Evidence map›Paper›PMID 40748762›Full record

ArticleSTAR protocols2025

Protocol for automated graph-based clustering of single-cell RNA-seq data with application in mouse intestinal stem cells.

Alexander L E Wang, Luca Zanella, Yosuke Ochiai, Leonardo Golinelli, Andrea Califano, Ermanno Malagola, Alessandro Vasciaveo

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in STAR protocols, 2025. 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. 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

7 authors.

Alexander L E WangDepartment of Systems Biology, Columbia University, New York, NY 10032, USA.
Luca ZanellaDepartment of Systems Biology, Columbia University, New York, NY 10032, USA.
Yosuke OchiaiDivision of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA.
Leonardo GolinelliNCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; Center for Data Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
Andrea CalifanoDepartment of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry & Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA; Chan Zuckerberg Biohub NY, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
Ermanno MalagolaDivision of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA; Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland.
Alessandro VasciaveoDepartment of Systems Biology, Columbia University, New York, NY 10032, USA; NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; Center for Data Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; Center for Therapeutics Discovery, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA. Electronic address: avasciaveo@sbpdiscovery.org.

Funding

Tumor Biology and Microenvironment ProgramP30CA013696 · NCI · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI Anil K Rustgi · 1985 to 2026
$115.3M
Predicting Cancer Cell Response to Endogenous and Exogenous Perturbations at the Single Cell LevelR35CA197745 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI ANDREA CALIFANO · 2015 to 2026
$11.5M
High-performance compute cluster for biomedical computingS10OD012351 · OD · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI CALIFANO, ANDREA · 2012 to 2012
$2.0M
High Performance Computing Cluster for Biomedical ResearchS10OD032433 · OD · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI CALIFANO, ANDREA · 2023 to 2023
$2.0M
Storage System for High Performance ComputingS10OD021764 · OD · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI CALIFANO, ANDREA · 2016 to 2016
$600k
NCI NIH HHS P30 CA013696NCI NIH HHS R35 CA197745NIH HHS S10 OD012351NIH HHS S10 OD021764NIH HHS S10 OD032433
6 · The paper itself

Abstract

We present a protocol for isolating highly purified crypt epithelial cells from the mouse intestine for single-cell RNA sequencing (scRNA-seq). Optimized for the mouse jejunum, it can be adapted to all intestinal tracts, including the colon. The pipeline incorporates automated community detection of cell populations (ACDC), a time- and memory-efficient Python package for automated graph-based optimal clustering of large scRNA-seq datasets. We demonstrate its usage to identify cellular populations in an intestinal stem cell dataset and generate publication-ready figures. For complete details on the use and execution of this protocol, please refer to Malagola et al.

Indexed as

IntestinesRNA-SeqSequence Analysis, RNASingle-Cell AnalysisStem CellsAnimalsCluster AnalysisMiceSingle-Cell Gene Expression AnalysisBioinformaticsCell BiologyCell DifferentiationCell isolationFlow CytometryGenomicsMolecular BiologyRNA-seqSequence analysisSingle CellStem Cells

Identifiers

PMID40748762
PMCPMC12337269

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
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.