Knockdown TNF family prognosis index crucial gene PDE4B promoted PANoptosis of ovarian carcinoma cell:Based in vitro and in vivo experiments by Qianqian Yu, Yunxiao Wang, Ting Fu, Dongyu Han, Linlin Wang, Lin Zhao, Yongle Xu

“…We conducted an analysis using bulk transcriptomic data of ovarian cancer and normal ovarian tissues, as well as single-cell sequencing data according to publicly available databases. …”
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Integrative analysis of single-cell and transcriptome sequencing with experimental validation reveals PKHD1L1 as a novel biomarker in lung adenocarcinoma by Xiangqian Zhang, Jie Wang, Hanyang Su, Xiaojin Liu

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Genetic parameters and identification of genomic regions and candidate genes associated with vaginal discharge score in Holstein cattle based on genomic and transcriptomic analyses by Junxing Zhang, Liyun Han, Hui Sheng, Hailiang Zhang, Luiz F. Brito, Shanshan Li, Guoshang Ji, Xingang Dan, Bei Cai, Yamei Hu, Yachun Wang, Yun Ma

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Biomarkers associated with cell-in-cell structure in kidney renal clear cell carcinoma based on transcriptome sequencing by Zehua Wang, Zhongxiao Zhang

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Single-dose VSV-based vaccine protects cynomolgus macaques from disease after Taï Forest virus infection by Paige Fletcher, Kyle L. O’Donnell, Brianna M. Doratt, Delphine C. Malherbe, Chad S. Clancy, Joseph F. Rhoderick, Friederike Feldmann, Patrick W. Hanley, Thomas G. Ksiazek, Thomas W. Geisbert, Ilhem Messaoudi, Andrea Marzi

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A single-cell landscape of the regenerating spinal cord of zebrafish by Lei Yao, Xinyi Cai, Saishuai Yang, Yixing Song, Lingyan Xing, Guicai Li, Zhiming Cui, Jiajia Chen

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Whole genome sequencing and single-cell transcriptomics identify KMT2D inactivation as a potential new driver for pituitary tumors: a case report by Maxime Brunner, Jenny Meylan-Merlini, Maude Muriset, Sergey Oreshkov, Andrea Messina, Mahmoud Messerer, Roy Daniel, Ekkehard Hewer, Jean Phillipe Brouland, Federico Santoni

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Histopathologic Evaluation and Single-cell Spatial Transcriptomics of the Colon Reveal Cellular and Molecular Abnormalities Linked to J-Pouch Failure in Patients With Inflammatory... by Andrea D. Olivas, Paul Chak Mou Ngai, Emily Schahrer, Junjie Xing, Mobarakeh Ghadiri, Kinga S. Olortegui, John F. Cursio, Shintaro Akiyama, Eugene B. Chang, Le Shen, Konstantin Umanskiy, David T. Rubin, David Zemmour, Christopher R. Weber

“…A subset of patients was profiled using single-cell spatial transcriptomics to map gene expression and immune cell interactions in relation to the risk of pouch failure. …”
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Single-cell transcriptome of mouse hippocampus identifies neural precursor-like cells, and reveals IL15Rα knock out-mediated neuron remodeling by Yanting Luo, Yadan Nie, Xuemei Huang, Haixia Wang, Zuoli Sun, Jian Yang, Yi He

“…Results To study how IL15Rα knock-out affects cellular function of the hippocampus in adult mice, we produced 64,399 single-cell transcriptomes from WT and KO mice and identified precursor-like neuron (PLN), a type of neural cells exhibiting precursor-like attributes, as well as four variant glial cell types. …”
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Metabolism-associated marker gene-based predictive model for prognosis, targeted therapy, and immune landscape in ovarian cancer: an integrative analysis of single-cell and bulk RN... by Lele Ling, Bingrong Li, Boliang Ke, Yinjie Hu, Kaiyong Zhang, Siwen Li, Te Liu, Peng Liu, Bimeng Zhang

“…The MRG-based prognostic model was further utilized for functional analysis of the model gene set, pan-cancer analysis of genomic variations, spatial transcriptomics analysis, as well as GO and KEGG enrichment analysis. …”
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Unveiling SSR4: a promising biomarker in esophageal squamous cell carcinoma by Jiaqi Zhang, Fang Jia, Chuqiao Li, Shunzhe Song, Aixia Gong

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APPLICATIONS OF TRANSCRIPTOMICS METHODS IN BREAST CANCER by Yeşim Gökmen Polar

“…Role of ncRNAs have been well documented in breast cancer. Using RNA sequencing and probe-based transcriptome analyses, several studies, including ours, have emphasized the role alternative splicing events in breast cancer progression. …”
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Distinct gene signatures define the epithelial cell features of mucinous appendiceal neoplasms and pseudomyxoma metastases by Carlos Ayala, Anuja Sathe, Xiangqi Bai, Susan M. Grimes, Jeanne Shen, George A. Poultsides, Byrne Lee, Hanlee P. Ji

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Comparison of spatial transcriptomics technologies using tumor cryosections by Anne Rademacher, Alik Huseynov, Michele Bortolomeazzi, Sina Jasmin Wille, Sabrina Schumacher, Pooja Sant, Denise Keitel, Konstantin Okonechnikov, David R. Ghasemi, Kristian W. Pajtler, Jan-Philipp Mallm, Karsten Rippe

“…Results Our analysis reveals that automated imaging-based spatial transcriptomics methods are well-suited to delineate the intricate MBEN microanatomy and capture cell-type-specific transcriptome profiles. …”
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Identification of Genetic Variants Based on Single Nucleotide Polymorphisms and Insertion-Deletion Events in TLR8, IRF10b, and GAPDH Genes Related to the Immune System in Rainbow T... by Najmeh Fazeli Moghadam, Ghodrat Rahimi Miyanji, Ayoub Farhadi, Ardeshir Nejati Jawarami, Elham Younesi Melardi

“…Some variants based on single nucleotide polymorphisms (SNPs), including synonymous, non-synonymous, and non-coding, as well as insertion-deletion (InDel) events resulting in RNA sequencing data, can be used as a desirable genetic marker in genetic differentiation analysis, especially in investigating allele-specific expression. …”
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Cell-specific transcriptional signatures of vascular cells in Alzheimer’s disease: perspectives, pathways, and therapeutic directions by Soumilee Chaudhuri, Minyoung Cho, Julia C. Stumpff, Paula J. Bice, Özkan İş, Nilüfer Ertekin-Taner, Andrew J. Saykin, Kwangsik Nho

“…We also discuss impaired cellular crosstalk between vascular cells and neuroglial units, as well as astrocytes in AD. Additionally, we contextualize the findings from single-cell studies of distinct endothelial cells, smooth muscle cells, fibroblasts, and pericytes in the human AD brain and highlight pathways for potential therapeutic interventions as a concerted multi-omic effort with spatial transcriptomics technology, neuroimaging, and neuropathology. …”
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SpaNorm: spatially-aware normalization for spatial transcriptomics data by Agus Salim, Dharmesh D. Bhuva, Carissa Chen, Chin Wee Tan, Pengyi Yang, Melissa J. Davis, Jean Y. H. Yang

“…SpaNorm is versatile and works equally well for multicellular and subcellular spatial transcriptomics data with relatively robust performance under different segmentation methods.…”
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The design of experiments for the transcriptome studies by high-throughput sequencing methods by P. N. Menshanov, N. N. Dygalo

“…The ENCODE guidelines (2011) as well as the recently published advances in the design of the studies of mammalian, animal and plant transcriptomes are also summarized in this review. …”
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Genome-wide identification of cell type-specific susceptibility genes for Juvenile dermatomyositis through the analysis of N6-methyladenosine-associated SNPs by Huan Zhang, Kedi Fan, Zhentao Zhang, Yufan Guo, Xingbo Mo

“…Additionally, differential expression analyses were conducted on bulk tissues, as well as single-cell transcriptomic data comprising 6 JDM patients and 11 juvenile controls (99,396 cells). …”
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A collaborative network analysis for the interpretation of transcriptomics data in Huntington’s disease by Ozan Ozisik, Nazli Sila Kara, Tooba Abbassi-Daloii, Morgane Térézol, Elsa C. Kuijper, Núria Queralt-Rosinach, Annika Jacobsen, Osman Ugur Sezerman, Marco Roos, Chris T. Evelo, Anaïs Baudot, Friederike Ehrhart, Eleni Mina

“…We analyzed a Huntington’s disease transcriptomics dataset using six network-based methods in a collaborative way. …”
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