Analysis of Whole Transcriptome Sequencing Data: Workflow and Software by In Seok Yang, Sangwoo Kim

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Whole blood transcriptomics analysis of Indonesians reveals translocated and pathogenic microbiota in blood by Katalina Bobowik, Muhamad Fachrul, Chelzie Crenna Darusallam, Pradiptajati Kusuma, Herawati Sudoyo, Clarissa A. Febinia, Safarina G. Malik, Christine A. Wells, Irene Gallego Romero

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Whole blood transcriptomics analysis of Indonesians reveals translocated and pathogenic microbiota in blood. by Katalina Bobowik, Muhamad Fachrul, Chelzie Crenna Darusallam, Pradiptajati Kusuma, Herawati Sudoyo, Clarissa A Febinia, Safarina G Malik, Christine A Wells, Irene Gallego Romero

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Whole-Transcriptome Analysis Reveals the Regulatory Network of Immune Response in Dapulian Pig by Tao Wang, Zhe Tian, Mubin Yu, Shuer Zhang, Min Zhang, Xiangwei Zhai, Wei Shen, Junjie Wang

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Integrative whole slide image and spatial transcriptomics analysis with QuST and QuPath by Chao-Hui Huang, Sara Lichtarge, Diane Fernandez

“…Abstract The integration of AI in digital pathology, particularly in whole slide image (WSI) and spatial transcriptomics (ST) analysis, holds immense potential for enhancing disease understanding. …”
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Comparative analysis of the whole transcriptome landscapes of muscle and adipose tissue in Qinchuan beef cattle by Ju Qiu, Zheng Ma, Zhipeng Hong, Xu Yin, Yun Chen, Hafiz Qadeer Ahmed, Linsen Zan, Anning Li

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The Exon-Based Transcriptomic Analysis of Parkinson’s Disease by Sulev Kõks

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Integrated analysis of whole genome and transcriptome sequencing reveals diverse transcriptomic aberrations driven by somatic genomic changes in liver cancers. by Yuichi Shiraishi, Akihiro Fujimoto, Mayuko Furuta, Hiroko Tanaka, Ken-ichi Chiba, Keith A Boroevich, Tetsuo Abe, Yoshiiku Kawakami, Masaki Ueno, Kunihito Gotoh, Shun-ichi Ariizumi, Tetsuo Shibuya, Kaoru Nakano, Aya Sasaki, Kazuhiro Maejima, Rina Kitada, Shinya Hayami, Yoshinobu Shigekawa, Shigeru Marubashi, Terumasa Yamada, Michiaki Kubo, Osamu Ishikawa, Hiroshi Aikata, Koji Arihiro, Hideki Ohdan, Masakazu Yamamoto, Hiroki Yamaue, Kazuaki Chayama, Tatsuhiko Tsunoda, Satoru Miyano, Hidewaki Nakagawa

“…In this study, we performed integrated and comparative analyses of whole genomes and transcriptomes of 22 hepatitis B virus (HBV)-related hepatocellular carcinomas (HCCs) and their matched controls. …”
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Comparative analysis of whole genomes and transcriptomes of Microsporum canis from invasive dermatophytosis and tinea capitis by Ruojun Wang, Weixia Liu, Xiao Liu, Zhe Wan, G. Sybren de Hoog, Ruoyu Li, Yinggai Song

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Joint analysis of whole-genome methylation and transcriptome in avian pullorum disease and validation of gene function by Jiongwen Wu, Weiming Liang, Aijun Liu, Xiaomeng Wang, Zhexia Fan, Xuerong Ma, Shuya Chen, Cheng Fang, Xiquan Zhang, Qingbin Luo

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Whole transcriptome analysis of breast tumors during neoadjuvant chemotherapy: association with response to preoperative chemotherapy by M. K. Ibragimova, M. M. Tsyganov, N. V. Litviakov

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Whole Blood Transcriptome Analysis in Dairy Ewes Fed a Dietary Grape Pomace Supplementation by Andrea Ianni, Francesca Bennato, Camillo Martino, Maria Antonietta Saletti, Francesco Pomilio, Giuseppe Martino

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Genome-wide transcriptomic response of whole blood to radiation by Ahmed Salah, Daniel Wollschläger, Maurizio Callari, Heinz Schmidberger, Federico Marini, Sebastian Zahnreich

“…Abstract Blood cells are affected in nearly all ionizing radiation exposure scenarios. Whole transcriptome data offer detailed insights into blood’s radiation response, crucial for radiotherapy and biodosimetry. …”
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A meta-analysis of whole blood transcriptome reveals genes associated with increased neutrophil activity and T cell suppression in sepsis by T. N. Shruthi, Anbazhagan Kolandaswamy, Prabakara Somanna

“…Hence our study was limited to transcriptome data derived solely from whole blood to understand the pathogenesis and immune regulation in sepsis. …”
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Differential Gene Expression Analysis of Whole Blood Transcriptome Between Young and Old Border Collie Dogs by Dávid Jónás, Kitti Tátrai, Zsófia Rékasi, Balázs Egyed, Eniko Kubinyi

“…Additionally, we recommend implementing pre-sequencing hemoglobin depletion to improve the analysis of whole blood in future studies.…”
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Identification of novel biomarkers involved in oral squamous cell carcinoma by whole transcriptome sequencing and bioinformatics analysis by Hongliang Du, Zhenze Wang, Mengyi Qi, Yunqing Pang, Qingling Lin, Dengqi He, Jing Wang

“…Methods Differentially expressed messenger RNAs (mRNAs), microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) (DE-mRNAs, DE-miRNAs, and DE-lncRNAs) between primary and control groups, as well as metastatic and primary groups, were identified using whole transcriptome sequencing data. Candidate OSCC genes were derived from DE-mRNAs. …”
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Whole genome and transcriptome analyses identify genetic markers associated with growth traits in Qinchuan black pig by Yaxin Wang, Guangquan Lv, Zhe Liu, Ye Cheng, Rongrong Ding, Gongshe Yang, Taiyong Yu

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Identification and validation of differentially expressed genes in allergic asthma pathogenesis using whole-transcriptome sequencing by Fang Cui, Rui Liu, Li Wang, Jing He, Yanxia Xu

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CRP deposition in human abdominal aortic aneurysm is associated with transcriptome alterations toward aneurysmal pathogenesis: insights from in situ spatial whole transcriptomic analysis by Eun Na Kim, Hee Young Seok, Joon Seo Lim, Jiwon Koh, Jeong Mo Bae, Chong Jai Kim, Ga-Hyeon Ryu, You Jung Ok, Jae-Sung Choi, Chung-Hyun Cho, Se Jin Oh

“…Normal aorta specimens obtained during heart transplantation were used as the control group [n = 3 (6 cores)]. Spatially resolved whole transcriptomic analysis was performed, focusing on CD68-positive macrophages, CD45-positive lymphocytes, and αSMA-positive vascular smooth muscle cells.ResultsSpatial whole transcriptomic analysis revealed significant differential expression of 1,086, 1,629, and 1,281 genes between high-CRP and low-CRP groups within CD68-, CD45-, and αSMA-positive cells, respectively. …”
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Whole Transcriptome-Based ceRNA Regulatory Network Analysis of Radiation-Induced Esophageal Epithelial Cell Injury by Lin H, Feng Y, Liu H, Zhang J, Zhang X, Ying X, Shi Y, Tan H, Tu W

“…Future work should focus on elucidating specific ceRNA interactions and exploring therapeutic potential for mitigating radiation-induced esophageal injury.Keywords: ionizing radiation, esophageal epithelial cells, radiation-induced injury, whole transcriptome, competitive endogenous RNA network…”
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