The Impact of Intramammary Escherichia coli Challenge on Liver and Mammary Transcriptome and Cross-Talk in Dairy Cows during Early Lactation Using RNAseq. by K M Moyes, P Sørensen, M Bionaz

“…Our objective was to identify the biological response and the cross-talk between liver and mammary tissue after intramammary infection (IMI) with Escherichia coli (E. coli) using RNAseq technology. Sixteen cows were inoculated with live E. coli into one mammary quarter at ~4-6 weeks in lactation. …”
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Dual RNAseq analyses at soma and germline levels reveal evolutionary innovations in the elephantiasis-agent Brugia malayi, and adaptation of its Wolbachia endosymbionts. by Germain Chevignon, Vincent Foray, Mercedes Maria Pérez-Jiménez, Silvia Libro, Matthew Chung, Jeremy M Foster, Frédéric Landmann

“…In order to better comprehend this symbiosis, we investigated the adaptation of wBm to the host nematode soma and germline, and we characterized these cellular environments to highlight their specificities. Dual RNAseq experiments were performed at the tissue-specific and ovarian developmental stage levels, reaching the resolution of the germline mitotic proliferation and meiotic differentiation stages. …”
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RNAseq based transcriptomics study of SMCs from carotid atherosclerotic plaque: BMP2 and IDs proteins are crucial regulators of plaque stability by Iraide Alloza, Haize Goikuria, Juan Luis Idro, Juan Carlos Triviño, José María Fernández Velasco, Elena Elizagaray, María García-Barcina, Genoveva Montoya-Murillo, Esther Sarasola, Reyes Vega Manrique, Maria del Mar Freijo, Koen Vandenbroeck

“…Comparative transcriptomics analysis of SMCs based on RNAseq technology identified 67 significant differentially expressed genes and 143 significant differentially expressed isoforms in symptomatic SMCs compared with asymptomatic. 37 of top-scoring genes were further validated by digital PCR. …”
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Quantitative RNAseq analysis of Ugandan KS tumors reveals KSHV gene expression dominated by transcription from the LTd downstream latency promoter. by Timothy M Rose, A Gregory Bruce, Serge Barcy, Matt Fitzgibbon, Lisa R Matsumoto, Minako Ikoma, Corey Casper, Jackson Orem, Warren Phipps

“…To investigate the role of KSHV in the development of KS, we obtained KS biopsies from ART-naïve, HIV-positive individuals in Uganda and analyzed the tumors using RNAseq to globally characterize the KSHV transcriptome. …”
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Comprehensive RNAseq analysis reveals PIK3CD promotes glioblastoma tumorigenesis by mediating PI3K-Akt signaling pathway by Zulfikar Azam, Wei Shao, Ho-keung Ng, Jing Wang, Zhong-ping Chen, Shing-shun Tony To

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Correction to: RNAseq and quantitative proteomic analysis of Dictyostelium knock-out cells lacking the core autophagy proteins ATG9 and/or ATG16 by Qiuhong Xiong, Ning Song, Ping Li, Sarah Fischer, Roman Konertz, Prerana Wagle, Gernot Glöckner, Changxin Wu, Ludwig Eichinger

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RNAseq of Deformed Wing Virus and Other Honey Bee-Associated Viruses in Eight Insect Taxa with or without <i>Varroa</i> Infestation by Laura E. Brettell, Declan C. Schroeder, Stephen J. Martin

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Single Nucleus RNA Sequence (snRNAseq) Analysis of the Spectrum of Trophoblast Lineages Generated From Human Pluripotent Stem Cells in vitro by Teka Khan, Teka Khan, Arun S. Seetharam, Arun S. Seetharam, Jie Zhou, Jie Zhou, Nathan J. Bivens, Danny J. Schust, Toshihiko Ezashi, Toshihiko Ezashi, Geetu Tuteja, R. Michael Roberts, R. Michael Roberts, R. Michael Roberts

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Live slow-frozen human tumor tissues viable for 2D, 3D, ex vivo cultures and single-cell RNAseq by Gaetana Restivo, Aizhan Tastanova, Zsolt Balázs, Federica Panebianco, Maren Diepenbruck, Caner Ercan, Bodgan-T. Preca, Jürg Hafner, Walter P. Weber, Christian Kurzeder, Marcus Vetter, Simone Münst Soysal, Christian Beisel, Mohamed Bentires-Alj, Salvatore Piscuoglio, Michael Krauthammer, Mitchell P. Levesque

“…Fresh vs. slow-frozen tissues from various malignancies are compared for the establishment of 2D, 3D and ex vivo cultures, as well as for scRNAseq analysis, and found to be comparable and suitable for cancer research.…”
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An integrated RNAseq-1H NMR metabolomics approach to understand soybean primary metabolism regulation in response to Rhizoctonia foliar blight disease by Tanya R. Copley, Konstantinos A. Aliferis, Daniel J. Kliebenstein, Suha H. Jabaji

“…Results Transcriptomics (RNAseq) and metabolomics (1H NMR) data were analyzed individually and by integration using bidirectional orthogonal projections to latent structures (O2PLS) to reveal possible links between the metabolome and transcriptome during early and late infection stages. …”
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Immunoglobulin characteristics and RNAseq data of FcRL4+ B cells sorted from synovial fluid and tissue of patients with rheumatoid arthritis by Khaled Amara, Elizabeth Clay, Lorraine Yeo, Daniel Ramsköld, Julia Spengler, Natalie Sippl, James Cameron, Lena Israelsson, Philip J. Titcombe, Caroline Grönwall, Ilfita Sahbudin, Andrew Filer, Karim Raza, Vivianne Malmström, Dagmar Scheel-Toellner

“…Furthermore a URL link to the RNAseq datasets submitted to GEO is included. Keywords: B cells, FcRL4, Rheumatoid arthritis, IRTA1…”
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Meta-analysis of microarray and RNAseq data reveal OsbZIP52 to mediate salt stress responses in sensitive, tolerant and halophyte rice varieties by Dipankor Chatterjee, Mohammad Umer Sharif Shohan, Nishat Tamanna, Zeba I. Seraj

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Single-cell RNAseq identifies clonally expanded antigen-specific T-cells following intradermal injection of gold nanoparticles loaded with diabetes autoantigen in humans by Stephanie J. Hanna, Terri C. Thayer, Terri C. Thayer, Emma J. S. Robinson, Ngoc-Nga Vinh, Nigel Williams, Laurie G. Landry, Robert Andrews, Qi Zhuang Siah, Pia Leete, Rebecca Wyatt, Martina A. McAteer, Maki Nakayama, F. Susan Wong, Jennie H. M. Yang, Timothy I. M. Tree, Johnny Ludvigsson, Colin M. Dayan, Danijela Tatovic

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<i>Leptosphaeria maculans</i>-<i>Brassica napus</i> Battle: A Comparison of Incompatible vs. Compatible Interactions Using Dual RNASeq by Kaluhannadige R. E. Padmathilake, Wannakuwattewaduge Gerard Dilantha Fernando

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The feasibility of developing biomarkers from peripheral blood mononuclear cell RNAseq data in children with juvenile idiopathic arthritis using machine learning approaches by Kerry E. Poppenberg, Kaiyu Jiang, Lu Li, Yijun Sun, Hui Meng, Carol A. Wallace, Teresa Hennon, James N. Jarvis

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735 Identification of a small molecule that prevents T cell exhaustion using machine learning algorithms paired with high-resolution single cell RNAseq by Daniel Treacy, Isabelle Le Mercier, Sunny Sun, Dongmei Xiao, Laura Isacco, Emilie Artru, Scott Steelman, Alex Wolf, Morag Stewart, Effie Tozzo

Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor by Biplabendu Das, Charissa de Bekker

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CellPalmSeq: A curated RNAseq database of palmitoylating and de-palmitoylating enzyme expression in human cell types and laboratory cell lines by Angela R. Wild, Peter W. Hogg, Stephane Flibotte, Shruti Kochhar, Rocio B. Hollman, Kurt Haas, Shernaz X. Bamji

“…We therefore created CellPalmSeq (https://cellpalmseq.med.ubc.ca), a curated RNAseq database and interactive webtool for visualization of the expression patterns of the genes that regulate palmitoylation across human single cell types, bulk tissue, cancer cell lines and commonly used laboratory non-human cell lines. …”
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OncoPeptVAC: A robust TCR binding algorithm to prioritize neoepitope using tumor mutation (DNAseq) and gene expression (RNAseq) data by Snigdha Majumder, Vasumathi Kode, Priyanka Shah, Anand Kumar, Ravi Gupta, Amit Chaudhuri, Papia Chakraborty

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Transcriptomic responses to environmental temperature by turtles with temperature-dependent and genotypic sex determination assessed by RNAseq inform the genetic architecture of embryonic gonadal development. by Srihari Radhakrishnan, Robert Literman, Jennifer Neuwald, Andrew Severin, Nicole Valenzuela

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