Article
Multidisciplinary Sciences
Gerda Kildisiute, Waleed M. Kholosy, Matthew D. Young, Kenny Roberts, Rasa Elmentaite, Sander R. van Hooff, Clarissa N. Pacyna, Eleonora Khabirova, Alice Piapi, Christine Thevanesan, Eva Bugallo-Blanco, Christina Burke, Lira Mamanova, Kaylee M. Keller, Karin P. S. Langenberg-Ververgaert, Philip Lijnzaad, Thanasis Margaritis, Frank C. P. Holstege, Michelle L. Tas, Marc H. W. A. Wijnen, Max M. van Noesel, Ignacio Del Valle, Giuseppe Barone, Reinier van der Linden, Catriona Duncan, John Anderson, John C. Achermann, Muzlifah Haniffa, Sarah A. Teichmann, Dyanne Rampling, Neil J. Sebire, Xiaoling He, Ronald R. de Krijger, Roger A. Barker, Kerstin B. Meyer, Omer Bayraktar, Karin Straathof, Jan J. Molenaar, Sam Behjati
Summary: The neuroblastoma cancer cells resemble fetal sympathoblasts, indicating a pan-neuroblastoma cancer cell state that could potentially be targeted for novel treatment strategies. The findings highlight the importance of understanding the phenotype of neuroblastoma cells for the development of immunotherapeutic and targeted avenues.
Article
Multidisciplinary Sciences
David Laehnemann, Johannes Koester, Ute Fischer, Arndt Borkhardt, Alice C. McHardy, Alexander Schoenhuth
Summary: ProSolo is a tool for calling single nucleotide variants from MDA single cell DNA sequencing data, which integrates all relevant MDA biases to achieve higher accuracy and reliability in single cells compared to existing tools.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Mohammadamin Edrisi, Monica V. Valecha, Sunkara B. Chowdary, Sergio Robledo, Huw A. Ogilvie, David Posada, Hamim Zafar, Luay Nakhleh
Summary: In this study, the authors developed a new scalable method called Phylovar for detecting single-nucleotide variants (SNVs) from sequencing datasets containing millions of loci. They showed that Phylovar outperforms existing methods in terms of running time and accuracy through benchmarking on simulated datasets. The authors also demonstrated the effectiveness of Phylovar on real biological datasets, detecting somatic SNVs in cancer cells and identifying SNVs associated with neurodegenerative diseases in neuron cells.
Article
Multidisciplinary Sciences
Zhigang Chen, Yi Zhang, Wenlu Li, Chenyi Gao, Fengbo Huang, Lu Cheng, Menglei Jin, Xiaoming Xu, Jian Huang
Summary: This study utilizes single cell RNA-seq to investigate the mechanisms of fibroadenoma (FA) and develops organoid models for studying treatment resistance. The study identifies dysregulation of epithelial cells in FAs and discovers hormone-responsive functional signatures as well as mechanisms of hormone resistance. The authors also develop a human expandable FA organoid system and find that combinations of inhibitors can suppress the viability of tamoxifen-resistant organoids.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Kailing Tu, Keying Lu, Qilin Zhang, Wei Huang, Dan Xie
Summary: A new variant detection method SCOUT was developed for single-cell genotyping, which does not require external data for SNV detection. By utilizing base count information from the neighboring genomic region, SCOUT improves variant detection performance and shows increased operating efficiency compared to other methods.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Etienne Sollier, Jack Kuipers, Koichi Takahashi, Niko Beerenwinkel, Katharina Jahn
Summary: This paper presents a new computational method, COMPASS, for inferring the joint phylogeny of single nucleotide variants and copy number alterations from targeted scDNAseq data. COMPASS was evaluated on simulated data and applied to real datasets, showing its effectiveness in detecting clonal and subclonal CNAs, and aiding in understanding tumor evolution and predicting drug resistance.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Kun Yin, Shanqing Huang, Weidong Ruan, Haopai Wei, He Dong, Dianyi Liang, Meijuan Zhao, Wei Qi, Chaoyong Yang, Zhi Zhu
Summary: Iso-seq is a rapid and uniform single-cell whole-genome sequencing method that uses a specially designed dual-well structure and a capillary-based centrifugal-driven droplet generator to isolate single cells and compartmentalize their genomes in droplets within 3 minutes. Iso-seq achieves high mapping ratio, broad coverage of the genome, and low coefficient of variation, making it promising for a wide variety of biological applications.
Article
Cell Biology
Daniel A. Bartlett, Vishnu Dileep, Tetsuya Handa, Yasuyuki Ohkawa, Hiroshi Kimura, Steven Henikoff, David M. Gilbert
Summary: The study introduces a high-throughput single-cell DNA binding site mapping method, TIP-seq, that is simple, cost-effective, and capable of multiplexing multiple samples per experiment.
JOURNAL OF CELL BIOLOGY
(2021)
Article
Biochemical Research Methods
Lei Zhang, Moonsook Lee, Alexander Y. Maslov, Cristina Montagna, Jan Vijg, Xiao Dong
Summary: This study presents a detailed protocol for single-cell whole-genome sequencing to discover and analyze somatic mutations in tissues and organs. The protocol includes steps such as single-cell isolation, whole-genome amplification, library preparation, and sequencing, as well as computational analyses. It provides high genomic coverage and accuracy compared to other single-cell amplification methods.
Article
Chemistry, Analytical
Furui Jin, Danke Xu
Summary: The study utilized cascaded DNA circuits on a bead array platform for signal amplification of miRNA, achieving high sensitivity detection in single cells. This method allows accurate quantification and identification of single nucleotide differences, providing new possibilities for disease treatment strategies.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Xiaowen Cao, Feng Chen, Jing Xue, Yue Zhao, Min Bai, Yongxi Zhao
Summary: Here, we present a hierarchical DNA branch assembly-encoded fluorescent nanoladders for denoised and highly multiplexed signal amplification of single-cell transcripts. Our method achieves independent RNA-primed rolling circle amplification without nonspecific amplification and allows for programmable DNA branch assembly to encode virtual signals for visualizing numbers of targets. We demonstrate accurate RNA profiling in different cancer cells and reveal diverse localization patterns for spatial regulation of transcripts.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Doina Ciobanu, Alicia Clum, Steven Ahrendt, William B. Andreopoulos, Asaf Salamov, Sandy Chan, C. Alisha Quandt, Brian Foster, Jan P. Meier-Kolthoff, Yung Tsu Tang, Patrick Schwientek, Gerald L. Benny, Matthew E. Smith, Diane Bauer, Shweta Deshpande, Kerrie Barry, Alex Copeland, Steven W. Singer, Tanja Woyke, Igor Grigoriev, Timothy Y. James, Jan-Fang Cheng
Summary: This study outlines a pipeline for targeted single-cell sequencing of poorly studied and uncultivated eukaryotic microorganisms found at low abundance. The pipeline consists of seven steps, each with quality review measures to ensure high genome quality at low cost. Genomes generated through this pipeline are shown to be almost as good as complete reference genomes for functional and comparative genomics of environmental microbial eukaryotes.
Article
Biochemical Research Methods
Teng Xu, Yuandong Li, Xiao Han, Lingyan Kan, Jing Ren, Luyang Sun, Zhidian Diao, Yuetong Ji, Pengfei Zhu, Jian Xu, Bo Ma
Summary: An optical tweezer-assisted pool-screening and single-cell isolation (OPSI) system has been established for precise, indexed isolation of individual bacterial, yeast or human cancer cells. The system achieves high purity and speed, is applicable to cells of different sizes, and can generate high-quality single-cell transcriptome profiles.
Article
Chemistry, Multidisciplinary
Yingfei Wang, Yanyun Fang, Yu Zhu, Shiyi Bi, Ying Liu, Huangxian Ju
Summary: By developing a hydrogel microbead-based strategy, simultaneous sensitive quantification of multiple miRNAs in single cells is achieved. The porous structure of the hydrogel microbeads effectively avoids nonspecific cross-reactions and enables successful differentiation of cellular heterogeneity and subpopulation discrimination in liver cancer cells and normal liver cells.
Article
Multidisciplinary Sciences
Yuguang Liu, Patricio Jeraldo, William Herbert, Samantha McDonough, Bruce Eckloff, Dirk Schulze-Makuch, Jean-Pierre De Vera, Charles Cockell, Thomas Leya, Mickael Baque, Jin Jen, Marina Walther-Antonio
Summary: Here, we report the use of microfluidic technology combined with single cell sequencing and de novo assembly to minimize the contamination and recover the complete genome of the Nostoc strain CCCryo 231-06 with high quality.
Article
Mycology
R. C. Van Court, M. S. Wiseman, K. W. Meyer, D. J. Ballhorn, K. R. Amses, J. C. Slot, B. T. M. Dentinger, R. Garibay-Orijel, J. K. Uehling
Summary: Therapeutic use of psilocybin has gained attention in recent international research, highlighting the importance of understanding psilocybin-producing fungi for consumer safety.
Article
Mycology
Gustavo H. Jeronimo, D. Rabern Simmons, Kevin R. Amses, Kensuke Seto, Timothy Y. James, Carmen L. A. Pires-Zottarelli, Joyce E. Longcore
Summary: Cladochytriales is a group of chytrids that includes both monocentric and polycentric lineages, commonly found in algae and decaying plant material in aquatic and terrestrial ecosystems. Recently, two polycentric chytrids with unique rhizomycelia structures were discovered on onion skin, distinct from known cladochytrialean genera or those in other orders. Phylogenetic analysis revealed that these two isolates belong to separate branches of a predominantly monocentric clade. The discovery of these new chytrids expands our understanding of their diversity and supports the unreliable nature of thalli's development as a taxonomic character.
MYCOLOGICAL PROGRESS
(2022)
