Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNAseq, RNA interference and irradiation approach. by Solana, J, Kao, D, Mihaylova, Y, Jaber-Hijazi, F, Malla, S, Wilson, R, Aboobaker, A

A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology by Blythe, M, Kao, D, Malla, S, Rowsell, J, Wilson, R, Evans, D, Jowett, J, Hall, A, Lemay, V, Lam, S, Aboobaker, A

“…Our experiments have defined an extensive planarian transcriptome that can be used as a template for RNAseq and can also help to annotate the S. mediterranea genome. …”

Comparative RNAseq Analysis of the Insect-Pathogenic Fungus Metarhizium anisopliae Reveals Specific Transcriptome Signatures of Filamentous and Yeast-Like Development by Natasha Sant’Anna Iwanicki, Italo Delalibera Júnior, Jørgen Eilenberg, Henrik H. De Fine Licht

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RNAseq Analysis of Novel 1,3,4-Oxadiazole Chalcogen Analogues Reveals Anti-Tubulin Properties on Cancer Cell Lines by Stefano Zoroddu, Luca Sanna, Valentina Bordoni, Weidong Lyu, Gabriele Murineddu, Gerard A. Pinna, Sonia Vanina Forcales, Arturo Sala, David J. Kelvin, Luigi Bagella

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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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Single-Cell and Bulk RNASeq Profiling of COVID-19 Patients Reveal Immune and Inflammatory Mechanisms of Infection-Induced Organ Damage by Alexandrea Bass, Yiran Liu, Sivanesan Dakshanamurthy

Subjects: “…single and bulk RNASeq cell profiling and analysis…”
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Meta-Transcriptomic Analysis of RNAseq Data Reveals Pacu and Loach Fish with Unusually High Levels of Myoglobin Expression in Skeletal Muscles by Rui-Yi Chen, Bui Thi Ngoc Hieu, Gilbert Audira, Bao Lou, Ming-Der Lin, Chung-Der Hsiao

“…RNAseq data were downloaded from the NCBI Sequence Read Archive (SRA) database, and de novo assembly was performed to generate transcript contigs. …”
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STAT3 exacerbates survival of cancer stem-like tumorspheres in EGFR-positive colorectal cancers: RNAseq analysis and therapeutic screening by Chun-Chia Cheng, Po-Nien Liao, Ai-Sheng Ho, Ken-Hong Lim, Jungshan Chang, Ying-Wen Su, Caleb Gon-Shen Chen, Ya-Wen Chiang, Bi-Ling Yang, Huan-Chau Lin, Yu-Cheng Chang, Chun-Chao Chang, Yi-Fang Chang

“…To identify the differential genes that maintain CSLCs, RNAseq analysis was conducted followed by bioinformatics analysis. …”
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Are Cell Junctions Implicated in the Regulation of Vitellogenin Uptake? Insights from an RNAseq-Based Study in Eel, <i>Anguilla australis</i> by Lucila Babio, P. Mark Lokman, Erin L. Damsteegt, Ludovic Dutoit

“…At the onset of puberty, ovarian follicles become competent to incorporate large amounts of vitellogenin (Vtg). Using an RNAseq-based approach, transcriptomes from pre-vitellogenic (PV) and early vitellogenic (EV) ovaries from wild-caught eel, <i>Anguilla australis</i>, were compared to investigate the expression of specific genes encoding cell junction proteins that could be involved in regulating Vtg uptake. …”
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Transcriptional and Translational Relationship in Environmental Stress: RNAseq and ITRAQ Proteomic Analysis Between Sexually Reproducing and Parthenogenetic Females in Moina micrura by Jingyi Jia, Xiangjiang Liu, Lu Li, Chengqiang Lei, Ying Dong, Guoqiang Wu, Guangfu Hu

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scFASTCORMICS: A Contextualization Algorithm to Reconstruct Metabolic Multi-Cell Population Models from Single-Cell RNAseq Data by Maria Pires Pacheco, Jimmy Ji, Tessy Prohaska, María Moscardó García, Thomas Sauter

Subjects: “…single-cell RNAseq…”
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Quality control recommendations for RNASeq using FFPE samples based on pre-sequencing lab metrics and post-sequencing bioinformatics metrics by Yuanhang Liu, Aditya Bhagwate, Stacey J. Winham, Melissa T. Stephens, Brent W. Harker, Samantha J. McDonough, Melody L. Stallings-Mann, Ethan P. Heinzen, Robert A. Vierkant, Tanya L. Hoskin, Marlene H. Frost, Jodi M. Carter, Michael E. Pfrender, Laurie Littlepage, Derek C. Radisky, Julie M. Cunningham, Amy C. Degnim, Chen Wang

“…Here we identified parameters that determine which FFPE samples have the potential for successful RNA extraction, library preparation, and generation of usable RNAseq data. Methods We optimized library preparation protocols designed for use with FFPE samples using seven FFPE and Fresh Frozen replicate pairs, and tested optimized protocols using a study set of 130 FFPE biopsies from women with benign breast disease. …”
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RNAseq reveals different transcriptomic responses to GA3 in early and midseason varieties before ripening initiation in sweet cherry fruits by Nathalie Kuhn, Jonathan Maldonado, Claudio Ponce, Macarena Arellano, Alson Time, Salvatore Multari, Stefan Martens, Esther Carrera, José Manuel Donoso, Boris Sagredo, Lee A. Meisel

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A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses by Mutasa-Göttgens Effie S, Joshi Anagha, Holmes Helen F, Hedden Peter, Göttgens Berthold

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Time-resolved and multi-tissue RNAseq provides new insights on the immune responses of European eels following infection with Aeromonas hydrophila by Fan Xiong, Lu Cao, Jing Xiong, Ya Fang Wu, Wen Shu Huang, Ming Xian Chang

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Dissociation and inDrops microfluidic encapsulation of human gut tissues for single-cell atlasing studies by Alan J. Simmons, Ken S. Lau

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Protocol for comprehensive RNA sequencing analysis of murine long non-coding RNAs during aging by Xinyue Lu, Qiuzhong Zhou, Jin Liu, Lei Sun

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Protocol to benchmark gene expression signature scoring techniques for single-cell RNA sequencing data in cancer by Nighat Noureen, Xiaojing Wang, Siyuan Zheng

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Exploring the RNA Gap for Improving Diagnostic Yield in Primary Immunodeficiencies by Jed J. Lye, Anthony Williams, Anthony Williams, Diana Baralle, Diana Baralle

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Prior metabolite extraction fully preserves RNAseq quality and enables integrative multi-‘omics analysis of the liver metabolic response to viral infection by Zachary B Madaj, Michael S. Dahabieh, Vijayvardhan Kamalumpundi, Brejnev Muhire, J. Pettinga, Rebecca A. Siwicki, Abigail E. Ellis, Christine Isaguirre, Martha L. Escobar Galvis, Lisa DeCamp, Russell G. Jones, Scott A. Givan, Marie Adams, Ryan D. Sheldon

“…Altogether, our data show that prior metabolite extraction preserves RNAseq data quality, which enables us to confidently perform integrated pathway enrichment analysis on metabolomics and RNAseq data from a single sample. …”
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