Sequencing articles within Nature Communications

Featured

  • Article
    | Open Access

    Understanding T cell behaviour in cancers is vital for improving immunotherapies. Here, the authors present spatially resolved T cell receptor sequencing (SPTCR-seq), a technology that annotates T cell receptors within the tumour ecosystem.

    • Jasim Kada Benotmane
    • , Jan Kueckelhaus
    •  & Dieter Henrik Heiland

  • Article
    | Open Access

    Mucosal associated invariant T (MAIT) cells reside in barrier organs, but their contribution to inflammatory processes in the kidneys is not fully known. Here authors find by single cell RNA sequencing that among the different MAIT cell subtypes found at steady state, a population with MAIT17 signature is expanded in both human crescentic glomerulonephritis and its mouse model, and these cells may play protective role in the disease.

    • Ann-Christin Gnirck
    • , Marie-Sophie Philipp
    •  & Jan-Eric Turner

  • Article
    | Open Access

    Identifying spatially variable genes (SVGs) is essential for linking molecular cell functions with tissue phenotypes. Here, authors introduce a non-parametric model that detects SVGs from two or three-dimensional spatial transcriptomics data by comparing gene expression patterns at granularities.

    • Juexin Wang
    • , Jinpu Li
    •  & Dong Xu

  • Article
    | Open Access

    The study reveals limitations in widely used RNA-seq aligners, which create 'phantom' introns in reference databases. The authors introduce EASTR, a computational tool that not only enhances alignment accuracy but also uncovers existing annotation errors. This improvement bolsters the dependability of subsequent RNA-seq analyses.

    • Ida Shinder
    • , Richard Hu
    •  & Mihaela Pertea

  • Article
    | Open Access

    Methylation is the dominant modification in mRNA and occurs at a variety of sites. Here, Hartstock et al. show that a clickable analogue of the key cosubstrate S-adenosyl-L-methionine (SAM) can be produced in cells, allowing for identification and mapping of different methylated nucleosides in mRNA.

    • Katja Hartstock
    • , Nadine A. Kueck
    •  & Andrea Rentmeister

  • Article
    | Open Access

    Uterine natural killer (NK) cells support tissue homeostasis in the uterus during pregnancy, but it is not fully known how they differentiate into potentially cytotoxic effector cells while avoiding tissue damage. Here authors show that Il21 receptor signalling via STAT3 activation governs their differentiation, while an apoptotic cell death program ensures that harm is limited.

    • Mengwei Han
    • , Luni Hu
    •  & Chao Zhong

  • Article
    | Open Access

    Unnatural base pairing xenonucleic acids (XNAs) can be used to expand life’s alphabet beyond ATGC. Here, authors show strategies for enzymatic synthesis and next-generation nanopore sequencing of XNA base pairs for reading and writing 12-letter DNA (ATGCBSPZXKJV).

    • Hinako Kawabe
    • , Christopher A. Thomas
    •  & Jorge A. Marchand

  • Article
    | Open Access

    Current methods to generate spheroids are associated with low production throughputs, limiting clinical and industrial translation. Here the authors present a clean ultra-high-throughput in-air microfluidic platform for mass production of lumenogenic embryoid bodies and functional cardiospheres.

    • Bas van Loo
    • , Simone A. ten Den
    •  & Jeroen Leijten

  • Article
    | Open Access

    mRNA vaccines must be rigorously analysed to measure their integrity and detect contaminants, which can be time-consuming and costly. Here, authors describe a method to analyse mRNA vaccine quality using long-read sequencing and a custom bioinformatic pipeline.

    • Helen M. Gunter
    • , Senel Idrisoglu
    •  & Tim R. Mercer

  • Article
    | Open Access

    Haplotype-resolved long, complex tandem repeats remain largely hidden despite their potential relevance to disease. Here, the authors reveal and analyze the genome-wide landscape of these repeats using a high-precision algorithm.

    • Kazuki Ichikawa
    • , Riki Kawahara
    •  & Shinichi Morishita

  • Article
    | Open Access

    During preclinical drug development, the ability of cancer cell lines to faithfully model human disease is important for identifying potential therapeutic strategies. Here, using transcriptomic datasets of over 1000 cell lines, the authors evaluate how representative each line is of its cancer type and present their cell line selection tool.

    • Han Jin
    • , Cheng Zhang
    •  & Adil Mardinoglu

  • Article
    | Open Access

    Rapid identification of pathogens in neonatal infection, and corresponding antimicrobial susceptibility profiles, would improve patient outcomes and assist in antibiotic stewardship. In this work, the authors utilize metagenomic next-generation sequencing of post-mortem tissue samples to identify pathogens associated with neonatal deaths.

    • Vicky L. Baillie
    • , Shabir A. Madhi
    •  & Courtney P. Olwagen

  • Article
    | Open Access

    Many expression deconvolution approaches have been developed to estimate % RNA contributions of diverse cell types to mixed RNA measurements. Here, the authors have developed a complementary approach called scProjection to recover cell type-specific expression profiles from mixed RNA measurements.

    • Nelson Johansen
    • , Hongru Hu
    •  & Gerald Quon

  • Article
    | Open Access

    Here the authors introduce a new method to study DNA in single cells by long-read sequencing. Their method gives a more complete view of the genomic structure of individual cells and allows to study genetic differences at the single-cell level.

    • Joanna Hård
    • , Jeff E. Mold
    •  & Adam Ameur

  • Article
    | Open Access

    Population level transcriptomics measurements miss bacterial heterogeneity. Here the authors report smRandom-seq, a droplet-based high-throughput single-microbe RNA-seq assay, using random primers for in situ cDNA generation, droplets for single-microbe barcoding, and CRISPR-based rRNA depletion.

    • Ziye Xu
    • , Yuting Wang
    •  & Yongcheng Wang

  • Article
    | Open Access

    Droplet microfluidics enables high-throughput single-cell sequencing, but often with increased noise. Here the authors report spinDrop (sorting picoinjection inDrop) to increase gene detection and reduce noise; they use this to generate a high-quality molecular atlas of mouse brain development.

    • Joachim De Jonghe
    • , Tomasz S. Kaminski
    •  & Florian Hollfelder

  • Article
    | Open Access

    Mosquito-borne viruses are serious global public health threats associated with severe atypical cardiovascular manifestations. Here, the authors dissect how chikungunya virus directly infects cardiac tissue leading to heart disease and define key host pathways involved in viral cardiac persistence and tissue damage.

    • Maria G. Noval
    • , Sophie N. Spector
    •  & Kenneth A. Stapleford

  • Article
    | Open Access

    Qu et al. present a detailed three-dimensional spatial transcriptome atlas of all major organs in the mouse embryo at E13.5, providing a better understanding of organ development and cellular interactions during mammalian development.

    • Fangfang Qu
    • , Wenjia Li
    •  & Guangdun Peng

  • Article
    | Open Access

    Accurate cell-type identification is vital for single-cell analysis. Here, the authors develop a computational pipeline called “LungMAP CellRef” for efficient, automated cell-type annotation of normal and disease human and mouse lung single-cell datasets.

    • Minzhe Guo
    • , Michael P. Morley
    •  & Yan Xu

  • Article
    | Open Access

    Chikungunya virus is endemic in Brazil and cases have been rapidly increasing in recent years. Here, the authors describe the expansion of a genomic surveillance program across the country allowing them to characterise the emergence and dispersal of two distinct subclades mainly seeded from the north eastern region.

    • Joilson Xavier
    • , Luiz Carlos Junior Alcantara
    •  & Marta Giovanetti

  • Article
    | Open Access

    There is a need for methods that allow the analysis of single-cell long-read sequencing data without depending on known barcode lists or short-read sequencing. Here, the authors develop scNanoGPS, a tool that can independently deconvolute long reads into single cells and single molecules, and apply it on tumour and cell line data.

    • Cheng-Kai Shiau
    • , Lina Lu
    •  & Ruli Gao

  • Article
    | Open Access

    Sequencing malaria parasites from low density infections in small amounts of dried blood is important for large-scale genomic surveillance. Here, the authors develop and validate a highly multiplexed droplet digital PCR-based amplicon deep sequencing assay and apply it to data from Zanzibar, Tanzania.

    • Aurel Holzschuh
    • , Anita Lerch
    •  & Cristian Koepfli

  • Article
    | Open Access

    Acorales is sister to all other monocots and contains only one family with just one genus, Acorus. Here, the authors assemble the genome of the diploid Ac. gramineus and the tetraploid Ac. calamus, reconstruct an ancestral monocot karyotype and gene toolkit, and discuss the origin and evolution of the two species and other monocots.

    • Liang Ma
    • , Ke-Wei Liu
    •  & Zhong-Jian Liu

  • Article
    | Open Access

    Monocots are one of the most diverse and dominant clades of flowering plants. Here, the authors assemble the genome of Acorus gramineus, confirm its phylogenetic position as sister to the rest of monocots and reveal the absence of tau (τ) whole-genome duplication observed in the majority of monocot clades.

    • Xing Guo
    • , Fang Wang
    •  & Huan Liu

  • Comment
    | Open Access

    Whole genome sequencing has enabled new insights into the genetic architecture of complex traits, especially through access to low-frequency and rare variation. This Comment highlights the key contributions from this technology and discusses considerations for its use and future perspectives.

    • Ozvan Bocher
    • , Cristen J. Willer
    •  & Eleftheria Zeggini

  • Article
    | Open Access

    Here, the authors provide an exome study of hand grip strength, a proxy of generalized muscle strength. They identify six exome-wide significant genes, with links to disease, and additivity of rare and common genetic variant effects on muscle strength.

    • Yunfeng Huang
    • , Dora Bodnar
    •  & Heiko Runz

  • Article
    | Open Access

    Importins are known to facilitate nucleocytoplasmic transport and cytoplasmic chaperoning of some proteins. Here, the authors uncover that these proteins also act as co-translational chaperones for specific sets of proteins, for example ribonucleic acid binding factors.

    • Maximilian Seidel
    • , Natalie Romanov
    •  & Martin Beck

  • Article
    | Open Access

    Compact RNA structural motifs control many aspects of gene expression, but methods for their identification are lacking. Here the authors present a sequencing-based terbium probing approach to detect complex 3D structural elements, which can be used to pinpoint potential riboregulatory elements.

    • Shivali Patel
    • , Alec N. Sexton
    •  & Anna Marie Pyle

  • Article
    | Open Access

    Village cultures, where multiple stem cell lines are cultured in a single dish, provide an elegant solution for population-scale studies. Here, authors show the utility of village models – showing that expression heterogeneity is largely a result of line-specific effects and not village cultures.

    • Drew R. Neavin
    • , Angela M. Steinmann
    •  & Joseph E. Powell

  • Article
    | Open Access

    Protein sequencing is one of the key aims of the nanopore field. Working toward this goal, here the authors report the direct identification of single amino acids in MoS2 nanopores with sub-1 Dalton resolution, as well as the discrimination of the amino acid isomers and amino acid phosphorylation.

    • Fushi Wang
    • , Chunxiao Zhao
    •  & Jiandong Feng

  • Article
    | Open Access

    Single cell sequencing can be used to better characterize immune cell progenitors. Here the authors characterize CLEC12Ahi pre-basophils downstream of pre-basophil and mast cell progenitors (pre-BMPs) but upstream of mature basophils and this population includes basophil progenitors (BaPs).

    • Kensuke Miyake
    • , Junya Ito
    •  & Hajime Karasuyama

  • Article
    | Open Access

    The contribution of cell-extrinsic factors during cellular reprogramming to human induced pluripotent stem cells has long been overlooked. Here, the authors show functional protein communication between reprogramming intermediates and the re-shaping of a permissive extracellular environment.

    • Francesco Panariello
    • , Onelia Gagliano
    •  & Nicola Elvassore

  • Article
    | Open Access

    Long-read single-cell RNA isoform sequencing can elucidate the intricate landscape of alternative RNA splicing in individual cells, but it suffers from a low read throughput. Here, the authors develop circular consensus sequencing methods to allow high-throughput and high-accuracy single-cell RNA isoform sequencing.

    • Zhuo-Xing Shi
    • , Zhi-Chao Chen
    •  & Yi-Zhi Liu

  • Article
    | Open Access

    Single-nucleus RNA-seq was used to profile 11 retinas with varying stages of age-related macular degeneration and 6 control retinas. The authors identified shared glial states across neurodegeneration, indicating that the retina provides a human system for investigating therapeutic approaches in neurodegeneration.

    • Manik Kuchroo
    • , Marcello DiStasio
    •  & Brian P. Hafler

  • Article
    | Open Access

    Methods to reanalyze scRNA-seq data in a spatial perspective are vital but lacking. Here, the authors develop scSpace, an integrative method that uses ST data as spatial reference to reconstruct the pseudo-space of scRNA-seq data and identify spatially variable cell subpopulations, providing insights into spatial heterogeneity from scRNA-seq data.

    • Jingyang Qian
    • , Jie Liao
    •  & Xiaohui Fan

  • Article
    | Open Access

    Efforts to convert aptamers into molecular switches using rational design are often unsuccessful. Here the authors describe a massively parallel screening-based strategy whereby millions of potential aptamer switches are synthesised, sequenced and screened directly on a flow-cell.

    • Alex M. Yoshikawa
    • , Alexandra E. Rangel
    •  & H. Tom Soh

  • Article
    | Open Access

    Stromal cells are essential for intestinal homeostasis. Here the authors describe the phenotype, transcriptional profile and location of stromal cell subsets in the adult murine small intestine and colon lamina propria and demonstrate that these cells derive from Gli1+ precursors present in embryonic day 12.5 intestine.

    • Simone Isling Pærregaard
    • , Line Wulff
    •  & William W. Agace

  • Article
    | Open Access

    Chemotherapy priming sensitizes triple-negative breast cancers to immune checkpoint blockade. However, immune suppressive myeloid cells may impede its optimal effect. Here authors characterise the immune suppressive myeloid cells via single-cell analyses of immune cells from low dose chemotherapy treated breast tumours and identify STAT1 signalling as a regulator for immune suppressive state.

    • Bhavana Palakurthi
    • , Shaneann R. Fross
    •  & Siyuan Zhang

Browse broader subjects

Browse narrower subjects

Browse Sequencing across other nature.com journals