ArticleBMC genomics2024
High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction.
Article in BMC genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Mitochondrial transcript abundance in breast cancer circulating tumour cells may reflect both blood-derived transcripts and biological heterogeneity.Clinical & experimental metastasis · 2026Article
- Evaluating the role of pretraining dataset size and diversity on single-cell foundation model performance.Nature methods · 2026Article
- ScQCenrich enables multi-metric quality control for single-cell RNA sequencing.Communications biology · 2026Article
- Loss of tumor-infiltrating lymphocytes and poor response to immunotherapy in IDH GOF mutant melanoma.JCI insight · 2026Article
- ModelingbioRxiv : the preprint server for biology · 2026Article
- Single-cell transcriptomics identifies regulatory T cell heterogeneity in gestational diabetes mellitus.Communications medicine · 2026Article
- Comparative analysis of nuclei isolation methods for brain single-nucleus RNA sequencing.Cell reports methods · 2026Article
- Integration of in situ hybridization and scRNA-seq data provides a 2D topographical map of the developing retina across species.bioRxiv : the preprint server for biology · 2026Article
- PITX2 dosage-dependent changes in pacemaker cell state underlie sinus node dysfunction and atrial arrhythmias.Nature communications · 2025Article
- Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance.bioRxiv : the preprint server for biology · 2025Article
- Monod: model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell sequencing data.Nature methods · 2025Article
- Single-cell foundation models: bringing artificial intelligence into cell biology.Experimental & molecular medicine · 2025Review
- QClus: a droplet filtering algorithm for enhanced snRNA-seq data quality in challenging samples.Nucleic acids research · 2025Article
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Authors and funding
2 authors.
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Abstract
The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we will show that prominent initiatives such as the Human Cell Atlas [1], the Tabula Sapiens [2] and the Tabula Muris [3] contain a significant amount of contamination products (frequently affecting the whole organ) in their data portals due to suboptimal quality filtering. Our work addresses a critical gap by advocating for more stringent quality filtering, highlighting the imperative for a shift from existing standards, which currently lean towards greater permissiveness. We will show the importance of incorporating cell intronic fraction in quality control -or MALAT1 expression otherwise- showcasing its informative nature and potential to elevate cell atlas data reliability. In summary, here, we unveil the hidden intronic landscape of every tissue and highlight the importance of more rigorous single-cell RNA-sequencing quality assessment in cell atlases to enhance their applicability in diverse downstream analyses.
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