Implementation and validation of single-cell genomics experiments in neuroscience

Marco Colonna; Genevieve Konopka; Shane A. Liddelow; Tomasz Nowakowski; Rajeshwar Awatramani; Helen S. Bateup; Cathryn R. Cadwell; Emre Caglayan; Jerry L. Chen; Jesse Gillis; Martin Kampmann; Fenna Krienen; Samuel E. Marsh; Michelle Monje; Michael R. O’Dea; Rickie Patani; Alex A. Pollen; Francisco J. Quintana; Marissa Scavuzzo; Matthew Schmitz; Steven A. Sloan; Paul J. Tesar; Jessica Tollkuhn; Maria Antonietta Tosches; Madeleine E. Urbanek; Jonathan M. Werner; Omer A. Bayraktar; Ozgun Gokce; Naomi Habib

doi:10.1038/s41593-024-01814-0

Implementation and validation of single-cell genomics experiments in neuroscience

Marco Colonna^*, Genevieve Konopka^*, Shane A. Liddelow^*, Tomasz Nowakowski^*, Rajeshwar Awatramani, Helen S. Bateup, Cathryn R. Cadwell, Emre Caglayan, Jerry L. Chen, Jesse Gillis, Martin Kampmann, Fenna Krienen, Samuel E. Marsh, Michelle Monje, Michael R. O’Dea, Rickie Patani, Alex A. Pollen, Francisco J. Quintana, Marissa Scavuzzo, Matthew SchmitzSteven A. Sloan, Paul J. Tesar, Jessica Tollkuhn, Maria Antonietta Tosches, Madeleine E. Urbanek, Jonathan M. Werner, Omer A. Bayraktar^*, Ozgun Gokce^*, Naomi Habib^*

^*Corresponding author for this work

Edmond & Lily Safra Center for Brain Sciences

Research output: Contribution to journal › Review article › peer-review

1 Scopus citations

Abstract

Single-cell or single-nucleus transcriptomics is a powerful tool for identifying cell types and cell states. However, hypotheses derived from these assays, including gene expression information, require validation, and their functional relevance needs to be established. The choice of validation depends on numerous factors. Here, we present types of orthogonal and functional validation experiment to strengthen preliminary findings obtained using single-cell and single-nucleus transcriptomics as well as the challenges and limitations of these approaches.

Original language	English
Article number	e8746
Pages (from-to)	2310-2325
Number of pages	16
Journal	Nature Neuroscience
Volume	27
Issue number	12
DOIs	https://doi.org/10.1038/s41593-024-01814-0
State	Published - Dec 2024

Bibliographical note

Publisher Copyright:
© Springer Nature America, Inc. 2024.

Access to Document

10.1038/s41593-024-01814-0

Cite this

Colonna, M., Konopka, G., Liddelow, S. A., Nowakowski, T., Awatramani, R., Bateup, H. S., Cadwell, C. R., Caglayan, E., Chen, J. L., Gillis, J., Kampmann, M., Krienen, F., Marsh, S. E., Monje, M., O’Dea, M. R., Patani, R., Pollen, A. A., Quintana, F. J., Scavuzzo, M., ... Habib, N. (2024). Implementation and validation of single-cell genomics experiments in neuroscience. Nature Neuroscience, 27(12), 2310-2325. Article e8746. https://doi.org/10.1038/s41593-024-01814-0

@article{182c1aa8cd204fa28857172c7c75eed4,

title = "Implementation and validation of single-cell genomics experiments in neuroscience",

abstract = "Single-cell or single-nucleus transcriptomics is a powerful tool for identifying cell types and cell states. However, hypotheses derived from these assays, including gene expression information, require validation, and their functional relevance needs to be established. The choice of validation depends on numerous factors. Here, we present types of orthogonal and functional validation experiment to strengthen preliminary findings obtained using single-cell and single-nucleus transcriptomics as well as the challenges and limitations of these approaches.",

author = "Marco Colonna and Genevieve Konopka and Liddelow, {Shane A.} and Tomasz Nowakowski and Rajeshwar Awatramani and Bateup, {Helen S.} and Cadwell, {Cathryn R.} and Emre Caglayan and Chen, {Jerry L.} and Jesse Gillis and Martin Kampmann and Fenna Krienen and Marsh, {Samuel E.} and Michelle Monje and O{\textquoteright}Dea, {Michael R.} and Rickie Patani and Pollen, {Alex A.} and Quintana, {Francisco J.} and Marissa Scavuzzo and Matthew Schmitz and Sloan, {Steven A.} and Tesar, {Paul J.} and Jessica Tollkuhn and Tosches, {Maria Antonietta} and Urbanek, {Madeleine E.} and Werner, {Jonathan M.} and Bayraktar, {Omer A.} and Ozgun Gokce and Naomi Habib",

note = "Publisher Copyright: {\textcopyright} Springer Nature America, Inc. 2024.",

year = "2024",

month = dec,

doi = "10.1038/s41593-024-01814-0",

language = "אנגלית",

volume = "27",

pages = "2310--2325",

journal = "Nature Neuroscience",

issn = "1097-6256",

publisher = "Nature Research",

number = "12",

}

Colonna, M, Konopka, G, Liddelow, SA, Nowakowski, T, Awatramani, R, Bateup, HS, Cadwell, CR, Caglayan, E, Chen, JL, Gillis, J, Kampmann, M, Krienen, F, Marsh, SE, Monje, M, O’Dea, MR, Patani, R, Pollen, AA, Quintana, FJ, Scavuzzo, M, Schmitz, M, Sloan, SA, Tesar, PJ, Tollkuhn, J, Tosches, MA, Urbanek, ME, Werner, JM, Bayraktar, OA, Gokce, O & Habib, N 2024, 'Implementation and validation of single-cell genomics experiments in neuroscience', Nature Neuroscience, vol. 27, no. 12, e8746, pp. 2310-2325. https://doi.org/10.1038/s41593-024-01814-0

TY - JOUR

T1 - Implementation and validation of single-cell genomics experiments in neuroscience

AU - Colonna, Marco

AU - Konopka, Genevieve

AU - Liddelow, Shane A.

AU - Nowakowski, Tomasz

AU - Awatramani, Rajeshwar

AU - Bateup, Helen S.

AU - Cadwell, Cathryn R.

AU - Caglayan, Emre

AU - Chen, Jerry L.

AU - Gillis, Jesse

AU - Kampmann, Martin

AU - Krienen, Fenna

AU - Marsh, Samuel E.

AU - Monje, Michelle

AU - O’Dea, Michael R.

AU - Patani, Rickie

AU - Pollen, Alex A.

AU - Quintana, Francisco J.

AU - Scavuzzo, Marissa

AU - Schmitz, Matthew

AU - Sloan, Steven A.

AU - Tesar, Paul J.

AU - Tollkuhn, Jessica

AU - Tosches, Maria Antonietta

AU - Urbanek, Madeleine E.

AU - Werner, Jonathan M.

AU - Bayraktar, Omer A.

AU - Gokce, Ozgun

AU - Habib, Naomi

PY - 2024/12

Y1 - 2024/12

N2 - Single-cell or single-nucleus transcriptomics is a powerful tool for identifying cell types and cell states. However, hypotheses derived from these assays, including gene expression information, require validation, and their functional relevance needs to be established. The choice of validation depends on numerous factors. Here, we present types of orthogonal and functional validation experiment to strengthen preliminary findings obtained using single-cell and single-nucleus transcriptomics as well as the challenges and limitations of these approaches.

AB - Single-cell or single-nucleus transcriptomics is a powerful tool for identifying cell types and cell states. However, hypotheses derived from these assays, including gene expression information, require validation, and their functional relevance needs to be established. The choice of validation depends on numerous factors. Here, we present types of orthogonal and functional validation experiment to strengthen preliminary findings obtained using single-cell and single-nucleus transcriptomics as well as the challenges and limitations of these approaches.

UR - http://www.scopus.com/inward/record.url?scp=85211136134&partnerID=8YFLogxK

U2 - 10.1038/s41593-024-01814-0

DO - 10.1038/s41593-024-01814-0

M3 - ???researchoutput.researchoutputtypes.contributiontojournal.systematicreview???

C2 - 39627589

AN - SCOPUS:85211136134

SN - 1097-6256

VL - 27

SP - 2310

EP - 2325

JO - Nature Neuroscience

JF - Nature Neuroscience

IS - 12

M1 - e8746

ER -

Implementation and validation of single-cell genomics experiments in neuroscience

Abstract

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this