RNA sequencing articles from across Nature Portfolio

The presence of multiple functional m⁶A modification sites on diverse HIV-1 RNA transcripts suggests a strategy to provide additional stability and resilience to HIV-1 replication.

Using a combination of single-cell and spatial transcriptomic analysis, Serrano et al. uncover transcriptional dynamics during the establishment of arbuscular mycorrhizal symbiosis.

Technical limitations of simultaneously multi-omics profiling lead to highly noisy multi-modal data and substantial costs. Here, authors proposed a versatile framework and data augmentation schemes, capable of single-cell cross-modality translation and multiple extensive applications.

As a major microenvironmental component in B cell lymphomas, T cells are highly relevant for current immunotherapeutic treatment strategies of such tumours. A study now provides an unprecedented multimodal insight into the composition and features of T cell subsets of the four main types of nodal B cell non-Hodgkin lymphoma.

We pinpoint PCR artifacts as the primary source of inaccurate quantification in both short- and long-read RNA sequencing, a problem that intensifies with an increase in PCR cycles in both bulk and single-cell sequencing contexts. To overcome this challenge, we engineered a novel unique molecular identifier (UMI) barcode composed of homotrimer nucleotide blocks. This design facilitates accurate quantification of RNA molecules, substantially improving molecular counting.

ARTR-seq uses antibody-guided in situ reverse transcription to efficiently and accurately identify RNA-binding protein target sites in as few as 20 cells, or in a formaldehyde-fixed tissue section. The high temporal resolution of ARTR-seq opens opportunities for the investigation of dynamic RNA-binding protein–RNA interactions.

Expression profiles of single live cells are generated from Raman microscopy using deep learning, enabling us to track expression dynamics along cell reprogramming or differentiation.

DARLIN enables the generation of a massive diversity of barcodes for in vivo lineage tracing and the combination with single-cell multi-omics measurements.

Spatial transcriptomics offers a glimpse of how microbiomes interact with their hosts.