Evidence map›Paper›PMID 39627589›Full record

ReviewNature neuroscience2024

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 and 19 more

Abstract readReview
PubMed Publisher
In one paragraph

Review in Nature neuroscience, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

9 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Review
  5. Article
  6. Review
  7. Article
  8. Review
  9. Focus on single-cell genomics.Nature neuroscience · 2024
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

29 authors.

Marco ColonnaDepartment of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA. mcolonna@wustl.edu.ORCID http://orcid.org/0000-0001-5222-4987
Genevieve KonopkaDepartment of Neuroscience, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA. genevieve.konopka@utsouthwestern.edu.ORCID http://orcid.org/0000-0002-3363-7302
Shane A LiddelowNeuroscience Institute, NYU Grossman School of Medicine, New York, NY, USA. shane.liddelow@nyulangone.org.ORCID http://orcid.org/0000-0002-0840-1437
Tomasz NowakowskiDepartment of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA. tomasz.nowakowski@ucsf.edu.ORCID http://orcid.org/0000-0003-2345-4964
Rajeshwar AwatramaniDepartment of Microbiology and Immunology, Northwestern University, Chicago, IL, USA.ORCID http://orcid.org/0000-0002-0713-2140
Helen S BateupDepartment of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-0135-0972
Cathryn R CadwellDepartment of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0003-1963-8285
Emre CaglayanDepartment of Neuroscience, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA.ORCID http://orcid.org/0000-0001-5340-8614
Jerry L ChenDepartment of Biomedical Engineering, Boston University, Boston, MA, USA.ORCID http://orcid.org/0000-0002-7409-7859
Jesse GillisDepartment of Physiology and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.ORCID http://orcid.org/0000-0002-0936-9774
Martin KampmannInstitute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-3819-7019
Fenna KrienenPrinceton Neuroscience Institute, Princeton University, Princeton, NJ, USA.ORCID http://orcid.org/0000-0002-1400-6820
Samuel E MarshF.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA.ORCID http://orcid.org/0000-0002-3012-6945
Michelle MonjeDepartment of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-3547-237X
Michael R O'DeaNeuroscience Institute, NYU Grossman School of Medicine, New York, NY, USA.ORCID http://orcid.org/0000-0002-6135-7607
Rickie PataniDepartment of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK.ORCID http://orcid.org/0000-0002-3825-7675
Alex A PollenEli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0003-3263-8634
Francisco J QuintanaAnn Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-8156-0736
Marissa ScavuzzoDepartment of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, OH, USA.
Matthew SchmitzEli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
Steven A SloanDepartment of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.ORCID http://orcid.org/0000-0001-7769-7684
Paul J TesarDepartment of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, OH, USA.ORCID http://orcid.org/0000-0003-1532-3155
Jessica TollkuhnCold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.ORCID http://orcid.org/0000-0001-5991-7620
Maria Antonietta ToschesDepartment of Biological Sciences, Columbia University, New York, NY, USA.ORCID http://orcid.org/0000-0001-6338-9357
Madeleine E UrbanekBiomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
Jonathan M WernerDepartment of Physiology and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.ORCID http://orcid.org/0000-0001-9248-6420
Omer A BayraktarWellcome Sanger Institute, Cambridge, UK. ob5@sanger.ac.uk.ORCID http://orcid.org/0000-0001-6055-277X
Ozgun GokceDepartment of Old Age Psychiatry and Cognitive Disorders, University Hospital Bonn, Bonn, Germany. ozgun.goekce@ukbonn.de.ORCID http://orcid.org/0000-0001-6319-404X
Naomi HabibEdmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. naomi.habib@mail.huji.ac.il.ORCID http://orcid.org/0000-0002-6049-2487

Funding

Modulating Glial Fate and Function in Development and DiseaseR35NS116842 · NINDS · CASE WESTERN RESERVE UNIVERSITY · PI Paul Joseph Tesar · 2020 to 2026
$5.3M
NINDS NIH HHS R35 NS116842
6 · The paper itself

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.

Indexed as

GenomicsNeurosciencesSingle-Cell AnalysisAnimalsGene Expression ProfilingHumansTranscriptome

Identifiers

PMID39627589

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.