ArticleScientific reports2022
An optimized protocol for single nuclei isolation from clinical biopsies for RNA-seq.
Article in Scientific reports, 2022. 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 16 papers.
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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.
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Who cites it
16 citing papers in PubMed, 21 citations in OpenAlex.
- RNAlater-compatible protocol for nuclei isolation from radical prostatectomy prostate cancer resections, enabling single-nucleus resolution RNA-seq.Scientific reports · 2026Article
- Optimized nuclei isolation and snRNA-seq reveal oligodendrocyte pathway dysregulation in MOGHE brain tissue from pediatric patients.Scientific reports · 2026Article
- Achilles tendon exhibits distinct transcriptomic changes with increased mitochondrial energy production under lunar gravity.NPJ microgravity · 2026Article
- Kidney diseases and single-cell sequencing research: a bibliometric analysis from 2015 to 2024.Renal failure · 2025Review
- Unravelling the pathogenic mechanisms in Graves' orbitopathy.European thyroid journal · 2025Review
- A versatile and efficient method to isolate nuclei from low-input cryopreserved tissues for single-nuclei transcriptomics.Scientific reports · 2025Article
- Single-Cell Transcriptomics Sheds Light on Tumor Evolution: Perspectives from City of Hope's Clinical Trial Teams.Journal of clinical medicine · 2024Article
- Effects of oxycodone on placental lineages: Evidence from the transcriptome profile of mouse trophoblast giant cells.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- G6PC3 is involved in spermatogenesis by maintaining meiotic sex chromosome inactivation.Acta biochimica et biophysica Sinica · 2024Article
- Advances in long-read single-cell transcriptomics.Human genetics · 2024Review
- Single nuclei transcriptomics delineates complex immune and kidney cell interactions contributing to kidney allograft fibrosis.Kidney international · 2023Article
- Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease.Nature reviews. Neurology · 2023Review
- Optimized nucleus isolation protocol from frozen mouse tissues for single nucleus RNA sequencing application.Frontiers in cell and developmental biology · 2023Article
- Multi-omic single cell sequencing: Overview and opportunities for kidney disease therapeutic development.Frontiers in molecular biosciences · 2023Review
- Single-cell transcriptomics in thyroid eye disease.Taiwan journal of ophthalmologyReview
- Management of Dysglycemia in a Pregnancy Complicated by Fanconi-Bickel Syndrome.AACE clinical case reportsArticle
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Single nuclei RNA sequencing (snRNA-seq) has evolved as a powerful tool to study complex human diseases. Single cell resolution enables the study of novel cell types, biological processes, cell trajectories, and cell-cell signaling pathways. snRNA-seq largely relies on the dissociation of intact nuclei from human tissues. However, the study of complex tissues using small core biopsies presents many technical challenges. Here, an optimized protocol for single nuclei isolation is presented for frozen and RNAlater preserved human kidney biopsies. The described protocol is fast, low cost, and time effective due to the elimination of cell sorting and ultra-centrifugation. Samples can be processed in 90 min or less. This method is effective for obtaining normal nuclei morphology without signs of structural damage. Using snRNA-seq, 16 distinct kidney cell clusters were recovered from normal and peri-transplant acute kidney injury allograft samples, including immune cell clusters. Quality control measurements demonstrated that these optimizations eliminated cellular debris and allowed for a high yield of high-quality nuclei and RNA for library preparation and sequencing. Cellular disassociation did not induce cellular stress responses, which recapitulated transcriptional patterns associated with standardized methods of nuclei isolation. Future applications of this protocol will allow for thorough investigations of small biobank biopsies, identifying cell-specific injury pathways and driving the discovery of novel diagnostics and therapeutic targets.
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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.