, Kenny, Sancho-Serra, Carmen, Engelbert, Justin, Marečková, Magda, Gruhn, Wolfram H., Botting, Rachel A., Li, Tong, Crespo, Berta, van Dongen, Stijn, Kiselev, Vladimir Yu, Prigmore, Elena, Herbert, Mary, Moffett, Ashley, Chédotal, Alain, Bayraktar, Omer Ali, Surani, Azim, Haniffa, Muzlifah, and Vento-Tormo, Roser

Published
2022
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8. Cell2location maps fine-grained cell types in spatial transcriptomics

Author

Kleshchevnikov, Vitalii, Shmatko, Artem, Dann, Emma, Aivazidis, Alexander, King, Hamish W., Li, Tong, Elmentaite, Rasa, Lomakin, Artem, Kedlian, Veronika, Gayoso, Adam, Jain, Mika Sarkin, Park, Jun Sung, Ramona, Lauma, Tuck, Elizabeth, Arutyunyan, Anna, Vento-Tormo, Roser, Gerstung, Moritz, James, Louisa, Stegle, Oliver, and Bayraktar, Omer Ali

Published
2022
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9. Cells of the human intestinal tract mapped across space and time

Author

Elmentaite, Rasa, Kumasaka, Natsuhiko, Roberts, Kenny, Fleming, Aaron, Dann, Emma, King, Hamish W., Kleshchevnikov, Vitalii, Dabrowska, Monika, Pritchard, Sophie, Bolt, Liam, Vieira, Sara F., Mamanova, Lira, Huang, Ni, Perrone, Francesca, Goh Kai’En, Issac, Lisgo, Steven N., Katan, Matilda, Leonard, Steven, Oliver, Thomas R. W., Hook, C. Elizabeth, Nayak, Komal, Campos, Lia S., Domínguez Conde, Cecilia, Stephenson, Emily, Engelbert, Justin, Botting, Rachel A., Polanski, Krzysztof, van Dongen, Stijn, Patel, Minal, Morgan, Michael D., Marioni, John C., Bayraktar, Omer Ali, Meyer, Kerstin B., He, Xiaoling, Barker, Roger A., Uhlig, Holm H., Mahbubani, Krishnaa T., Saeb-Parsy, Kourosh, Zilbauer, Matthias, Clatworthy, Menna R., Haniffa, Muzlifah, James, Kylie R., and Teichmann, Sarah A.

Published
2021
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10. A human embryonic limb cell atlas resolved in space and time

Author

Zhang, Bao, primary, He, Peng, additional, Lawrence, John E. G., additional, Wang, Shuaiyu, additional, Tuck, Elizabeth, additional, Williams, Brian A., additional, Roberts, Kenny, additional, Kleshchevnikov, Vitalii, additional, Mamanova, Lira, additional, Bolt, Liam, additional, Polanski, Krzysztof, additional, Li, Tong, additional, Elmentaite, Rasa, additional, Fasouli, Eirini S., additional, Prete, Martin, additional, He, Xiaoling, additional, Yayon, Nadav, additional, Fu, Yixi, additional, Yang, Hao, additional, Liang, Chen, additional, Zhang, Hui, additional, Blain, Raphael, additional, Chedotal, Alain, additional, FitzPatrick, David R., additional, Firth, Helen, additional, Dean, Andrew, additional, Bayraktar, Omer Ali, additional, Marioni, John C., additional, Barker, Roger A., additional, Storer, Mekayla A., additional, Wold, Barbara J., additional, Zhang, Hongbo, additional, and Teichmann, Sarah A., additional

Published
2023
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11. Cells of the adult human heart

Author

Litviňuková, Monika, Talavera-López, Carlos, Maatz, Henrike, Reichart, Daniel, Worth, Catherine L., Lindberg, Eric L., Kanda, Masatoshi, Polanski, Krzysztof, Heinig, Matthias, Lee, Michael, Nadelmann, Emily R., Roberts, Kenny, Tuck, Liz, Fasouli, Eirini S., DeLaughter, Daniel M., McDonough, Barbara, Wakimoto, Hiroko, Gorham, Joshua M., Samari, Sara, Mahbubani, Krishnaa T., Saeb-Parsy, Kourosh, Patone, Giannino, Boyle, Joseph J., Zhang, Hongbo, Zhang, Hao, Viveiros, Anissa, Oudit, Gavin Y., Bayraktar, Omer Ali, Seidman, J. G., Seidman, Christine E., Noseda, Michela, Hubner, Norbert, and Teichmann, Sarah A.

Published
2020
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12. Astrocyte development and heterogeneity.

Author

Bayraktar, Omer Ali, Fuentealba, Luis C, Alvarez-Buylla, Arturo, and Rowitch, David H

Subjects
Cerebral Ventricles, Spinal Cord, Neuroglia, Astrocytes, Animals, Mammals, Humans, Models, Neurological, Adult, Neural Stem Cells, Brain Disorders, Stem Cell Research - Nonembryonic - Non-Human, Stem Cell Research, Neurosciences, Underpinning research, 1.1 Normal biological development and functioning, Neurological
Abstract

Astrocytes have many roles within the brain parenchyma, and a subpopulation restricted to germinal niches functions as neural stem cells (NSCs) that produce various types of neuronal progeny in relation to spatiotemporal factors. A growing body of evidence supports the concept of morphological and molecular differences between astrocytes in different brain regions, which might relate to their derivation from regionally patterned radial glia. Indeed, the notion that astrocytes are molecularly and functionally heterogeneous could help explain how the central nervous system (CNS) retains embryonic positional information into adulthood. Here, we discuss recent evidence for regionally encoded functions of astrocytes in the developing and adult CNS to provide an integrated concept of the origin and possible function of astrocyte heterogeneity. We focus on the regionalization of NSCs in the ventricular-subventricular zone (V-SVZ) of the adult mammalian brain and emerging evidence for a segmental organization of astrocytes in the developing spinal cord and forebrain. We propose that astrocytes' diversity will provide fundamental clues to understand regional brain organization and function.

Published
2014

14. WebAtlas pipeline for integrated single cell and spatial transcriptomic data

Author

Li, Tong, primary, Horsfall, David, additional, Basurto-Lozada, Daniela, additional, Roberts, Kenny, additional, Prete, Martin, additional, Lawrence, John E G, additional, He, Peng, additional, Tuck, Elisabeth, additional, Moore, Josh, additional, Ghazanfar, Shila, additional, Teichmann, Sarah, additional, Haniffa, Muzlifah, additional, and Bayraktar, Omer Ali, additional

Published
2023
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15. Distinct lung cell signatures define the temporal evolution of diffuse alveolar damage in fatal COVID-19

Author

Milross, Luke, primary, Hunter, Bethany, additional, McDonald, David, additional, Merces, George, additional, Thompson, Amanda, additional, Hilkens, Catharien M.U., additional, Wills, John, additional, Rees, Paul, additional, Jiwa, Kasim, additional, Cooper, Nigel, additional, Majo, Joaquim, additional, Ashwin, Helen, additional, Duncan, Christopher J.A., additional, Kaye, Paul M., additional, Bayraktar, Omer Ali, additional, Filby, Andrew, additional, and Fisher, Andrew J., additional

Published
2023
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16. Identification of a protein expression signature distinguishing early from organising diffuse alveolar damage in COVID-19 patients

Author

Ashwin, Helen, primary, Milross, Luke, additional, Wilson, Julie, additional, Majo, Joaquim, additional, Hang Lee, Jimmy Tsz, additional, Calder, Grant, additional, Hunter, Bethany, additional, James, Sally, additional, Lagos, Dimitris, additional, Signoret, Nathalie, additional, Filby, Andrew, additional, Bayraktar, Omer Ali, additional, Fisher, Andrew J, additional, and Kaye, Paul M, additional

Published
2023
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17. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche

Author

Madissoon, Elo, primary, Oliver, Amanda J., additional, Kleshchevnikov, Vitalii, additional, Wilbrey-Clark, Anna, additional, Polanski, Krzysztof, additional, Richoz, Nathan, additional, Ribeiro Orsi, Ana, additional, Mamanova, Lira, additional, Bolt, Liam, additional, Elmentaite, Rasa, additional, Pett, J. Patrick, additional, Huang, Ni, additional, Xu, Chuan, additional, He, Peng, additional, Dabrowska, Monika, additional, Pritchard, Sophie, additional, Tuck, Liz, additional, Prigmore, Elena, additional, Perera, Shani, additional, Knights, Andrew, additional, Oszlanczi, Agnes, additional, Hunter, Adam, additional, Vieira, Sara F., additional, Patel, Minal, additional, Lindeboom, Rik G. H., additional, Campos, Lia S., additional, Matsuo, Kazuhiko, additional, Nakayama, Takashi, additional, Yoshida, Masahiro, additional, Worlock, Kaylee B., additional, Nikolić, Marko Z., additional, Georgakopoulos, Nikitas, additional, Mahbubani, Krishnaa T., additional, Saeb-Parsy, Kourosh, additional, Bayraktar, Omer Ali, additional, Clatworthy, Menna R., additional, Stegle, Oliver, additional, Kumasaka, Natsuhiko, additional, Teichmann, Sarah A., additional, and Meyer, Kerstin B., additional

Published
2022
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18. Identification of a protein expression signature distinguishing early from organising diffuse alveolar damage in COVID-19 patients

Author

Ashwin, Helen, primary, Milross, Luke, additional, Wilson, Julie, additional, Majo, Joaquim, additional, Hang Lee, Jimmy Tsz, additional, Calder, Grant, additional, Hunter, Bethany, additional, James, Sally, additional, Lagos, Dimitris, additional, Signoret, Nathalie, additional, Filby, Andrew, additional, Bayraktar, Omer Ali, additional, Fisher, Andrew J., additional, and Kaye, Paul M., additional

Published
2022
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19. Spatially resolved single-cell multiomics map of human trophoblast differentiation in early pregnancy

Author

Arutyunyan, Anna, primary, Roberts, Kenny, additional, Sheridan, Megan A, additional, Kats, Ilia, additional, Garcia-Alonso, Luz, additional, Velten, Britta, additional, Hoo, Regina, additional, Lozano, Kevin Troulé, additional, Handfield, Louis-Francois, additional, Marconato, Luca, additional, Tuck, Elizabeth, additional, Gardner, Lucy, additional, Mazzeo, Cecilia Icoresi, additional, Kelava, Iva, additional, Prigmore, Elena, additional, Teichmann, Sarah A, additional, Bayraktar, Omer Ali, additional, Moffett, Ashley, additional, Stegle, Oliver, additional, Turco, Margherita Y, additional, and Vento-Tormo, Roser, additional

Published
2022
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21. A spatial multi-omics atlas of the human lung reveals a novel gland-associated immune niche

Author

Meyer, Kerstin, primary, Madissoon, Elo, additional, Oliver, Amanda, additional, Kleshchevnikov, Vitalii, additional, Wilbrey-Clark, Anna, additional, Polański, Krzysztof, additional, Richoz, Nathan, additional, Orsi, Ana Elisa Ribeiro, additional, Mamanova, Lira, additional, Bolt, Liam, additional, Elmentaite, Rasa, additional, Pett, Jan, additional, Huang, Ni, additional, Xu, Chuan, additional, He, Peng, additional, Dabrowska, Monika, additional, Pritchard, Sophie, additional, Tuck, Elizabeth, additional, Prigmore, Elena, additional, Perera, Shani, additional, Knights, Andrew, additional, Oszlanczi, Agnes, additional, Hunter, Adam, additional, Vieira, Sara Filipa, additional, Patel, Minal, additional, Yoshida, Masahiro, additional, Worlock, Kaylee, additional, Lindeboom, Rik, additional, Nikolic, Marko, additional, Georgakopoulos, Nikitas, additional, Mahbubani, Krishna, additional, Saeb-Parsy, Kourosh, additional, Bayraktar, Omer Ali, additional, Clatworthy, Menna, additional, Stegle, Oliver, additional, Kumasaka, Natsuhiko, additional, and Teichmann, Sarah, additional

Published
2022
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22. Loss of function variant in SMIM1 is associated with reduced energy expenditure and weight gain

Author

Frontini, Mattia, primary, Stefanucci, Luca, additional, Moslemi, Camous, additional, Tome, Ana, additional, Virtue, Samuel, additional, Gleadall, Nicholas, additional, Watson, Laura, additional, Kwa, Jing, additional, Burden, Frances, additional, Farrow, Samantha, additional, Chen, Ji, additional, Võsa, Urmo, additional, Burling, Keith, additional, Baker, Peter, additional, Warner, James, additional, Frary, Amy, additional, Rehnstrom, Karola, additional, Ashford, Sofie, additional, Piper, Jo, additional, Biggs, Gail, additional, Erber, Wendy, additional, Hoffman, Gary, additional, Schoenmakers, Nadia, additional, Erikstrup, Christian, additional, Rieneck, Klaus, additional, Dziegiel, Morten, additional, Ullum, Henrik, additional, Azzu, Vian, additional, Vacca, Michele, additional, Bayraktar, Omer Ali, additional, Vidal-Puig, Antonio, additional, Ostrowski, Sisse, additional, Astle, William, additional, Olsson, Martin L., additional, Storry, Jill R., additional, Pedersen, Ole, additional, Ouwehand, Willem, additional, Chatterjee, Krishna, additional, and Vuckovic, Dragana, additional

Published
2022
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23. A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche

Author

Madissoon, Elo, primary, Oliver, Amanda J., additional, Kleshchevnikov, Vitalii, additional, Wilbrey-Clark, Anna, additional, Polanski, Krzysztof, additional, Orsi, Ana Ribeiro, additional, Mamanova, Lira, additional, Bolt, Liam, additional, Richoz, Nathan, additional, Elmentaite, Rasa, additional, Pett, J. Patrick, additional, Huang, Ni, additional, He, Peng, additional, Dabrowska, Monika, additional, Pritchard, Sophie, additional, Tuck, Liz, additional, Prigmore, Elena, additional, Knights, Andrew, additional, Oszlanczi, Agnes, additional, Hunter, Adam, additional, Vieira, Sara F., additional, Patel, Minal, additional, Georgakopoulos, Nikitas, additional, Mahbubani, Krishnaa, additional, Saeb-Parsy, Kourosh, additional, Clatworthy, Menna, additional, Bayraktar, Omer Ali, additional, Stegle, Oliver, additional, Kumasaka, Natsuhiko, additional, Teichmann, Sarah A., additional, and Meyer, Kerstin B., additional

Published
2021
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24. Single-cell roadmap of human gonadal development

Author

Vento-Tormo, Roser, primary, Garcia-Alonso, Luz, additional, Lorenzi, Valentina, additional, Mazzeo, Cecilia, additional, Sancho-Serra, Carmen, additional, Roberts, Kenny, additional, Engelbert, Justin, additional, Alves-Lopes, João, additional, Marečková, Magda, additional, Botting, Rachel, additional, Li, Tong, additional, Crespo, Berta, additional, Dongen, Stijn van, additional, Kiselev, Vladimir, additional, Prigmore, Elena, additional, Moffett, Ashley, additional, Herbert, Mary, additional, Bayraktar, Omer Ali, additional, Surani, Azim, additional, and Haniffa, Muzlifah, additional

Published
2021
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25. Spatial genomics maps the structure, character and evolution of cancer clones

Author

Lomakin, Artem, primary, Svedlund, Jessica, additional, Strell, Carina, additional, Gataric, Milana, additional, Shmatko, Artem, additional, Park, Jun Sung, additional, Ju, Young Seok, additional, Dentro, Stefan, additional, Kleshchevnikov, Vitalii, additional, Vaskivskyi, Vasyl, additional, Li, Tong, additional, Bayraktar, Omer Ali, additional, Moore, Luiza, additional, Pinder, Sarah, additional, Richardson, Andrea L, additional, Campbell, Peter J, additional, Gerstung, Moritz, additional, Nilsson, Mats, additional, and Yates, Lucy R, additional

Published
2021
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27. Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn’s Disease

Author

Elmentaite, Rasa, primary, Ross, Alexander D.B., additional, Roberts, Kenny, additional, James, Kylie R., additional, Ortmann, Daniel, additional, Gomes, Tomás, additional, Nayak, Komal, additional, Tuck, Liz, additional, Pritchard, Sophie, additional, Bayraktar, Omer Ali, additional, Heuschkel, Robert, additional, Vallier, Ludovic, additional, Teichmann, Sarah A., additional, and Zilbauer, Matthias, additional

Published
2020
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28. Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics

Author

Kleshchevnikov, Vitalii, primary, Shmatko, Artem, additional, Dann, Emma, additional, Aivazidis, Alexander, additional, King, Hamish W, additional, Li, Tong, additional, Lomakin, Artem, additional, Kedlian, Veronika, additional, Jain, Mika Sarkin, additional, Park, Jun Sung, additional, Ramona, Lauma, additional, Tuck, Elizabeth, additional, Arutyunyan, Anna, additional, Vento-Tormo, Roser, additional, Gerstung, Moritz, additional, James, Louisa, additional, Stegle, Oliver, additional, and Bayraktar, Omer Ali, additional

Published
2020
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30. Single-cell in situ transcriptomic map of astrocyte cortical layer diversity

Author

Bayraktar, Omer Ali, primary, Bartels, Theresa, additional, Polioudakis, Damon, additional, Holmqvist, Staffan, additional, Haim, Lucile Ben, additional, Young, Adam M.H., additional, Prakash, Kirti, additional, Brown, Alexander, additional, Paredes, Mercedes F., additional, Kawaguchi, Riki, additional, Stockley, John, additional, Sabeur, Khalida, additional, Chang, Sandra M., additional, Huang, Eric, additional, Hutchinson, Peter, additional, Ullian, Erik M., additional, Geschwind, Daniel H., additional, Coppola, Giovanni, additional, and Rowitch, David H., additional

Published
2018
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35. Drosophila type II neuroblast lineages keep Prospero levels low to generate large clones that contribute to the adult brain central complex.

Author

Bayraktar, Omer Ali, Boone, Jason Q., Drummond, Michael L., and Doe, Chris Q.

Subjects
*HOMEOSTASIS, *PHYSIOLOGICAL control systems, *NEURAL stem cells, *MULTIPOTENT stem cells, *DEVELOPMENTAL neurobiology
Abstract

Tissue homeostasis depends on the ability of stem cells to properly regulate self-renewal versus differentiation. Drosophila neural stem cells (neuroblasts) are a model system to study self-renewal and differentiation. Recent work has identified two types of larval neuroblasts that have different self-renewal/differentiation properties. Type I neuroblasts bud off a series of small basal daughter cells (ganglion mother cells) that each generate two neurons. Type II neuroblasts bud off small basal daughter cells called intermediate progenitors (INPs), with each INP generating 6 to 12 neurons. Type I neuroblasts and INPs have nuclear Asense and cytoplasmic Prospero, whereas type II neuroblasts lack both these transcription factors. Here we test whether Prospero distinguishes type I/II neuroblast identity or proliferation profile, using several newly characterized Gal4 lines. We misexpress prospero using the 19H09- Gal4 line (expressed in type II neuroblasts but no adjacent type I neuroblasts) or 9D11-Gal4 line (expressed in INPs but not type II neuroblasts). We find that differential prospero expression does not distinguish type I and type II neuroblast identities, but Prospero regulates proliferation in both type I and type II neuroblast lineages. In addition, we use 9D11 lineage tracing to show that type II lineages generate both small-field and large-field neurons within the adult central complex, a brain region required for locomotion, flight, and visual pattern memory. [ABSTRACT FROM AUTHOR]

Published
2010
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36. Single-cell roadmap of human gonadal development

Author

Garcia-Alonso, Luz, Lorenzi, Valentina, Mazzeo, Cecilia Icoresi, Alves-Lopes, João Pedro, Roberts, Kenny, Sancho-Serra, Carmen, Engelbert, Justin, Marečková, Magda, Gruhn, Wolfram H, Botting, Rachel A, Li, Tong, Crespo, Berta, Van Dongen, Stijn, Kiselev, Vladimir Yu, Prigmore, Elena, Herbert, Mary, Moffett, Ashley, Chédotal, Alain, Bayraktar, Omer Ali, Surani, Azim, Haniffa, Muzlifah, Vento-Tormo, Roser, Lorenzi, Valentina [0000-0002-3111-4006], Roberts, Kenny [0000-0001-6155-0821], Marečková, Magda [0000-0002-4897-5013], Gruhn, Wolfram H [0000-0001-6072-1916], Botting, Rachel A [0000-0001-9595-4605], Li, Tong [0000-0002-8240-4476], Crespo, Berta [0000-0003-0006-009X], Prigmore, Elena [0000-0001-8870-0316], Moffett, Ashley [0000-0002-8388-9073], Chédotal, Alain [0000-0001-7577-3794], Bayraktar, Omer Ali [0000-0001-6055-277X], Vento-Tormo, Roser [0000-0002-9870-8474], Apollo - University of Cambridge Repository, and Surani, Azim [0000-0002-8640-4318]

Subjects
Male, Sex Differentiation, Immunoglobulins, 45/23, 38/91, 14/32, Mice, PAX8 Transcription Factor, Pregnancy, 631/136/142, Testis, Animals, Humans, Cell Lineage, Receptors, Immunologic, Granulosa Cells, Membrane Glycoproteins, Multidisciplinary, Macrophages, Ovary, article, Membrane Proteins, 45/15, Chromatin, Pregnancy Trimester, First, Germ Cells, Microscopy, Fluorescence, Pregnancy Trimester, Second, Female, 38/39, 64/60, Single-Cell Analysis, 631/80, Transcriptome
Abstract

Gonadal development is a complex process that involves sex determination followed by divergent maturation into either testes or ovaries1. Historically, limited tissue accessibility, a lack of reliable in vitro models and critical differences between humans and mice have hampered our knowledge of human gonadogenesis, despite its importance in gonadal conditions and infertility. Here, we generated a comprehensive map of first- and second-trimester human gonads using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays and fluorescent microscopy. We extracted human-specific regulatory programmes that control the development of germline and somatic cell lineages by profiling equivalent developmental stages in mice. In both species, we define the somatic cell states present at the time of sex specification, including the bipotent early supporting population that, in males, upregulates the testis-determining factor SRY and sPAX8s, a gonadal lineage located at the gonadal–mesonephric interface. In females, we resolve the cellular and molecular events that give rise to the first and second waves of granulosa cells that compartmentalize the developing ovary to modulate germ cell differentiation. In males, we identify human SIGLEC15+ and TREM2+ fetal testicular macrophages, which signal to somatic cells outside and inside the developing testis cords, respectively. This study provides a comprehensive spatiotemporal map of human and mouse gonadal differentiation, which can guide in vitro gonadogenesis.

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37. Cells of the adult human heart

Author

Litviňuková, Monika, Talavera-López, Carlos, Maatz, Henrike, Reichart, Daniel, Worth, Catherine L., Lindberg, Eric L., Kanda, Masatoshi, Polanski, Krzysztof, Heinig, Matthias, Lee, Michael, Nadelmann, Emily R., Roberts, Kenny, Tuck, Liz, Fasouli, Eirini S., DeLaughter, Daniel M., McDonough, Barbara, Wakimoto, Hiroko, Gorham, Joshua M., Samari, Sara, Mahbubani, Krishnaa T., Saeb-Parsy, Kourosh, Patone, Giannino, Boyle, Joseph J., Zhang, Hongbo, Zhang, Hao, Viveiros, Anissa, Oudit, Gavin Y., Bayraktar, Omer Ali, Seidman, J. G., Seidman, Christine E., Noseda, Michela, Hubner, Norbert, and Teichmann, Sarah A.

Subjects
631/208/199, 14/32, 45/62, 692/308/2056, article, 13, 3. Good health, 38/91
Abstract

Cardiovascular disease is the leading cause of death worldwide. Advanced insights into disease mechanisms and therapeutic strategies require a deeper understanding of the molecular processes involved in the healthy heart. Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavour. Here, using state-of-the-art analyses of large-scale single-cell and single-nucleus transcriptomes, we characterize six anatomical adult heart regions. Our results highlight the cellular heterogeneity of cardiomyocytes, pericytes and fibroblasts, and reveal distinct atrial and ventricular subsets of cells with diverse developmental origins and specialized properties. We define the complexity of the cardiac vasculature and its changes along the arterio-venous axis. In the immune compartment, we identify cardiac-resident macrophages with inflammatory and protective transcriptional signatures. Furthermore, analyses of cell-to-cell interactions highlight different networks of macrophages, fibroblasts and cardiomyocytes between atria and ventricles that are distinct from those of skeletal muscle. Our human cardiac cell atlas improves our understanding of the human heart and provides a valuable reference for future studies.

38. Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map

Author

Bayraktar, Omer Ali, Bartels, Theresa, Holmqvist, Staffan, Kleshchevnikov, Vitalii, Martirosyan, Araks, Polioudakis, Damon, Ben Haim, Lucile, Young, Adam MH, Batiuk, Mykhailo Y, Prakash, Kirti, Brown, Alexander, Roberts, Kenny, Paredes, Mercedes F, Kawaguchi, Riki, Stockley, John H, Sabeur, Khalida, Chang, Sandra M, Huang, Eric, Hutchinson, Peter, Ullian, Erik M, Hemberg, Martin, Coppola, Giovanni, Holt, Matthew G, Geschwind, Daniel H, and Rowitch, David H

Subjects
Cerebral Cortex, Neurons, Brain Mapping, Mice, Astrocytes, Animals, Humans, Transcriptome, 3. Good health
Abstract

Although the cerebral cortex is organized into six excitatory neuronal layers, it is unclear whether glial cells show distinct layering. In the present study, we developed a high-content pipeline, the large-area spatial transcriptomic (LaST) map, which can quantify single-cell gene expression in situ. Screening 46 candidate genes for astrocyte diversity across the mouse cortex, we identified superficial, mid and deep astrocyte identities in gradient layer patterns that were distinct from those of neurons. Astrocyte layer features, established in the early postnatal cortex, mostly persisted in adult mouse and human cortex. Single-cell RNA sequencing and spatial reconstruction analysis further confirmed the presence of astrocyte layers in the adult cortex. Satb2 and Reeler mutations that shifted neuronal post-mitotic development were sufficient to alter glial layering, indicating an instructive role for neuronal cues. Finally, astrocyte layer patterns diverged between mouse cortical regions. These findings indicate that excitatory neurons and astrocytes are organized into distinct lineage-associated laminae.

39. Cells of the adult human heart

Author

Litviňuková, Monika, Talavera-López, Carlos, Maatz, Henrike, Reichart, Daniel, Worth, Catherine L, Lindberg, Eric L, Kanda, Masatoshi, Polanski, Krzysztof, Heinig, Matthias, Lee, Michael, Nadelmann, Emily R, Roberts, Kenny, Tuck, Liz, Fasouli, Eirini S, DeLaughter, Daniel M, McDonough, Barbara, Wakimoto, Hiroko, Gorham, Joshua M, Samari, Sara, Mahbubani, Krishnaa T, Saeb-Parsy, Kourosh, Patone, Giannino, Boyle, Joseph J, Zhang, Hongbo, Zhang, Hao, Viveiros, Anissa, Oudit, Gavin Y, Bayraktar, Omer Ali, Seidman, JG, Seidman, Christine E, Noseda, Michela, Hubner, Norbert, and Teichmann, Sarah A

Subjects
Adult, Male, Heart Ventricles, Epithelium, Adipocytes, Homeostasis, Humans, Myocytes, Cardiac, Heart Atria, Muscle, Skeletal, Neurons, SARS-CoV-2, Gene Expression Profiling, Macrophages, Myocardium, Epithelial Cells, Fibroblasts, 3. Good health, Female, Angiotensin-Converting Enzyme 2, Single-Cell Analysis, Stromal Cells, Pericytes, Transcriptome, Genome-Wide Association Study, Receptors, Coronavirus
Abstract

Cardiovascular disease is the leading cause of death worldwide. Advanced insights into disease mechanisms and therapeutic strategies require a deeper understanding of the molecular processes involved in the healthy heart. Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavour. Here, using state-of-the-art analyses of large-scale single-cell and single-nucleus transcriptomes, we characterize six anatomical adult heart regions. Our results highlight the cellular heterogeneity of cardiomyocytes, pericytes and fibroblasts, and reveal distinct atrial and ventricular subsets of cells with diverse developmental origins and specialized properties. We define the complexity of the cardiac vasculature and its changes along the arterio-venous axis. In the immune compartment, we identify cardiac-resident macrophages with inflammatory and protective transcriptional signatures. Furthermore, analyses of cell-to-cell interactions highlight different networks of macrophages, fibroblasts and cardiomyocytes between atria and ventricles that are distinct from those of skeletal muscle. Our human cardiac cell atlas improves our understanding of the human heart and provides a valuable reference for future studies.

40. Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn's Disease

Author

Elmentaite, Rasa, Ross, Alexander DB, Roberts, Kenny, James, Kylie R, Ortmann, Daniel, Gomes, Tomás, Nayak, Komal, Tuck, Liz, Pritchard, Sophie, Bayraktar, Omer Ali, Heuschkel, Robert, Vallier, Ludovic, Teichmann, Sarah A, and Zilbauer, Matthias

Subjects
intestinal stem cells, Adolescent, human fetal gut development, pediatric Crohn's disease, single-cell RNA sequencing, 3. Good health, Receptors, G-Protein-Coupled, Crohn Disease, inflammatory bowel disease, intestinal organoids, villus formation, Humans, RNA-Seq, Intestinal Mucosa, Single-Cell Analysis, Child, Transcriptome, Cells, Cultured, Transcription Factors
Abstract

Human gut development requires the orchestrated interaction of differentiating cell types. Here, we generate an in-depth single-cell map of the developing human intestine at 6-10 weeks post-conception. Our analysis reveals the transcriptional profile of cycling epithelial precursor cells; distinct from LGR5-expressing cells. We propose that these cells may contribute to differentiated cell subsets via the generation of LGR5-expressing stem cells and receive signals from surrounding mesenchymal cells. Furthermore, we draw parallels between the transcriptomes of ex vivo tissues and in vitro fetal organoids, revealing the maturation of organoid cultures in a dish. Lastly, we compare scRNA-seq profiles from pediatric Crohn's disease epithelium alongside matched healthy controls to reveal disease-associated changes in the epithelial composition. Contrasting these with the fetal profiles reveals the re-activation of fetal transcription factors in Crohn's disease. Our study provides a resource available at www.gutcellatlas.org, and underscores the importance of unraveling fetal development in understanding disease.

41. Cells of the adult human heart

Author

Litviňuková, Monika, Talavera-López, Carlos, Maatz, Henrike, Reichart, Daniel, Worth, Catherine L., Lindberg, Eric L., Kanda, Masatoshi, Polanski, Krzysztof, Heinig, Matthias, Lee, Michael, Nadelmann, Emily R., Roberts, Kenny, Tuck, Liz, Fasouli, Eirini S., DeLaughter, Daniel M., McDonough, Barbara, Wakimoto, Hiroko, Gorham, Joshua M., Samari, Sara, Mahbubani, Krishnaa T., Saeb-Parsy, Kourosh, Patone, Giannino, Boyle, Joseph J., Zhang, Hongbo, Zhang, Hao, Viveiros, Anissa, Oudit, Gavin Y., Bayraktar, Omer Ali, Seidman, J. G., Seidman, Christine E., Noseda, Michela, Hubner, Norbert, and Teichmann, Sarah A.

Subjects
631/208/199, 14/32, 45/62, 692/308/2056, article, 13, 3. Good health, 38/91
Abstract

Cardiovascular disease is the leading cause of death worldwide. Advanced insights into disease mechanisms and therapeutic strategies require a deeper understanding of the molecular processes involved in the healthy heart. Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavour. Here, using state-of-the-art analyses of large-scale single-cell and single-nucleus transcriptomes, we characterize six anatomical adult heart regions. Our results highlight the cellular heterogeneity of cardiomyocytes, pericytes and fibroblasts, and reveal distinct atrial and ventricular subsets of cells with diverse developmental origins and specialized properties. We define the complexity of the cardiac vasculature and its changes along the arterio-venous axis. In the immune compartment, we identify cardiac-resident macrophages with inflammatory and protective transcriptional signatures. Furthermore, analyses of cell-to-cell interactions highlight different networks of macrophages, fibroblasts and cardiomyocytes between atria and ventricles that are distinct from those of skeletal muscle. Our human cardiac cell atlas improves our understanding of the human heart and provides a valuable reference for future studies.

42. Cells of the human intestinal tract mapped across space and time

Author

Cecilia Domínguez Conde, Ni Huang, Omer Ali Bayraktar, Krishnaa T. Mahbubani, Holm H. Uhlig, Justin Engelbert, Steven Leonard, Emma Dann, Minal Patel, Aaron M. Fleming, Sara F. Vieira, C. Elizabeth Hook, Sarah A. Teichmann, Lia S. Campos, Emily Stephenson, Issac Goh Kai’En, Sophie Pritchard, Stijn van Dongen, Michael D Morgan, Kourosh Saeb-Parsy, Krzysztof Polanski, Rasa Elmentaite, Kenny Roberts, John C. Marioni, Thomas R. W. Oliver, Natsuhiko Kumasaka, Matthias Zilbauer, Roger A. Barker, Francesca Perrone, Kylie R. James, Kerstin B Meyer, Muzlifah Haniffa, Komal Nayak, Menna R. Clatworthy, Vitalii Kleshchevnikov, Steven Lisgo, Liam Bolt, Lira Mamanova, Xiaoling He, Monika Dabrowska, Rachel A. Botting, Matilda Katan, Hamish W King, Elmentaite, Rasa [0000-0001-7366-5466], Kumasaka, Natsuhiko [0000-0002-3557-0375], Roberts, Kenny [0000-0001-6155-0821], Dann, Emma [0000-0002-7400-7438], King, Hamish W. [0000-0001-5972-8926], Bolt, Liam [0000-0001-7293-0774], Vieira, Sara F. [0000-0002-1021-3021], Mamanova, Lira [0000-0003-1463-8622], Katan, Matilda [0000-0001-9992-8375], Oliver, Thomas R. W. [0000-0003-4306-0102], Domínguez Conde, Cecilia [0000-0002-8684-4655], Botting, Rachel A. [0000-0001-9595-4605], Polanski, Krzysztof [0000-0002-2586-9576], Morgan, Michael D. [0000-0003-0757-0711], Marioni, John C. [0000-0001-9092-0852], Bayraktar, Omer Ali [0000-0001-6055-277X], Meyer, Kerstin B. [0000-0001-5906-1498], Uhlig, Holm H. [0000-0002-6111-7355], Mahbubani, Krishnaa T. [0000-0002-1327-2334], Saeb-Parsy, Kourosh [0000-0002-0633-3696], Zilbauer, Matthias [0000-0002-7272-0547], Haniffa, Muzlifah [0000-0002-3927-2084], James, Kylie R. [0000-0002-7107-0650], Teichmann, Sarah A. [0000-0002-6294-6366], Apollo - University of Cambridge Repository, King, Hamish W [0000-0001-5972-8926], Vieira, Sara F [0000-0002-1021-3021], Oliver, Thomas RW [0000-0003-4306-0102], Botting, Rachel A [0000-0001-9595-4605], Morgan, Michael D [0000-0003-0757-0711], Marioni, John C [0000-0001-9092-0852], Meyer, Kerstin B [0000-0001-5906-1498], Uhlig, Holm H [0000-0002-6111-7355], Mahbubani, Krishnaa T [0000-0002-1327-2334], James, Kylie R [0000-0002-7107-0650], Teichmann, Sarah A [0000-0002-6294-6366], and Oliver, Thomas R W [0000-0003-4306-0102]

Subjects
Aging, Time Factors, Organogenesis, Cell, Datasets as Topic, Inflammatory bowel disease, 14, Enteric Nervous System, Mice, Crohn Disease, Child, 631/114/2391, health care economics and organizations, Crohn's disease, Multidisciplinary, article, humanities, Cell biology, Intestines, medicine.anatomical_structure, Health, Female, 38/39, medicine.symptom, 631/136, Signal Transduction, Adult, Cellular signalling networks, education, Inflammation, Biology, 38/91, 14/32, Immune system, Fetus, Spatio-Temporal Analysis, 692/699/1503/257/1402, Developmental biology, medicine, Animals, Humans, 45, Receptors, IgG, Epithelial Cells, medicine.disease, Embryonic stem cell, Gastrointestinal Microbiome, Mice, Inbred C57BL, Metagenome, Enteric nervous system, Lymph Nodes
Abstract

Funder: Medical Research Council, The cellular landscape of the human intestinal tract is dynamic throughout life, developing in utero and changing in response to functional requirements and environmental exposures. Here, to comprehensively map cell lineages, we use single-cell RNA sequencing and antigen receptor analysis of almost half a million cells from up to 5 anatomical regions in the developing and up to 11 distinct anatomical regions in the healthy paediatric and adult human gut. This reveals the existence of transcriptionally distinct BEST4 epithelial cells throughout the human intestinal tract. Furthermore, we implicate IgG sensing as a function of intestinal tuft cells. We describe neural cell populations in the developing enteric nervous system, and predict cell-type-specific expression of genes associated with Hirschsprung's disease. Finally, using a systems approach, we identify key cell players that drive the formation of secondary lymphoid tissue in early human development. We show that these programs are adopted in inflammatory bowel disease to recruit and retain immune cells at the site of inflammation. This catalogue of intestinal cells will provide new insights into cellular programs in development, homeostasis and disease.

Published
2021
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43. Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map

Author

Matthew Holt, John H. Stockley, Riki Kawaguchi, Araks Martirosyan, Lucile Ben Haim, Martin Hemberg, Peter J. Hutchinson, Vitalii Kleshchevnikov, Khalida Sabeur, Kirti Prakash, Mykhailo Y. Batiuk, Theresa Bartels, Adam Young, Daniel H. Geschwind, Eric J. Huang, Staffan Holmqvist, Kenny Roberts, Omer Ali Bayraktar, Mercedes F. Paredes, David H. Rowitch, Sandra Chang, Giovanni Coppola, Damon Polioudakis, Erik M. Ullian, Alexander Brown, Bayraktar, Omer Ali [0000-0001-6055-277X], Holmqvist, Staffan [0000-0001-6709-6666], Kleshchevnikov, Vitalii [0000-0001-9110-7441], Batiuk, Mykhailo Y [0000-0001-6681-4048], Roberts, Kenny [0000-0001-6155-0821], Stockley, John H [0000-0002-7385-8310], Huang, Eric [0000-0002-5381-3801], Hemberg, Martin [0000-0001-8895-5239], Holt, Matthew G [0000-0002-8958-4027], Geschwind, Daniel H [0000-0003-2896-3450], Rowitch, David H [0000-0002-0079-0060], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Candidate gene, 1.1 Normal biological development and functioning, Biology, Article, Transcriptome, 03 medical and health sciences, Mice, 0302 clinical medicine, Reeler, Underpinning research, Cortex (anatomy), Gene expression, medicine, Genetics, Psychology, Animals, Humans, Cerebral Cortex, Neurons, Brain Mapping, Neurology & Neurosurgery, General Neuroscience, Human Genome, Neurosciences, 3. Good health, Brain Disorders, 030104 developmental biology, medicine.anatomical_structure, Cerebral cortex, Astrocytes, Neurological, Excitatory postsynaptic potential, Cognitive Sciences, Neuroscience, 030217 neurology & neurosurgery, Astrocyte, Biotechnology
Abstract

Although the cerebral cortex is organized into six excitatory neuronal layers, it is unclear whether glial cells show distinct layering. In the present study, we developed a high-content pipeline, the large-area spatial transcriptomic (LaST) map, which can quantify single-cell gene expression in situ. Screening 46 candidate genes for astrocyte diversity across the mouse cortex, we identified superficial, mid and deep astrocyte identities in gradient layer patterns that were distinct from those of neurons. Astrocyte layer features, established in the early postnatal cortex, mostly persisted in adult mouse and human cortex. Single-cell RNA sequencing and spatial reconstruction analysis further confirmed the presence of astrocyte layers in the adult cortex. Satb2 and Reeler mutations that shifted neuronal post-mitotic development were sufficient to alter glial layering, indicating an instructive role for neuronal cues. Finally, astrocyte layer patterns diverged between mouse cortical regions. These findings indicate that excitatory neurons and astrocytes are organized into distinct lineage-associated laminae. ispartof: NATURE NEUROSCIENCE vol:23 issue:4 pages:500-+ ispartof: location:United States status: published

Published
2018

44. Generation of Mammalian Astrocyte Functional Heterogeneity.

Author

Bartels T, Rowitch DH, and Bayraktar OA

Abstract

Mammalian astrocytes have regional roles within the brain parenchyma. Indeed, the notion that astrocytes are molecularly heterogeneous could help explain how the central nervous system (CNS) retains embryonic positional information through development into specialized regions into adulthood. A growing body of evidence supports the concept of morphological and molecular differences between astrocytes in different brain regions, which might relate to their derivation from regionally patterned radial glia and/or local neuron inductive cues. Here, we review evidence for regionally encoded functions of astrocytes to provide an integrated concept on lineage origins and heterogeneity to understand regional brain organization, as well as emerging technologies to identify and further investigate novel roles for astrocytes., (Copyright © 2024 Cold Spring Harbor Laboratory Press; all rights reserved.)

Published
2024
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45. Automation of Multiplexed RNAscope Single-Molecule Fluorescent In Situ Hybridization and Immunohistochemistry for Spatial Tissue Mapping.

Author

Roberts K and Bayraktar OA

Subjects
Humans, Image Processing, Computer-Assisted, RNA genetics, Signal-To-Noise Ratio, Immunohistochemistry methods, In Situ Hybridization, Fluorescence methods, RNA isolation & purification, Single Molecule Imaging methods
Abstract

In situ transcriptomic methods hold immense promise for spatially resolved mapping of cell types across human tissues. Here, we describe a protocol for automated single-molecule fluorescent in situ hybridization (smFISH) on standard histology sections at high throughput. We focus on the RNAscope smFISH assay that combines branched DNA amplification with tyramide signal amplification (TSA) to obtain high signal-to-noise ratio for tissue imaging. We describe the use of the robotic Leica BOND RX system for automation of liquid handling and the combination of the RNAscope assay with TSA-based immunohistochemistry without the need for specialized demultiplexed imaging.

Published
2020
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