Use of next-generation sequencing in genomic studies of polyploid crops: cotton as an example by Zhu Qianhao, Danny Llewellyn, Iain Wilson

“…Next-generation sequencing (NGS) technologies provide enormous power and new potential to access the complex polyploid genomes and transcriptomes of major crops, including cotton. This article summarises the applications of NGS in cotton genomic studies, including genome sequencing and resequencing, transcriptomic analysis, small RNA sequencing and miRNA identification, and identification of single nucleotide polymorphisms. …”
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Comprehensive characterization of NK cell-related genes in cutaneous melanoma identified a novel prognostic signature for predicting the prognosis, immunotherapy, and chemotherapy... by Haili Ma, Jian Liu, Huan Jin, Min Zhang, Qian Liang, Zhiqiang Guo

“…Methods RNA-sequencing data and clinical information of CM patients were retrieved from The Cancer Genome Atlas (TCGA) database, while expression profiles from normal skin specimens were obtained from the Genotype-Tissue Expression (GTEx) database. Single-cell transcriptomes from CM were analyzed in conjunction with immune genes to identify NKIGs. …”
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Cancer stem cells and tumor-associated macrophages as mates in tumor progression: mechanisms of crosstalk and advanced bioinformatic tools to dissect their phenotypes and interacti... by Francesco Verona, Sebastiano Di Bella, Roberto Schirano, Camilla Manfredi, Francesca Angeloro, Giulia Bozzari, Matilde Todaro, Matilde Todaro, Giuseppe Giannini, Giuseppe Giannini, Giorgio Stassi, Veronica Veschi

“…Nowadays, the integration of biological and computational data obtained by cutting-edge technologies (single-cell RNA sequencing, spatial transcriptomics, trajectory analysis) has significantly improved the comprehension of the biunivocal multicellular dialogue, providing a comprehensive view of the heterogeneity and dynamics of CSCs, and uncovering alternative mechanisms of immune evasion and therapeutic resistance. …”
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Comparative transcriptome analysis of PBMCs in cats diagnosed with and recovered from FIPV by Ju Young Lee, Hyeong Ryeol Cho, Hong-Geun Oh, Jeong Ho Hwang

“…GS-441524 the parent drug of remdesivir and a competitive inhibitor of nucleoside triphosphates in viral RNA synthesis is a well-known treatment for FIP. However, comparative transcriptome and gene ontology analyses of normal (Normal), FIP-diseased (FIPD), and FIP-recovered (FIPR) cats have not yet been conducted. …”
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Benchmarking spatial transcriptomics technologies with the multi-sample SpatialBenchVisium dataset by Mei R. M. Du, Changqing Wang, Charity W. Law, Daniela Amann-Zalcenstein, Casey J. A. Anttila, Ling Ling, Peter F. Hickey, Callum J. Sargeant, Yunshun Chen, Lisa J. Ioannidis, Pradeep Rajasekhar, Raymond K. H. Yip, Kelly L. Rogers, Diana S. Hansen, Rory Bowden, Matthew E. Ritchie

“…Among the array of spatial capture technologies available is 10x Genomics’ Visium platform, a popular method which enables transcriptome-wide profiling of tissue sections. Visium offers a range of sample handling and library construction methods which introduces a need for benchmarking to compare data quality and assess how well the technology can recover expected tissue features and biological signatures. …”
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Endogenous Ribonucleases: Therapeutic Targeting of the Transcriptome Through Oligonucleotide-Triggered RNA Inactivation by Daria A. Chiglintseva, Olga A. Patutina, Marina A. Zenkova

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Transcriptome and DNA methylation profiling during the NSN to SN transition in mouse oocytes by Hannah Demond, Soumen Khan, Juan Castillo-Fernandez, Courtney W. Hanna, Gavin Kelsey

“…Transcriptome analysis showed a lower number of detected transcripts in SN compared with NSN oocytes as well as downregulation of 576 genes, which were enriched for processes related to mRNA processing. …”
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Hippocampal Transcriptome Analysis in a Mouse Model of Chronic Unpredictable Stress Insomnia by Shuo Zhang, Changqing Tong, Na Cao, Dong Tian, Linshan Du, Ya Xu, Weiguang Wang, Zijie Chen, Shuangqing Zhai

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Comparative transcriptomic and proteomic analyses of hypoxia response in wild and cultivated tomato roots by Zhihan Zhang, Yabing Hou, Hao Yin, Song Lu, Daliang Liu, Lin Cheng, Houlin Yu, Tao Li, Yiyong Zhao

“…To elucidate the molecular mechanisms underlying these contrasting phenotypes, as well as the impact of positive selection and protein-protein interactions of differentially expressed genes (DEGs) and proteins (DEPs), we conducted transcriptomic and proteomic analyses of root samples from a wild tomato accession, T178 (S. habrochaites), and a cultivated tomato variety, Fenzhenzhu (S. lycopersicum, FZZ). …”
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Bile acid synthesis, modulation, and dementia: A metabolomic, transcriptomic, and pharmacoepidemiologic study. by Vijay R Varma, Youjin Wang, Yang An, Sudhir Varma, Murat Bilgel, Jimit Doshi, Cristina Legido-Quigley, João C Delgado, Anup M Oommen, Jackson A Roberts, Dean F Wong, Christos Davatzikos, Susan M Resnick, Juan C Troncoso, Olga Pletnikova, Richard O'Brien, Eelko Hak, Brenda N Baak, Ruth Pfeiffer, Priyanka Baloni, Siamak Mohmoudiandehkordi, Kwangsik Nho, Rima Kaddurah-Daouk, David A Bennett, Shahinaz M Gadalla, Madhav Thambisetty

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Integrating multiple “omics” analysis for plant metabolites and their functions by ZHOU Guoyan, HU Wangxiong, XU Jianhong, XUE Qingzhong

“…Instead of relying only on a single analytical technique, identification of the metabolites needs integrating multiple “omics”. …”
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Identifying key palmitoylation-associated genes in endometriosis through genomic data analysis by Jinyan Kai, Jiaqi Su, Yinping You, Xiaoliang Liang, Haitao Huang, Jie Fang, Qiong Chen

“…Methods This study integrated transcriptomic analysis and Mendelian randomization (MR) to identify a causal gene set implicated in endometriosis. …”
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Comparative Transcriptomics Analysis of Foot-and-Mouth Disease Virus-Infected Cell Model Systems by Haibin Ma, Zhenzhen Zheng, Min Liu, Mengsi Zhang, Xiaoyun Qu, Jingqiang Ren, Ming Liao

“…The FMDV genome, composed of single-stranded RNA, consists of approximately 8500 nucleotides and harbors a single open reading frame (ORF) encoding both structural and non-structural proteins vital for the virus’s pathogenicity and replication. …”
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Transcriptomic and proteomic characterization of cell and protein biomarkers of checkpoint inhibitor-induced liver injury by Changhua Ji, Steven Kumpf, Jessie Qian, Joel D. Federspiel, Mark Sheehan, Darien Capunitan, Edmond Atallah, Stuart Astbury, Seda Arat, Elias Oziolor, Mireia Fernandez Ocana, Shashi K. Ramaiah, Jane Grove, Guruprasad P. Aithal, Thomas A. Lanz

“…PBMCs were sequenced for by transcriptomic and T cell receptor repertoire (bulk and single-cell immune profiling), and extracellular vesicle (EV) enrichment from plasma was analyzed by mass spectroscopy proteomics. …”
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Transcriptomic Redox Dysregulation in a Rat Model of Metabolic Syndrome-Associated Kidney Injury by Chien-Lin Lu, Yi-Yun Wang, Yih-Jeng Tsai, Hsuan-Ting Chen, Ming-Chieh Ma, Wen-Bin Wu

“…In this study, we established a rat model of MetS using a high-fat diet combined with a single-dose streptozotocin injection in male Wistar rats. …”
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Cross-tissue transcriptome-wide analysis reveals novel insights into thyroid cancer etiology by Yue Zhu, Yu Luo, Yuye Zhang, Yixuan Wang, Zhangqi Gu, Jinyan Liu, Ancheng Qin, Weifeng Qian

“…Methods We performed a transcriptome-wide association study (TWAS) to identify the susceptibility genes for TC. …”
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PLXDC1+ Tumor‐Associated Pancreatic Stellate Cells Promote Desmoplastic and Immunosuppressive Niche in Pancreatic Ductal Adenocarcinoma by Yanhua Du, Yizhou Zhao, Judong Li, Jiaxin Wang, Shenglan You, Yao Zhang, Li Zhang, Jihong Yang, Hamid Alinejad‐Rokny, Shujie Cheng, Chenghao Shao, Duowu Zou, Youqiong Ye

“…PSCs heterogeneity and functions are characterized through bulk, single‐cell, and spatial transcriptomes, as well as in situ sequencing. …”
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Primary and metastatic cellular landscapes in human pancreatic cancer by Nina G. Steele, Veerin R. Sirihorachai, Ahmed M. Elhossiny, Ian M. Loveless, Padma Kadiyala, Monica Bonilla, Emily L. Lasse-Opsahl, Carinna Solano Vargas, Katelyn L. Donahue, Samantha B. Kemp, Valerie Gunchick, Yatrik M. Shah, Timothy L. Frankel, Filip Bednar, Arvind Rao, Benjamin L. Allen, Jiaqi Shi, Vaibhav Sahai, Howard C. Crawford, Eileen S. Carpenter, Marina Pasca di Magliano

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High-resolution mapping of single cells in spatial context by Jincan Ke, Jian Xu, Jia Liu, Yumeng Yang, Chenkai Guo, Bingbing Xie, Guizhong Cui, Guangdun Peng, Shengbao Suo

“…Particularly, CMAP handles scenarios well where discrepancies exist between single-cell and spatial transcriptomics data. …”
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Exploring biomarkers and molecular mechanisms of Type 2 diabetes mellitus promotes colorectal cancer progression based on transcriptomics by Simin Luo, Yuhong Zhu, Zhanli Guo, Chuan Zheng, Xi Fu, Fengming You, Xueke Li

“…Immune infiltration analysis suggested that its expression related to the proportion of M2 macrophages. Single-cell transcriptome analysis revealed a close association of COX11 expression with endothelial cells and macrophages. …”
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