Evidence map›Paper›PMID 42386990›Full record

ArticleNature biotechnology2026

A genome-scale CRISPRi perturbation atlas of human induced pluripotent stem cells.

Sami Nourreddine, Yesh Doctor, Amir Dailamy, Yi-Hung Lee, Jan N Hansen, Rebecca Chinn, Antoine Forget, Benjamin Polacco, Monita Muralidharan, Alina Sigaeva and 12 more

Abstract read
PubMed Publisher
In one paragraph

Article in Nature biotechnology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Multiplexed Pan Soluble Ligandome Assaying via OASIS.bioRxiv : the preprint server for biology · 2025
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

22 authors.

Sami Nourreddine *Department of Bioengineering, University of California San Diego, San Diego, CA, USA.
Yesh Doctor *Department of Bioengineering, University of California San Diego, San Diego, CA, USA.
Amir DailamyDepartment of Developmental Biology, Stanford University, Stanford, CA, USA.
Yi-Hung LeeDepartment of Bioengineering, University of California San Diego, San Diego, CA, USA.
Jan N HansenDepartment of Bioengineering, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-0489-7535
Rebecca ChinnDepartment of Bioengineering, University of California San Diego, San Diego, CA, USA.
Antoine ForgetQuantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
Benjamin PolaccoQuantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0003-1570-9234
Monita MuralidharanQuantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
Alina SigaevaDivision of Cellular and Clinical Proteomics, Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden.
Sushant SunderDepartment of Bioengineering, University of California San Diego, San Diego, CA, USA.
Emily PanDepartment of Bioengineering, University of California San Diego, San Diego, CA, USA.ORCID http://orcid.org/0009-0000-5477-1685
Jiahao GaoSchool of Medicine, University of California San Diego, San Diego, CA, USA.ORCID http://orcid.org/0000-0002-6311-3526
Jake Y ChenDepartment of Computer Science, The University of Alabama at Birmingham, Birmingham, VA, USA.ORCID http://orcid.org/0000-0001-8829-7504
Timothy ClarkDepartment of Medicine, University of Virginia, Charlottesville, VA, USA.
Jillian ParkerSchool of Medicine, University of California San Diego, San Diego, CA, USA.
Kirsten ObernierQuantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
Christian MetalloDepartment of Bioengineering, University of California San Diego, San Diego, CA, USA.ORCID http://orcid.org/0000-0003-2404-3040
Trey IdekerDepartment of Bioengineering, University of California San Diego, San Diego, CA, USA.ORCID http://orcid.org/0000-0002-1708-8454
Emma LundbergDepartment of Bioengineering, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-7034-0850
Nevan KroganQuantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0003-4902-337X
Prashant MaliDepartment of Bioengineering, University of California San Diego, San Diego, CA, USA. pmali@ucsd.edu.ORCID http://orcid.org/0000-0002-3383-1287

Funding

Bridge2AI: Cell Maps for AI (CM4AI) Data Generation ProjectOT2OD032742 · OD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Jean-Christophe Bélisle-Pipon, TIMOTHY W CLARK · 2022 to 2026
$21.5M
Next generation massively multiplexed combinatorial genetic screensR01HG012351 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Trey Ideker, Prashant Mali · 2023 to 2026
$2.7M
Systematic functional mapping and interrogation of oncogenic intrinsically disordered regionsR01CA310063 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Hannah Kathryn Carter, Prashant Mali · 2026 to 2026
$662k
California Institute for Regenerative Medicine (CIRM) DISC4-19271NCI NIH HHS R01 CA310063NHGRI NIH HHS R01 HG012351NIH HHS OT2 OD032742U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) R01CA310063U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) R01HG012351U.S. Department of Health & Human Services | NIH | NIH Office of the Director (OD) OT2OD032742
6 · The paper itself

Abstract

Comprehensively mapping the relationship between genotype and phenotype offers essential insights into how a cell's state arises from its genetic components. Toward this goal, we generated an expressed genome-scale CRISPRi perturbation cell atlas in KOLF2.1J human induced pluripotent stem cells, mapping transcriptional phenotypes associated with 11,692 perturbed genes across >2.5 million single cells. Using correlations among perturbed phenotypes, we created a cell map of the pluripotent state, demonstrating rich recapitulation of functionally related protein complexes. We then explored the atlas to uncover metabolic factor ZBTB41 and pluripotency regulator RNF7, validating their functions through metabolic tracing, immunofluorescence and protein-protein interaction assays. Lastly, we leveraged the atlas to generate a genome-scale screen of A-to-I RNA-editing modulators assayed through direct transcriptome-wide RNA editing, uncovering and mechanistically validating DBR1 as a potent regulator. Taken together, our data provide a comprehensive resource for interrogating the regulatory networks governing pluripotency, which is accessible at https://y-doctor.github.io/KOLF2.1J_Perturbation_Cell_Atlas/ .

Identifiers

PMID42386990

What Socratic 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 Socratic graph.