ArticleNature communications2021
Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 26 papers.
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.
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.
Who cites it
26 citing papers in PubMed, 43 citations in OpenAlex.
- High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow.Genome research · 2025Article
- Mapping T cell dynamics to molecular profiles through behavior-guided transcriptomics.Nature protocols · 2025Review
- Temporal and spatial omics technologies for 4D profiling.Nature methods · 2025Review
- Assessing the safety of microbiome perturbations.Microbial genomics · 2025Review
- Single-cell omics technologies - Fundamentals on how to create single-cell looking glasses for reproductive health.American journal of obstetrics and gynecology · 2025Review
- scTrends: A living review of commercial single-cell and spatial 'omic technologies.Cell genomics · 2024Review
- Spatial oncology: Translating contextual biology to the clinic.Cancer cell · 2024Review
- Tenascin-C in the early lung cancer tumor microenvironment promotes progression through integrin αvβ1 and FAK.bioRxiv : the preprint server for biology · 2024Article
- Next-Generation Sequencing-Based Spatial Transcriptomics: A Perspective from Barcoding Chemistry.JACS Au · 2024Review
- Secretory GFP reconstitution labeling of neighboring cells interrogates cell-cell interactions in metastatic niches.Nature communications · 2023Article
- Fragment-sequencing unveils local tissue microenvironments at single-cell resolution.Nature communications · 2023Article
- Bridging live-cell imaging and next-generation cancer treatment.Nature reviews. Cancer · 2023Review
- Spatiotemporal single-cell tracking analysis in 3D tissues to reveal heterogeneous cellular response to mechanical stimuli.Science advances · 2023Article
- Spatial transcriptomics in development and disease.Molecular biomedicine · 2023Review
- New discoveries in the field of metabolism by applying single-cell and spatial omics.Journal of pharmaceutical analysis · 2023Review
- Human pluripotent stem cell (hPSC) and organoid models of autism: opportunities and limitations.Translational psychiatry · 2023Review
- Review
- Making In Vitro Tumor Models Whole Again.Advanced healthcare materials · 2023Review
- High-throughput co-culture system for analysis of spatiotemporal cell-cell signaling.Biosensors & bioelectronics · 2023Article
- Alliance of Heart and Endoderm: Multilineage Organoids to Model Co-development.Circulation research · 2023Review
Corrections and comments
- Erratum issued
Authors and funding
15 authors at 7 institutions in 2 countries.
Funding
Abstract
A cell's phenotype and function are influenced by dynamic interactions with its microenvironment. To examine cellular spatiotemporal activity, we developed SPACECAT-Spatially PhotoActivatable Color Encoded Cell Address Tags-to annotate, track, and isolate cells while preserving viability. In SPACECAT, samples are stained with photocaged fluorescent molecules, and cells are labeled by uncaging those molecules with user-patterned near-UV light. SPACECAT offers single-cell precision and temporal stability across diverse cell and tissue types. Illustratively, we target crypt-like regions in patient-derived intestinal organoids to enrich for stem-like and actively mitotic cells, matching literature expectations. Moreover, we apply SPACECAT to ex vivo tissue sections from four healthy organs and an autochthonous lung tumor model. Lastly, we provide a computational framework to identify spatially-biased transcriptome patterns and enriched phenotypes. This minimally perturbative and broadly applicable method links cellular spatiotemporal and/or behavioral phenotypes with diverse downstream assays, enabling insights into the connections between tissue microenvironments and (dys)function.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.