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

“…Numerous studies have examined RNA features using whole transcriptome sequencing (RNA-seq) approaches. …”
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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

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Profiling of the microRNA transcriptome in feline whole blood by Åsa Ohlsson, Sofia Hanås, Bodil S. Holst, Julie Lorent, Göran Andersson, Katja Höglund, Anna Tidholm, Ingrid Ljungvall, Jens Häggström

“…Characterization of the whole blood (WB) miRNA-transcriptome (miRNome) in cats is lacking, which limits the potential use of miRNAs as biomarkers for diseases such as feline cardiovascular disease. …”
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Influence of Pregnancy on Whole-Transcriptome Sequencing in the Mammary Gland of Kazakh Mares by Zhenyu Zhang, Zhixin Lu, Xinkui Yao, Linling Li, Jun Meng, Jianwen Wang, Yaqi Zeng, Wanlu Ren

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Whole genome and transcriptome profiling in advanced pancreatic cancer patients on the COMPASS trial by Jennifer J. Knox, Gun Ho Jang, Robert C. Grant, Amy Zhang, Lucy Ma, Elena Elimova, Raymond Jang, Malcolm Moore, James Biagi, Mustapha Tehfe, Ravi Ramjeesingh, Erica S. Tsang, Spring Holter, Stephanie Ramotar, Shawn Hutchinson, Sheng-Ben Liang, Ilinca M. Lungu, Shari Moura, Yifan Wang, Sheron Perera, Michelle Chan-Seng-Yue, Maryam Monajemzadeh, Kyaw Aung, Rebecca Prince, Joan Miguel Romero, Jesus Fuentes-Antras, Galileo A. Gonzalez Conchas, Sarah Picardo, Ricardo Gonzalez, Sangeet Ghai, Korosh Khalili, Tae Kyoung Kim, Karen Ng, John Bartlett, Trevor J. Pugh, Sangeetha N. Kalimuthu, Sandra E. Fischer, Julie M. Wilson, Anna Dodd, George Zogopoulos, Barbara T. Grünwald, Faiyaz Notta, Steven Gallinger, Grainne M. O’Kane

“…Abstract Integrated whole genome and transcriptome sequencing can unveil distinct molecular subgroups in pancreatic cancer (PDAC). …”
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Translational and clinical comparison of whole genome and transcriptome to panel sequencing in precision oncology by Irina A. Kerle, Thomas Gross, Anja Kögler, Jonas S. Arnold, Maximilian Werner, Jan-Niklas Eckardt, Elena E. Möhrmann, Marie Arlt, Barbara Hutter, Jennifer Hüllein, Daniela Richter, Martin M. K. Schneider, Mario Hlevnjak, Lino Möhrmann, Dorothea Hanf, Christoph E. Heilig, Simon Kreutzfeldt, Maria-Veronica Teleanu, Evelin Schröck, Daniel Hübschmann, Peter Horak, Christoph Heining, Stefan Fröhling, Hanno Glimm

“…In this study, we compared whole-exome/whole-genome (WES/WGS) and transcriptome sequencing (TS) with broad panel sequencing by resequencing the same tumor DNA and RNA as well as normal tissue DNA for germline assessment, from 20 patients with rare or advanced tumors, who were originally sequenced by WES/WGS ± TS within the DKFZ/NCT/DKTK MASTER program from 2015 to 2020. …”
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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

“…Unequal investment in medical funding throughout Indonesia, particularly in rural areas, has resulted in under-reporting of cases, making surveillance challenging. Here, we use transcriptome data from 117 healthy individuals living on the islands of Mentawai, Sumba, and the Indonesian side of New Guinea Island to explore which pathogens are present within whole blood. …”
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Whole transcriptome sequencing: Optimizing molecular classification and management of rare skin cancers by B. Louveau, F. Jouenne, A. Sadoux, M. Mancini, C. Reger de Moura, B. Baroudjian, L. Da Meda, J. Brayet, P. Vilquin, C. Lebbé, M. Battistella, S. Mourah

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Whole-blood transcriptome profiling reveals signatures of metformin and its therapeutic response. by Monta Briviba, Laura Ansone, Ivars Silamikelis, Vita Rovite, Ilze Elbere, Laila Silamikele, Ineta Kalnina, Davids Fridmanis, Jelizaveta Sokolovska, Ilze Konrade, Valdis Pirags, Janis Klovins

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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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Whole-cell response of coronavirus-infected BMDCs through proteomic and transcriptomic analyses by Yanxi Ji, Yanxi Ji, Yuzhen Zhang, Yongjia Tong, Yongjia Tong, Liu Cao, Lanyi Zeng, Yiran Xu, Xiao Guo, Tiefeng Xu, Zhidong Tang, Zhen Zhang, Zhen Zhang, Lin Guo, Deyin Guo, Huabin Zhao, Yu Chen, Xiaolu Zhao, Xiaolu Zhao

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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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Whole transcriptome sequencing to uncover CircRNA expression patterns linked to schizophrenia pathogenesis by Jianxiong Long, Bing Shen, Fangping Liao, Hong Cai, Jiale Li, Rumei Lu, Zhicheng Zhong, Zukang Gong, Jianfeng Xu

“…Abstract Background No objective diagnostic indicators have been identified for schizophrenia (SCZ) because of the complexity of its pathogenesis. Whole-transcriptome analysis may help identify early diagnostic markers. …”
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Expression regulation network in papillae of sea cucumbers: Whole-transcriptome and DNA methylation datasets by Wenhong Mai, Jingxian Sun, Bingyu Ning, Tanjun Zhao, Haochen Yang, Liyuan Ren, Zengdong Wang, Cao Cheng, Ange Zou, Yaoyao Zhan, Yaqing Chang

“…Average clean bases of whole-transcriptome (16.35 G) and DNA methylome (28.92 G) were obtained using RNA sequencing and whole-genome bisulfite sequencing techniques. …”
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Whole-transcriptome insights into follicle selection: deciphering key regulatory networks in Luxi gamecock by Yiya Wang

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Whole blood transcriptome profile identifies motor neurone disease RNA biomarker signatures by Sulev Kõks, Sulev Kõks, Karin Rallmann, Mari Muldmaa, Mari Muldmaa, Jack Price, Abigail L. Pfaff, Abigail L. Pfaff, Pille Taba

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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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A new technique for obtaining whole pathogen transcriptomes from infected host tissues by Tatyana L. Azhikina, Timofey A. Skvortsov, Tatyana V. Radaeva, Andrey V. Mardanov, Nikolay V. Ravin, Alexander S. Apt, Eugene D. Sverdlov

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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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