ArticleCommunications biology2021
smiFISH and embryo segmentation for single-cell multi-gene RNA quantification in arthropods.
Article in Communications biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed, 34 citations in OpenAlex.
- NAA50-mediated SLU7 stabilization promotes cisplatin resistance in bladder cancer via regulating MAP3K3 mRNA nuclear export and p38 MAPK activation.Cellular oncology (Dordrecht, Netherlands) · 2026Article
- The Cappuccino interactome reveals an intracellular role for Semaphorin-2a inbioRxiv : the preprint server for biology · 2026Article
- Decoding the molecular logic of rapidly evolving ZAD zinc finger proteins inScience advances · 2026Article
- The transcriptomics of phenotypic nonspecificity in Drosophila melanogaster.G3 (Bethesda, Md.) · 2025Article
- DHX36 modulates stress granule assembly independent of recruitment of mRNAs with G-quadruplex sequence motifs.Nucleic acids research · 2025Article
- A toolkit for mapping cell identities in relation to neighbors reveals conserved patterning of neuromesodermal progenitor populations.PLoS biology · 2025Article
- Impact of G-tract RNAs and the DHX36 helicase on stress granule composition and formation.bioRxiv : the preprint server for biology · 2025Article
- Optimizing Confocal Imaging Protocols for Muscle Fiber Typing in the Mouse Masseter Muscle.Bio-protocol · 2025Article
- EB-SUN, a new microtubule plus-end tracking protein inMolecular biology of the cell · 2024Article
- EB-SUN, a New Microtubule Plus-End Tracking Protein inbioRxiv : the preprint server for biology · 2024Article
- The kinesin-3 KIF1C undergoes liquid-liquid phase separation for accumulation of specific transcripts at the cell periphery.The EMBO journal · 2024Article
- Enhancer-promoter interactions can form independently of genomic distance and be functional across TAD boundaries.Nucleic acids research · 2024Article
- The dynamic duo of microtubule polymerase Mini spindles/XMAP215 and cytoplasmic dynein is essential for maintainingProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Improved enzymatic labeling of fluorescent in situ hybridization probes applied to the visualization of retained introns in cells.RNA (New York, N.Y.) · 2023Article
- Article
- Dynamic interplay between non-coding enhancer transcription and gene activity in development.Nature communications · 2023Article
- Combined modelling of mRNA decay dynamics and single-molecule imaging in the Drosophila embryo uncovers a role for P-bodies in 5' to 3' degradation.PLoS biology · 2023Article
- The GATA factor ELT-3 specifies endoderm in Caenorhabditis angaria in an ancestral gene network.Development (Cambridge, England) · 2022Article
- An expanded toolkit foreLife · 2022Article
- Modelling the structure of Short Gastrulation and generation of a toolkit for studying its function in Drosophila.Biology open · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Recently, advances in fluorescent in-situ hybridization techniques and in imaging technology have enabled visualization and counting of individual RNA molecules in single cells. This has greatly enhanced the resolution in our understanding of transcriptional processes. Here, we adapt a recently published smiFISH protocol (single-molecule inexpensive fluorescent in-situ hybridization) to whole embryos across a range of arthropod model species, and also to non-embryonic tissues. Using multiple fluorophores with distinct spectra and white light laser confocal imaging, we simultaneously detect and separate single RNAs from up to eight different genes in a whole embryo. We also combine smiFISH with cell membrane immunofluorescence, and present an imaging and analysis pipeline for 3D cell segmentation and single-cell RNA counting in whole blastoderm embryos. Finally, using whole embryo single-cell RNA count data, we propose two alternative single-cell variability measures to the commonly used Fano factor, and compare the capacity of these three measures to address different aspects of single-cell expression variability.
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.