LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 7 of total 7

Search options

  1. Article ; Online: Protocol for flow cytometry-assisted single-nucleus RNA sequencing of human and mouse adipose tissue with sample multiplexing.

    Gulko, Anton / Essene, Adam / Belmont-Rausch, Dylan Matthew / Veregge, Molly / Pant, Deepti / Tenen, Danielle / Kapel, Benedicte Schultz / Emont, Margo P / Pers, Tune H / Rosen, Evan D / Tsai, Linus T

    STAR protocols

    2024  Volume 5, Issue 1, Page(s) 102893

    Abstract: Adipocyte size and fragility and commercial kit costs impose significant limitations on single-cell RNA sequencing of adipose tissue. Accordingly, we developed a workflow to isolate and sample-barcode nuclei from individual adipose tissue samples, ... ...

    Abstract Adipocyte size and fragility and commercial kit costs impose significant limitations on single-cell RNA sequencing of adipose tissue. Accordingly, we developed a workflow to isolate and sample-barcode nuclei from individual adipose tissue samples, integrating flow cytometry for quality control, counting, and precise nuclei pooling for direct loading onto the popular 10× Chromium controller. This approach can eliminate batch confounding, and significantly reduces poor-quality nuclei, ambient RNA contamination, and droplet loading-associated reagent waste, resulting in pronounced improvements in information content and cost efficiency.
    MeSH term(s) Animals ; Mice ; Humans ; Flow Cytometry/methods ; Sequence Analysis, RNA/methods ; Cell Nucleus/genetics ; RNA ; Adipose Tissue
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2024-02-27
    Publishing country United States
    Document type Journal Article
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2024.102893
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  2. Article ; Online: A spatially-resolved transcriptional atlas of the murine dorsal pons at single-cell resolution.

    Nardone, Stefano / De Luca, Roberto / Zito, Antonino / Klymko, Nataliya / Nicoloutsopoulos, Dimitris / Amsalem, Oren / Brannigan, Cory / Resch, Jon M / Jacobs, Christopher L / Pant, Deepti / Veregge, Molly / Srinivasan, Harini / Grippo, Ryan M / Yang, Zongfang / Zeidel, Mark L / Andermann, Mark L / Harris, Kenneth D / Tsai, Linus T / Arrigoni, Elda /
    Verstegen, Anne M J / Saper, Clifford B / Lowell, Bradford B

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 1966

    Abstract: The "dorsal pons", or "dorsal pontine tegmentum" (dPnTg), is part of the brainstem. It is a complex, densely packed region whose nuclei are involved in regulating many vital functions. Notable among them are the parabrachial nucleus, the Kölliker Fuse, ... ...

    Abstract The "dorsal pons", or "dorsal pontine tegmentum" (dPnTg), is part of the brainstem. It is a complex, densely packed region whose nuclei are involved in regulating many vital functions. Notable among them are the parabrachial nucleus, the Kölliker Fuse, the Barrington nucleus, the locus coeruleus, and the dorsal, laterodorsal, and ventral tegmental nuclei. In this study, we applied single-nucleus RNA-seq (snRNA-seq) to resolve neuronal subtypes based on their unique transcriptional profiles and then used multiplexed error robust fluorescence in situ hybridization (MERFISH) to map them spatially. We sampled ~1 million cells across the dPnTg and defined the spatial distribution of over 120 neuronal subtypes. Our analysis identified an unpredicted high transcriptional diversity in this region and pinpointed the unique marker genes of many neuronal subtypes. We also demonstrated that many neuronal subtypes are transcriptionally similar between humans and mice, enhancing this study's translational value. Finally, we developed a freely accessible, GPU and CPU-powered dashboard ( http://harvard.heavy.ai:6273/ ) that combines interactive visual analytics and hardware-accelerated SQL into a data science framework to allow the scientific community to query and gain insights into the data.
    MeSH term(s) Humans ; Animals ; Mice ; In Situ Hybridization, Fluorescence ; Pontine Tegmentum ; Brain Stem ; Locus Coeruleus ; Parabrachial Nucleus ; Ascomycota
    Language English
    Publishing date 2024-03-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-45907-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  3. Article: A spatially-resolved transcriptional atlas of the murine dorsal pons at single-cell resolution.

    Nardone, Stefano / De Luca, Roberto / Zito, Antonino / Klymko, Nataliya / Nicoloutsopoulos, Dimitris / Amsalem, Oren / Brannigan, Cory / Resch, Jon M / Jacobs, Christopher L / Pant, Deepti / Veregge, Molly / Srinivasan, Harini / Grippo, Ryan M / Yang, Zongfang / Zeidel, Mark L / Andermann, Mark L / Harris, Kenneth D / Tsai, Linus T / Arrigoni, Elda /
    Verstegen, Anne M J / Saper, Clifford B / Lowell, Bradford B

    bioRxiv : the preprint server for biology

    2023  

    Abstract: The "dorsal pons", or "dorsal pontine tegmentum" (dPnTg), is part of the brainstem. It is a complex, densely packed region whose nuclei are involved in regulating many vital functions. Notable among them are the parabrachial nucleus, the Kölliker Fuse, ... ...

    Abstract The "dorsal pons", or "dorsal pontine tegmentum" (dPnTg), is part of the brainstem. It is a complex, densely packed region whose nuclei are involved in regulating many vital functions. Notable among them are the parabrachial nucleus, the Kölliker Fuse, the Barrington nucleus, the locus coeruleus, and the dorsal, laterodorsal, and ventral tegmental nuclei. In this study, we applied single-nucleus RNA-seq (snRNA-seq) to resolve neuronal subtypes based on their unique transcriptional profiles and then used multiplexed error robust fluorescence in situ hybridization (MERFISH) to map them spatially. We sampled ~1 million cells across the dPnTg and defined the spatial distribution of over 120 neuronal subtypes. Our analysis identified an unpredicted high transcriptional diversity in this region and pinpointed many neuronal subtypes' unique marker genes. We also demonstrated that many neuronal subtypes are transcriptionally similar between humans and mice, enhancing this study's translational value. Finally, we developed a freely accessible, GPU and CPU-powered dashboard (http://harvard.heavy.ai:6273/) that combines interactive visual analytics and hardware-accelerated SQL into a data science framework to allow the scientific community to query and gain insights into the data.
    Language English
    Publishing date 2023-11-17
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.09.18.558047
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  4. Article ; Online: Author Correction: A single-cell atlas of human and mouse white adipose tissue.

    Emont, Margo P / Jacobs, Christopher / Essene, Adam L / Pant, Deepti / Tenen, Danielle / Colleluori, Georgia / Di Vincenzo, Angelica / Jørgensen, Anja M / Dashti, Hesam / Stefek, Adam / McGonagle, Elizabeth / Strobel, Sophie / Laber, Samantha / Agrawal, Saaket / Westcott, Gregory P / Kar, Amrita / Veregge, Molly L / Gulko, Anton / Srinivasan, Harini /
    Kramer, Zachary / De Filippis, Eleanna / Merkel, Erin / Ducie, Jennifer / Boyd, Christopher G / Gourash, William / Courcoulas, Anita / Lin, Samuel J / Lee, Bernard T / Morris, Donald / Tobias, Adam / Khera, Amit V / Claussnitzer, Melina / Pers, Tune H / Giordano, Antonio / Ashenberg, Orr / Regev, Aviv / Tsai, Linus T / Rosen, Evan D

    Nature

    2023  Volume 620, Issue 7973, Page(s) E14

    Language English
    Publishing date 2023-07-26
    Publishing country England
    Document type Published Erratum
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-023-06445-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 26: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 9: Show issues
    Zs.MO 244: Show issues

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  5. Article ; Online: A single-cell atlas of human and mouse white adipose tissue.

    Emont, Margo P / Jacobs, Christopher / Essene, Adam L / Pant, Deepti / Tenen, Danielle / Colleluori, Georgia / Di Vincenzo, Angelica / Jørgensen, Anja M / Dashti, Hesam / Stefek, Adam / McGonagle, Elizabeth / Strobel, Sophie / Laber, Samantha / Agrawal, Saaket / Westcott, Gregory P / Kar, Amrita / Veregge, Molly L / Gulko, Anton / Srinivasan, Harini /
    Kramer, Zachary / De Filippis, Eleanna / Merkel, Erin / Ducie, Jennifer / Boyd, Christopher G / Gourash, William / Courcoulas, Anita / Lin, Samuel J / Lee, Bernard T / Morris, Donald / Tobias, Adam / Khera, Amit V / Claussnitzer, Melina / Pers, Tune H / Giordano, Antonio / Ashenberg, Orr / Regev, Aviv / Tsai, Linus T / Rosen, Evan D

    Nature

    2022  Volume 603, Issue 7903, Page(s) 926–933

    Abstract: White adipose tissue, once regarded as morphologically and functionally bland, is now recognized to be dynamic, plastic and heterogenous, and is involved in a wide array of biological processes including energy homeostasis, glucose and lipid handling, ... ...

    Abstract White adipose tissue, once regarded as morphologically and functionally bland, is now recognized to be dynamic, plastic and heterogenous, and is involved in a wide array of biological processes including energy homeostasis, glucose and lipid handling, blood pressure control and host defence
    MeSH term(s) Adipose Tissue/metabolism ; Adipose Tissue, White/metabolism ; Adiposity ; Animals ; Atlases as Topic ; Diabetes Mellitus, Type 2/metabolism ; Humans ; Insulin Resistance ; Metabolic Diseases ; Mice ; Obesity/metabolism
    Language English
    Publishing date 2022-03-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-022-04518-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 26: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 9: Show issues
    Zs.MO 244: Show issues

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  6. Article: A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients.

    Pita-Juarez, Yered / Karagkouni, Dimitra / Kalavros, Nikolaos / Melms, Johannes C / Niezen, Sebastian / Delorey, Toni M / Essene, Adam L / Brook, Olga R / Pant, Deepti / Skelton-Badlani, Disha / Naderi, Pourya / Huang, Pinzhu / Pan, Liuliu / Hether, Tyler / Andrews, Tallulah S / Ziegler, Carly G K / Reeves, Jason / Myloserdnyy, Andriy / Chen, Rachel /
    Nam, Andy / Phelan, Stefan / Liang, Yan / Amin, Amit Dipak / Biermann, Jana / Hibshoosh, Hanina / Veregge, Molly / Kramer, Zachary / Jacobs, Christopher / Yalcin, Yusuf / Phillips, Devan / Slyper, Michal / Subramanian, Ayshwarya / Ashenberg, Orr / Bloom-Ackermann, Zohar / Tran, Victoria M / Gomez, James / Sturm, Alexander / Zhang, Shuting / Fleming, Stephen J / Warren, Sarah / Beechem, Joseph / Hung, Deborah / Babadi, Mehrtash / Padera, Robert F / MacParland, Sonya A / Bader, Gary D / Imad, Nasser / Solomon, Isaac H / Miller, Eric / Riedel, Stefan / Porter, Caroline B M / Villani, Alexandra-Chloé / Tsai, Linus T-Y / Hide, Winston / Szabo, Gyongyi / Hecht, Jonathan / Rozenblatt-Rosen, Orit / Shalek, Alex K / Izar, Benjamin / Regev, Aviv / Popov, Yury / Jiang, Z Gordon / Vlachos, Ioannis S

    bioRxiv : the preprint server for biology

    2022  

    Abstract: The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spatial ... ...

    Abstract The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 decedents. We identified hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells. Integrated analysis and comparisons with healthy controls revealed extensive changes in the cellular composition and expression states in COVID-19 liver, reflecting hepatocellular injury, ductular reaction, pathologic vascular expansion, and fibrogenesis. We also observed Kupffer cell proliferation and erythrocyte progenitors for the first time in a human liver single-cell atlas, resembling similar responses in liver injury in mice and in sepsis, respectively. Despite the absence of a clinical acute liver injury phenotype, endothelial cell composition was dramatically impacted in COVID-19, concomitantly with extensive alterations and profibrogenic activation of reactive cholangiocytes and mesenchymal cells. Our atlas provides novel insights into liver physiology and pathology in COVID-19 and forms a foundational resource for its investigation and understanding.
    Language English
    Publishing date 2022-10-28
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2022.10.27.514070
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  7. Article ; Online: A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients

    Pita-Juarez, Yered / Karagkouni, Dimitra / Kalavros, Nikolaos / Melms, Johannes C. / Niezen, Sebastian / Delorey, Toni M. / Essene, Adam L / Brook, Olga R. / Pant, Deepti / Skelton-Badlani, Disha / Naderi, Pourya / Huang, Pinzhu / Pan, Liuliu / Hether, Tyler / Andrews, Tallulah S. / Ziegler, Carly G.K. / Reeves, Jason / Myloserdnyy, Andriy / Chen, Rachel /
    Nam, Andy / Phelan, Stefan / Liang, Yan / Amin, Amit Dipak / Biermann, Jana / Hibshoosh, Hanina / Veregge, Molly / Kramer, Zachary / Jacobs, Christopher / Yalcin, Yusuf / Phillips, Devan / Slyper, Michal / Subramanian, Ayshwarya / Ashenberg, Orr / Bloom-Ackermann, Zohar / Tran, Victoria M. / Gomez, James / Sturm, Alexander / Zhang, Shuting / Fleming, Stephen J. / Warren, Sarah / Beechem, Joseph / Hung, Deborah / Babadi, Mehrtash / Padera, Robert F. / MacParland, Sonya A. / Bader, Gary D. / Imad, Nasser / Solomon, Isaac H. / Miller, Eric / Riedel, Stefan / Porter, Caroline B.M. / Villani, Alexandra-Chloé / Tsai, Linus T.-Y. / Hide, Winston / Szabo, Gyongyi / Hecht, Jonathan / Rozenblatt-Rosen, Orit / Shalek, Alex K. / Izar, Benjamin / Regev, Aviv / Popov, Yury / Jiang, Z. Gordon / Vlachos, Ioannis S.

    bioRxiv

    Abstract: The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spatial ... ...

    Abstract The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 decedents. We identified hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells. Integrated analysis and comparisons with healthy controls revealed extensive changes in the cellular composition and expression states in COVID-19 liver, reflecting hepatocellular injury, ductular reaction, pathologic vascular expansion, and fibrogenesis. We also observed Kupffer cell proliferation and erythrocyte progenitors for the first time in a human liver single-cell atlas, resembling similar responses in liver injury in mice and in sepsis, respectively. Despite the absence of a clinical acute liver injury phenotype, endothelial cell composition was dramatically impacted in COVID-19, concomitantly with extensive alterations and profibrogenic activation of reactive cholangiocytes and mesenchymal cells. Our atlas provides novel insights into liver physiology and pathology in COVID-19 and forms a foundational resource for its investigation and understanding.
    Keywords covid19
    Language English
    Publishing date 2022-10-28
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2022.10.27.514070
    Database COVID19

    Full text online

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top