Protocol to isolate live single cells while retaining spatial information by combining cell photolabeling and FACS.

Pilar Baldominos, Olga Barreiro, Ulrich von Andrian, Rafael Sirera, Paula Montero-Llopis, Judith Agudo

Abstract read

In one paragraph

Article in STAR protocols, 2022. 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

6 authors.

Pilar BaldominosDepartment of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.

Olga BarreiroDepartment of Immunology, Harvard Medical School, Boston, MA 02215, USA; Center for Immune Imaging, Harvard Medical School, Boston, MA 02215, USA. Electronic address: olga_barreiro@hms.harvard.edu.

Ulrich von AndrianDepartment of Immunology, Harvard Medical School, Boston, MA 02215, USA; Center for Immune Imaging, Harvard Medical School, Boston, MA 02215, USA.

Rafael SireraUnidad Mixta TRIAL, Centro Investigación Príncipe Felipe-Fundación Investigación, Hospital General Universitario de Valencia, Valencia, Spain; Centro de Investigación Biomédica en Red Cáncer, CIBERONC, Madrid, Spain; Department of Biotechnology, Universitat Politècnica de València, 46022 Valencia, Spain.

Paula Montero-LlopisMicRoN Core, Harvard Medical School, Boston, MA 02215, USA.

Judith AgudoDepartment of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Immunology, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center at Harvard, Boston, MA 02215, USA. Electronic address: judith_agudo@dfci.harvard.edu.

Funding

Tissue and Pathology CoreP50CA168504 · NCI · DANA-FARBER CANCER INST · PI Nabihah Tayob · 2013 to 2026

$30.1M

NCI NIH HHS P50 CA168504

6 · The paper itself

Abstract

Single-cell techniques have revolutionized biology; however, the required sample processing inherently implies the loss of spatial localization. Here, using an approach called photoconversion of areas to dissect micro-environments (PADME), we detail steps to isolate live single cells from a primary breast tumor while retaining spatial information by combining cell photolabeling and FACS (fluorescence-activated cell sorting). These live cells can be subsequently used for myriad techniques, from flow cytometry to single-cell RNA sequencing or other single cell "omics" approach. For complete details on the use and execution of this protocol, please refer to Baldominos et al. (2022).

Indexed as

Flow CytometryBiotechnology and bioengineeringCancerCell isolationFlow cytometry/Mass cytometryImmunologyMicroscopyMolecular/Chemical probesSingle cell

Identifiers

PMID36325581

DOI10.1016/j.xpro.2022.101795

PMCPMC9619724

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LicenceCC BY-NC-ND

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Registered trials

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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.