Evidence map›Paper›PMID 42647169›Full record

ArticleSTAR protocols2026

Protocol to identify genes required for cardiomyocyte development using Perturb-Seq.

Sushama Sivakumar, Lei Wang, Huan Zhao, Mpathi Nzima, David C Park, Yihan Wang, Anjana Sundarrajan, Chikara Takeuchi, Minnie Deng, W Lee Kraus and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in STAR protocols, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

12 authors.

Sushama SivakumarDepartment of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, Dallas, TX, USA. Electronic address: sushama.sivakumar@utsouthwestern.edu.
Lei WangCecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Huan ZhaoCecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Mpathi NzimaCecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
David C ParkDepartment of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Yihan WangCecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Anjana SundarrajanCecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Chikara TakeuchiCecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Minnie DengDepartment of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
W Lee KrausCecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Gary C HonCecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA; Lyda Hill Department of Bioinformatics, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA. Electronic address: gary.hon@utsouthwestern.edu.
Nikhil V MunshiDepartment of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA; Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA. Electronic address: nikhil.munshi@utsouthwestern.edu.

Funding

Multiscale functional characterization of genomic variation in human developmental disordersUM1HG011996 · NHGRI · UT SOUTHWESTERN MEDICAL CENTER · PI Gary Chung Hon, WILLIAM Lee KRAUS · 2021 to 2026
$10.5M
Combinatorial Biology of Gene Regulation for Cellular EngineeringDP2GM128203 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI HON, GARY CHUNG · 2017 to 2021
$2.9M
Diversity Supplement- Analysis of transcriptional and chromatin accessibility during atrioventricular node formatR01HL136604 · NHLBI · UT SOUTHWESTERN MEDICAL CENTER · PI MUNSHI, NIKHIL VILAS · 2017 to 2021
$2.1M
Exploring Mechanisms of Cardiac Pacemaker Cell Fate DeterminationR01HL151650 · NHLBI · UT SOUTHWESTERN MEDICAL CENTER · PI MUNSHI, NIKHIL VILAS · 2021 to 2025
$2.1M
Systematic Assessment of Combinatorial Transcription Factor ActivityR56HG012768 · NHGRI · UT SOUTHWESTERN MEDICAL CENTER · PI HON, GARY CHUNG, MUNSHI, NIKHIL VILAS · 2023 to 2023
$400k
NHGRI NIH HHS R56 HG012768NHGRI NIH HHS UM1 HG011996NHLBI NIH HHS R01 HL136604NHLBI NIH HHS R01 HL151650NIGMS NIH HHS DP2 GM128203
6 · The paper itself

Abstract

While Perturb-Seq combines CRISPR-based screening with single-cell RNA sequencing (scRNA-seq), large-scale experiments are costly and its application during development is complicated by differentiation heterogeneity. Here, we present a protocol to identify genes required for cardiomyocyte development using Perturb-Seq. We describe steps for sgRNA (single guide RNA) library cloning and infection, cardiomyocyte differentiation, cell hashing, super loading, and scRNA-seq. We then detail procedures for sequencing, mapping, and data analysis. For complete details on the use and execution of this protocol, please refer to Sivakumar et al.

Indexed as

Cell DifferentiationCRISPRGene ExpressionGenomicsHigh Throughput ScreeningMolecular BiologyRNAseqSequencingStem Cells

Identifiers

PMID42647169
PMCPMC13543896

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.