SLaP mapper: A webserver for identifying and quantifying spliced-leader addition and polyadenylation site usage in kinetoplastid genomes. by Fiebig, M, Gluenz, E, Carrington, M, Kelly, S

“…SLaP mapper only requires raw read data from paired-end Illumina RNAseq and performs all read processing, mapping, quality control, quantification, and analysis in a fully automated pipeline. …”

The Plasmodium falciparum transcriptome in severe malaria reveals altered expression of genes involved in important processes including surface antigen-encoding var genes by Tonkin-Hill, GQ, Trianty, L, Noviyanti, R, Nguyen, HHT, Sebayang, BF, Lampah, DA, Marfurt, J, Cobbold, SA, Rambhatla, JS, McConville, MJ, Rogerson, SJ, Brown, GV, Day, KP, Price, RN, Anstey, NM, Papenfuss, AT, Duffy, MF

“…Here, we used RNA sequencing (RNAseq) to analyse gene expression in 44 parasite isolates that caused severe and uncomplicated malaria in Papuan patients. …”

tauFisher predicts circadian time from a single sample of bulk and single-cell pseudobulk transcriptomic data by Junyan Duan, Michelle N. Ngo, Satya Swaroop Karri, Lam C. Tsoi, Johann E. Gudjonsson, Babak Shahbaba, John Lowengrub, Bogi Andersen

“…Given its robustness and generalizability across assay platforms, experimental setups, and tissue types, as well as its potential application in single-cell RNAseq data analysis, tauFisher is a promising tool that facilitates circadian medicine and research.…”
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Recovery of synaptic loss and depressive-like behavior induced by GATA1 through blocking of the neuroinflammatory response by Koeul Choi, Joonhee Lee, Gukdo Kim, Younghyun Lim, Hyo Jung Kang

“…Through the combined analyses of ChIPseq, mRNAseq, and small RNAseq, we profiled genes that are potentially affected by GATA1 in cultured cortical neurons, and Gene Ontology (GO) analysis revealed that GATA1 might be associated with immune-related functions. …”
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Identification of a pancreatic stellate cell gene signature and lncRNA interactions associated with type 2 diabetes progression by Jinjun Qiu, Peng Zhu, Peng Zhu, Xing Shi, Jinquan Xia, Shaowei Dong, Liqun Chen

“…This study aims to identify gene expression patterns specific to T2D pancreatic islet cells and to explore the potential role of pancreatic stellate cells (PSCs) in T2D progression through regulatory networks involving lncRNA-mRNA interactions.MethodsIn this study, we screened for upregulated genes in T2D pancreatic islet samples using bulk sequencing (bulkseq) datasets and mapped these gene expression profiles onto three T2D single-cell RNA sequencing (scRNAseq) datasets. The identified T2D-specific gene features were further validated in an additional T2D scRNAseq dataset, a T1D scRNAseq dataset, and a T2D bulkseq dataset. …”
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Alterations in Protein Translation and Carboxylic Acid Catabolic Processes in Diabetic Kidney Disease by Kimberly S. Collins, Michael T. Eadon, Ying-Hua Cheng, Daria Barwinska, Ricardo Melo Ferreira, Thomas W. McCarthy, Danielle Janosevic, Farooq Syed, Bernhard Maier, Tarek M. El-Achkar, Katherine J. Kelly, Carrie L. Phillips, Takashi Hato, Timothy A. Sutton, Pierre C. Dagher

“…Using single nuclear RNA sequencing (snRNAseq) of kidneys from db/db mice, we prioritized additional pathways identified in human DKD. …”
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Technical optimization of spatially resolved single-cell transcriptomic datasets to study clinical liver disease by Brittany Rocque, Kate Guion, Pranay Singh, Sarah Bangerth, Lauren Pickard, Jashdeep Bhattacharjee, Sofia Eguizabal, Carly Weaver, Shefali Chopra, Shengmei Zhou, Rohit Kohli, Linda Sher, Omid Akbari, Burcin Ekser, Juliet A. Emamaullee

“…Single cell mapping of the spatial transcriptome using paired snRNAseq data generated a spatially resolved, single cell dataset with 24 unique liver cell phenotypes. …”
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T-Cell-Based Platform for Functional Screening of T-Cell Receptors Identified in Single-Cell RNA Sequencing Data Sets of Tumor-Infiltrating T-Cells by Aaron Rodriguez Ehrenfried, Stefan Zens, Laura Steffens, Hannes Kehm, Alina Paul, Claudia Lauenstein, Michael Volkmar, Isabel Poschke, Zibo Meng, Rienk Offringa

“…The advent of single-cell RNA sequencing (scRNAseq) has enabled in-depth gene expression analysis of several thousand cells isolated from tissues. …”
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DIFFERENTIAL GENE EXPRESSION AND PATHWAYS ENRICHMENT ANALYSIS IN TWO RNA-SEQ DATASETS OF JAK2V617F POSITIVE CELL LINE, TREATED WITH RUXOLITINIB, INDICATE FOCAL ADHESION PATHWAY MOD... by MEL Silva, ACMM Valente, R Tognon-Ribeiro

“…Both datasets are from RNAseq in HEL cells (JAK2 V617F-positive) treated with DMSO and Ruxo 0.5 uM for 48h. …”
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Staphylococcal Enterotoxins Enhance Biofilm Formation by <i>Staphylococcus aureus</i> in Platelet Concentrates by Sylvia Ighem Chi, Sandra Ramirez-Arcos

“…A hybrid approach of comparative RNAseq analyses and CRISPR mutagenesis of SE genes was employed to investigate the effect of SEs in <i>S. aureus</i> growth and biofilm formation in PCs. …”
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High percentage of blood-based T-cell receptor gamma V9-JP recombinations associated with amyotrophic lateral sclerosis: extensive retention of the JP KKIK amino acid motif by George Blanck, Taha I. Huda, Konrad J. Cios, George Angelakakis, Joanna J. Song

“…Exome and RNAseq files prepared from blood samples can be mined for adaptive immune receptor recombinations and thus for the complementarity determining region-3 (CDR3) amino acid (AA) sequences, important for antigen binding. …”
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Unveiling novel double-negative prostate cancer subtypes through single-cell RNA sequencing analysis by Siyuan Cheng, Lin Li, Yunshin Yeh, Yingli Shi, Omar Franco, Eva Corey, Xiuping Yu

“…Abstract Recent advancements in single-cell RNA sequencing (scRNAseq) have facilitated the discovery of previously unrecognized subtypes within prostate cancer (PCa), offering new insights into cancer heterogeneity and progression. …”
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Immunotherapy that improves response to chemotherapy in high-grade serous ovarian cancer by Samar Elorbany, Chiara Berlato, Larissa S. Carnevalli, Eleni Maniati, Simon T. Barry, Jun Wang, Ranjit Manchanda, Julia Kzhyshkowska, Frances Balkwill

“…Abstract Single-cell RNA sequencing (scRNAseq) of tumour-infiltrating immune cells in high-grade serous ovarian cancer (HGSOC) omental biopsies reveals potential targets that could enhance response to neo-adjuvant chemotherapy (NACT). …”
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Single-Cell Molecular Profiling of Head and Neck Squamous Cell Carcinoma Reveals Five Dysregulated Signaling Pathways Associated With Circulating Tumor Cells by Andres Stucky PhD, Chi T. Viet DDS, MD, PhD, Bradley E. Aouizerat PhD, Yi Ye PhD, Coleen Doan MD, Tarun Mundluru PhD, Parish Sedhiazadeh MD, Uttam K. Sinha MD, Xuelian Chen MD, Xi Zhang MD, PhD, Shengwen Calvin Li PhD, Jin Cai MD, Jiang F. Zhong PhD

“…Results Specifically, we revealed metastatic HNSCC patients have complex CTCs that could be defined through gene expression and mutational gene profiling derived from completed single-cell RNASeq (scRNASeq) that served to confirm molecular pathways inherent in these CTCs. …”
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A data-driven method for quantifying the impact of a genetic circuit on its host by Dorfan, Yuval, Espah Borujeni, Amin, Park, YongJin, Saxena, Uma, Gondon, Ben, Voigt, Christopher A., Yeung, Enoch

“…In this work we utilize Koopman operator theory to construct data-driven models of transcriptomic-level dynamics from noisy and temporally sparse RNAseq measurements. We show how Koopman models can be used to quantify impact on genetic circuits. …”
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Discordant genome assemblies drastically alter the interpretation of single-cell RNA sequencing data which can be mitigated by a novel integration method by Potts, HG, Lemieux, ME, Rice, ES, Warren, W, Choudhury, RP, Mommersteeg, MTM

“…Multiple-genome assemblies are especially problematic for researchers studying the genetic makeup of individual cells, as single-cell RNA sequencing (scRNAseq) requires sequenced reads to be mapped and aligned to a single reference genome. …”

Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii. by Boinett, C, Cain, A, Hawkey, J, Do Hoang, N, Khanh, N, Thanh, D, Dordel, J, Campbell, J, Lan, N, Mayho, M, Langridge, G, Hadfield, J, Chau, N, Thwaites, G, Parkhill, J, Thomson, N, Holt, K, Baker, S

“…We aimed to identify the mechanisms associated with colistin resistance in A. baumannii using multiple high-throughput-sequencing technologies, including transposon-directed insertion site sequencing (TraDIS), RNA sequencing (RNAseq) and whole-genome sequencing (WGS) to investigate the genotypic changes of colistin resistance in A. baumannii. …”

Single-cell RNA sequencing analysis identifies one subpopulation of endothelial cells that proliferates and another that undergoes the endothelial-mesenchymal transition in regener... by Thanh Minh Nguyen, Xiaoxiao Geng, Yuhua Wei, Lei Ye, Daniel J. Garry, Jianyi Zhang, Jianyi Zhang

“…Background: In our previous work, we demonstrated that when newborn pigs undergo apical resection (AR) on postnatal day 1 (P1), the animals’ hearts were completely recover from a myocardial infarction (MI) that occurs on postnatal day 28 (P28); single-nucleus RNA sequencing (snRNAseq) data suggested that this recovery was achieved by regeneration of pig cardiomyocyte subpopulations in response to MI. …”
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The MicroRNA <i>miR-277</i> Controls Physiology and Pathology of the Adult <i>Drosophila</i> Midgut by Regulating the Expression of Fatty Acid β-Oxidation-Related Genes in Intestin... by Lisa Zipper, Sai Batchu, Nida Hatice Kaya, Zeus Andrea Antonello, Tobias Reiff

“…Our initial in silico analysis of single cell RNAseq data and functional experiments identify the <i>microRNA miR-277</i> as a posttranscriptional regulator of fatty acid β-oxidation (FAO) in the intestinal lineage. …”
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Performance comparison of high throughput single-cell RNA-Seq platforms in complex tissues by Yolanda Colino-Sanguino, Laura Rodriguez de la Fuente, Brian Gloss, Andrew M.K. Law, Kristina Handler, Marina Pajic, Robert Salomon, David Gallego-Ortega, Fatima Valdes-Mora

“…However, there are limited studies that have comprehensively compared the performance of different scRNAseq systems in complex tissues. Here, we present a systematic comparison of two well-established high throughput 3′-scRNAseq platforms: 10× Chromium and BD Rhapsody, using tumours that present high cell diversity. …”
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