Single–cell RNA sequencing and spatial transcriptomics reveal cancer-associated fibroblasts in glioblastoma with protumoral effects.
Bacterial droplet-based single–cell RNA-seq reveals antibiotic-associated heterogeneous cellular states.
ASGARD is A Single–cell Guided Pipeline to Aid Repurposing of Drugs.
ScRNA-seq and ST-seq in liver research.
From ‘Omics to Multi–omics Technologies: the Discovery of Novel Causal Mediators.
Single–cell spatial explorer: easy exploration of spatial and multimodal transcriptomics.
Screening cell–cell communication in spatial transcriptomics via collective optimal transport.
RNA methylation influences TDP43 binding and disease pathogenesis in models of amyotrophic lateral sclerosis and frontotemporal dementia.
Spatial and single–cell transcriptomics decipher the cellular environment containing HLA-G+ cancer cells and SPP1+ macrophages in colorectal cancer.
Lineage-specific regulatory changes in hypertrophic cardiomyopathy unraveled by single-nucleus RNA-seq and spatial transcriptomics.
Afriat A, Zuzarte-Luís V, Bahar Halpern K, Buchauer L, Marques S, Chora ÂF, Lahree A, Amit I, Mota MM, Itzkovitz S.Nature. 2022 Nov;611(7936):563-569. doi: 10.1038/s41586-022-05406-5. Epub 2022 Nov 9.PMID: 36352220
Abstract: Malaria infection involves an obligatory, yet clinically silent liver stage<sup>1,2</sup>. Hepatocytes operate in repeating units termed lobules, exhibiting heterogeneous gene expression patterns along the lobule axis<sup>3</sup>, but the effects of hepatocyte zonation on parasite development at the molecular level remain unknown. Here we combine single-cell RNA sequencing<sup>4</sup> and single-molecule transcript imaging<sup>5</sup> to characterize the host and parasite temporal expression programmes….LEARN MORE
April 8, 2022
. Single-cell RNA-seq reveals cell type–specific molecular and genetic associations to lupus
Abstract: Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease. Knowledge of circulating immune cell types and states associated with SLE remains incomplete. We profiled more than 1.2 million peripheral blood mononuclear cells (162 cases, 99 controls) with multiplexed single-cell RNA sequencing (mux-seq). …see Link for more information…
Also Highlighted in an article on Genomeweb. Find it HERE
April 1, 2022
Research Techniques Made Simple: Spatial Transcriptomics
Arianna J Piñeiro 1, Aubrey E Houser 1, Andrew L Ji 2PMID: 35331388 PMCID: PMC8969263 (available on 2023-04-01) DOI: 10.1016/j.jid.2021.12.014
Abstract: Transcriptome profiling of tissues and single cells facilitates interrogation of gene expression changes within diverse biological contexts. However, spatial information is often lost during tissue homogenization or dissociation. Recent advances in transcriptome profiling preserve the in situ spatial contexts…..Please see link for more information.
March 22, 2022
Multiplexed droplet single-cell sequencing (Mux-Seq) of normal and transplant kidney.
Abstract: Maintenance of systemic homeostasis by kidney requires the coordinated response of diverse cell types. The use of single-cell RNA sequencing (scRNAseq) for patient tissue samples remains fraught with difficulties with cell isolation, purity, and experimental bias. The ability to characterize immune and parenchymal cells during transplant rejection will be invaluable…..Please see link for more information.
March 15, 2022
Single-cell transcriptomics reveals distinct effector profiles of infiltrating T cells in lupus skin and kidney.
March 11, 2022
Single-Cell RNA Sequencing with Spatial Transcriptomics of Cancer Tissues.
Abstract: Single-cell RNA sequencing (RNA-seq) techniques can perform analysis of transcriptome at the single-cell level and possess an unprecedented potential for exploring signatures involved in tumor development and progression. These techniques can perform sequence analysis of transcripts with a better resolution that could increase understanding of the cellular diversity found in the tumor microenvironment …Please see link for more information.
November 14, 2021
Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration
David W McKellar 1, Lauren D Walter 2, Leo T Song 1, Madhav Mantri 3, Michael F Z Wang 3, Iwijn De Vlaminck # 4, Benjamin D Cosgrove # 5
Skeletal muscle repair is driven by the coordinated self-renewal and fusion of myogenic stem and progenitor cells. Single-cell gene expression analyses of myogenesis have been hampered by the poor sampling of rare and transient cell states that are critical for muscle repair, and do not inform the spatial context that is important for myogenic differentiation. Here, we demonstrate how large-scale integration of single-cell and spatial transcriptomic data can overcome these limitations. ……Please see link for more information.
October 29, 2021
Single-Cell Proteomic Analysis Dissects the Complexity of Tumor Microenvironment in Muscle Invasive Bladder Cancer
Muscle invasive bladder cancer (MIBC) is a malignancy with considerable heterogeneity. The MIBC tumor microenvironment (TME) is highly complex, comprising diverse phenotypes and spatial architectures. The complexity of the MIBC TME must be characterized to provide potential targets for precision therapy. Herein, an integrated combination of mass cytometry and imaging mass cytometry was used to analyze tumor cells, immune cells, and TME spatial characteristics of 44 MIBC patients. We detected tumor and immune cell clusters with abnormal phenotypes. ….Please see link for more information