Evidence map›Paper›PMID 41218606›Full record

ArticleCell reports methods2025

Simultaneous capture of single cell RNA-seq, ATAC-seq, and CRISPR perturbation enables multiomic screens to identify gene regulatory relationships.

Kaivalya Shevade, Yeqing Angela Yang, Kevin Feng, Karl Mader, Volkan Sevim, Jacob Parsons, Gunisha Arora, Hasnaa Elfawy, Rachel Mace, Scot Federman and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Review
  2. Review
  3. Review
  4. bioRxiv : the preprint server for biology · 2026
    Article
  5. Review
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

14 authors.

Kaivalya ShevadeLaboratory for Genomics Research, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA.
Yeqing Angela YangLaboratory for Genomics Research, San Francisco, CA 94158, USA; GSK, San Francisco, CA, USA. Electronic address: yeqingyang2016@gmail.com.
Kevin FengLaboratory for Genomics Research, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA.
Karl MaderLaboratory for Genomics Research, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA.
Volkan SevimLaboratory for Genomics Research, San Francisco, CA 94158, USA; GSK, San Francisco, CA, USA.
Jacob ParsonsGSK, Collegeville, PA, USA.
Gunisha AroraLaboratory for Genomics Research, San Francisco, CA 94158, USA; GSK, San Francisco, CA, USA.
Hasnaa ElfawyLaboratory for Genomics Research, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA.
Rachel MaceLaboratory for Genomics Research, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA.
Scot FedermanLaboratory for Genomics Research, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA.
Rustam EsanovLaboratory for Genomics Research, San Francisco, CA 94158, USA; GSK, San Francisco, CA, USA.
Shawn ShaferLaboratory for Genomics Research, San Francisco, CA 94158, USA; GSK, San Francisco, CA, USA.
Eric D ChowDepartment of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA; Center for Advanced Technology, University of California, San Francisco, CA 94158, USA. Electronic address: eric.chow@ucsf.edu.
Laralynne PrzybylaLaboratory for Genomics Research, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Here, we introduce CRISPR and transcriptomics-assay for transposase-accessible chromatin (CAT-ATAC), a technique that adds CRISPR guide RNA (gRNA) capture to the existing 10× Genomics Multiome assay, generating linked transcriptome, chromatin accessibility, and perturbation identity data from the same individual cells. We demonstrate up to 77% capture rate for both arrayed and pooled delivery of lentiviral gRNAs in induced pluripotent stem cells (iPSCs) and cancer cell lines. This capability allows us to construct gene regulatory networks (GRNs) in cells under drug and genetic perturbations. By applying CAT-ATAC, we identified a GRN associated with dasatinib resistance, indirectly activated by the HIC2 gene. Using loss-of-function experiments, we further validated that ZFPM2, a component of the predicted GRN, also contributes to dasatinib resistance. CAT-ATAC can thus be used to generate high-content multidimensional genotype-phenotype maps to reveal gene and cellular interactions and functions.

Indexed as

Chromatin Immunoprecipitation SequencingClustered Regularly Interspaced Short Palindromic RepeatsCRISPR-Cas SystemsGene Regulatory NetworksRNA-SeqSingle-Cell AnalysisCell Line, TumorChromatinDasatinibHumansInduced Pluripotent Stem CellsRNA, Guide, CRISPR-Cas SystemsTransposasesChromatinDasatinibRNA, Guide, CRISPR-Cas SystemsTransposasesCP: biotechnologyCP: cancer biologyCRISPRguide RNAmultiomeperturb-seqsingle cell

Identifiers

PMID41218606
PMCPMC12859477

What Socratic holds

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LicenceCC BY
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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.