Transcriptomics articles from across Nature Portfolio

Transcriptomics is the study of the transcriptome—the complete set of RNA transcripts that are produced by the genome, under specific circumstances or in a specific cell—using high-throughput methods, such as microarray analysis. Comparison of transcriptomes allows the identification of genes that are differentially expressed in distinct cell populations, or in response to different treatments.

Featured

News & Views | 02 March 2023

Designing spatial transcriptomic experiments
- Dario Righelli
- , Andrea Sottosanti
- & Davide Risso
Nature Methods 20, 355-356

Latest Research and Reviews

Research
25 March 2023 | Open Access

The endocannabinoid system promotes hepatocyte progenitor cell proliferation and maturation by modulating cellular energetics
- Bani Mukhopadhyay
- , Kellie Holovac
- & George Kunos
Cell Death Discovery 9, 104
Research
25 March 2023 | Open Access

Neurotrophin signaling is a central mechanism of salivary dysfunction after irradiation that disrupts myoepithelial cells
- Alejandro M. Chibly
- , Vaishali N. Patel
- & Matthew P. Hoffman
npj Regenerative Medicine 8, 17
Research
23 March 2023 | Open Access

Pan-cancer classification of single cells in the tumour microenvironment

The accuracy and granularity of classifying cell types in the tumour microenvironment (TME) from single-cell RNA-seq data is impacted by heterogeneity among cancer cells and similarities among functionally related immune cells. Here, the authors develop scATOMIC, a tumour and TME cell type classifier based on a hierarchical approach that can be applied to pan-cancer datasets.
- Ido Nofech-Mozes
- , David Soave
- & Sagi Abelson
Nature Communications 14, 1615
Research
18 March 2023 | Open Access

Spatial transcriptomics using multiplexed deterministic barcoding in tissue

Examining the spatially resolved transcriptome of tissue sections promises advances in biomedical research. Here, the authors present xDBiT, a versatile, microfluidics-based approach to cost-effectively measure the spatial transcriptome of multiple tissue sections in parallel.
- Johannes Wirth
- , Nina Huber
- & Matthias Meier
Nature Communications 14, 1523
Research
16 March 2023 | Open Access

Identification of two early blood biomarkers ACHE and CLEC12A for improved risk stratification of critically ill COVID-19 patients
- Simone Kattner
- , Jan Müller
- & Kai Sohn
Scientific Reports 13, 4388
Research
15 March 2023 | Open Access

Mycophenolic acid directly protects podocytes by preserving the actin cytoskeleton and increasing cell survival
- Seif El Din Abo Zed
- , Agnes Hackl
- & Lutz T. Weber
Scientific Reports 13, 4281

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News and Comment

News & Views | 02 March 2023

Designing spatial transcriptomic experiments

Optimal design of spatial transcriptomic experiments allows statistical evaluation of the impact of various biological and technological features on the discovery of cell phenotypes.
- Dario Righelli
- , Andrea Sottosanti
- & Davide Risso
Nature Methods 20, 355-356
News | 28 February 2023

Did flu come from fish? Genetics points to influenza’s aquatic origin

Corals, sturgeon and other aquatic creatures harbour signs of infection by influenza and its distant relatives.
- Ewen Callaway
Nature
News & Views | 23 February 2023

Meta-analysis of harmonized brain transcriptomics data prioritizes therapeutic target genes

A meta-analysis of harmonized human brain RNA-seq datasets creates expression quantitative trait locus (eQTL) maps for multiple ancestries and brain regions, predicts cell-type-dependent eQTLs and produces gene networks. This prioritizes genes for multiple brain-related diseases, serving as a promising step toward the identification of central nervous system (CNS) drug targets.

Nature Genetics 55, 363-364
Research Highlights | 22 February 2023

Sex and age affect circadian gene expression

A paper in Science reports that circadian gene expression in humans is affected by sex and age, findings that might explain differential disease prevalence among these groups and have implications for treatment.
- Dorothy Clyde
Nature Reviews Genetics 24, 208
Research Highlights | 16 February 2023

Epitranscriptomics of cancer microniches

In this Tools of the Trade article, Lee describes Select-seq, a novel method for generating epitranscriptomic data from microniches within the tumour. The author reveals how the method can be used to identify novel biomarkers from rare cell subpopulations such as cancer stem cells in tumours.
- Amos Chungwon Lee
Nature Reviews Cancer 23, 189
News & Views | 14 February 2023

Precise mapping of molecular and cellular brain changes in Alzheimer’s disease

STARmap PLUS is a new spatial gene mapping method combined with histological staining. With STARmap PLUS, we created high-resolution, comprehensive maps of altered molecular pathways and reactive cells in a mouse model of Alzheimer’s disease. These maps enabled us to infer the trajectories of biological processes and cell states during disease progression.

Nature Neuroscience 26, 371-372

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Transcriptomics articles from across Nature Portfolio

Featured

Designing spatial transcriptomic experiments

Latest Research and Reviews

The endocannabinoid system promotes hepatocyte progenitor cell proliferation and maturation by modulating cellular energetics

Neurotrophin signaling is a central mechanism of salivary dysfunction after irradiation that disrupts myoepithelial cells

Pan-cancer classification of single cells in the tumour microenvironment

Spatial transcriptomics using multiplexed deterministic barcoding in tissue

Identification of two early blood biomarkers ACHE and CLEC12A for improved risk stratification of critically ill COVID-19 patients

Mycophenolic acid directly protects podocytes by preserving the actin cytoskeleton and increasing cell survival

News and Comment

Designing spatial transcriptomic experiments

Did flu come from fish? Genetics points to influenza’s aquatic origin

Meta-analysis of harmonized brain transcriptomics data prioritizes therapeutic target genes

Sex and age affect circadian gene expression

Epitranscriptomics of cancer microniches

Precise mapping of molecular and cellular brain changes in Alzheimer’s disease

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