ArticleScientific reports2019
Evaluation of ultra-low input RNA sequencing for the study of human T cell transcriptome.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- New insight into RNA biomarkers in neuropathic pain: a clinician-neuroscientist roadmap to translational testing and treatment monitoring a clinical review.Frontiers in pain research (Lausanne, Switzerland) · 2026Review
- Kinome analysis of Madurella mycetomatis identified kinases in the cell wall integrity pathway as novel potential therapeutic drug targets in eumycetoma caused by Madurella mycetomatis.PLoS neglected tropical diseases · 2025Article
- The role of non-coding RNAs in the regulation of cell death pathways in melanoma.Discover oncology · 2025Review
- The impact of PCR duplication on RNAseq data generated using NovaSeq 6000, NovaSeq X, AVITI, and G4 sequencers.Genome biology · 2025Article
- A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics.Nature communications · 2025Article
- Integration of RNAseq transcriptomics andChemical science · 2025Article
- Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3.BMC genomics · 2024Article
- Comparative analysis of cell-cell communication at single-cell resolution.Nature biotechnology · 2024Article
- Dissecting the Immune System through Gene Regulation.Advances in experimental medicine and biology · 2024Article
- Gene expression changes in therapeutic ultrasound-treated venous leg ulcers.Frontiers in medicine · 2023Article
- Meso-seq for in-depth transcriptomics in ultra-low amounts of FACS-purified neuronal nuclei.Cell reports methods · 2022Article
- HIV-1 Drug Resistance Assay Using Ion Torrent Next Generation Sequencing and On-Instrument End-to-End Analysis Software.Journal of clinical microbiology · 2022Article
- Metabolic and functional impairment of CD8Journal of leukocyte biology · 2022Article
- Sensitive and accurate analysis of gene expression signatures enabled by oligonucleotide-labelled cDNA.RNA biology · 2022Article
- Advances in Genomics for Drug Development.Genes · 2020Review
- Transcriptional Profiling of CD8+ CMV-Specific T Cell Functional Subsets Obtained Using a Modified Method for Isolating High-Quality RNA From Fixed and Permeabilized Cells.Frontiers in immunology · 2020Article
- Functional Genomics of Healthy and Pathological Fetal Membranes.Frontiers in physiology · 2020Review
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Deeper understanding of T cell biology is crucial for the development of new therapeutics. Human naïve T cells have low RNA content and their numbers can be limiting; therefore we set out to determine the parameters for robust ultra-low input RNA sequencing. We performed transcriptome profiling at different cell inputs and compared three protocols: Switching Mechanism at 5' End of RNA Template technology (SMART) with two different library preparation methods (Nextera and Clontech), and AmpliSeq technology. As the cell input decreased the number of detected coding genes decreased with SMART, while stayed constant with AmpliSeq. However, SMART enables detection of non-coding genes, which is not feasible for AmpliSeq. The detection is dependent on gene abundance, but not transcript length. The consistency between technical replicates and cell inputs was comparable across methods above 1 K but highly variable at 100 cell input. Sensitivity of detection for differentially expressed genes decreased dramatically with decreased cell inputs in all protocols, support that additional approaches, such as pathway enrichment, are important for data interpretation at ultra-low input. Finally, T cell activation signature was detected at 1 K cell input and above in all protocols, with AmpliSeq showing better detection at 100 cells.
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