Aging and head and neck cancer insights from single cell and spatial transcriptomic analyses by Yi Pei, Zhuying Mou, Lai Jiang, Jinyan Yang, Yuheng Gu, Jie Min, Lingyi Sunzhang, Nan Xiong, Xiang Xu, Hao Chi, Ke Xu, Sinian Liu, Huiyan Luo

“…For the spatial transcriptome data, SCTransform and RunPCA were applied to examine the metabolic activities of the cells. …”
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Complete genome and transcriptome datasets of Streptococcus salivarius strains from healthy Korean subjects by Eun-Young Jang, Ji-Hoi Moon, Jae-Hyung Lee

“…Our dataset includes transcriptomic data that reveal functional gene expression patterns under standard growth conditions. …”
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Dissecting crosstalk induced by cell-cell communication using single-cell transcriptomic data by Jiawen Hou, Wei Zhao, Qing Nie

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Genomic, transcriptomic and epigenomic signatures of ageing and cold adaptation in the Antarctic clam Laternula elliptica by Victoria A. Sleight, Melody S. Clark, Meghan K. Yap-Chiongco, Frances Turner, Kevin M. Kocot

“…In this study, we describe and analyse the genome of L. elliptica and use it as a tool to understand transcriptomic responses to shell damage across different age cohorts. …”
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A comparison of anatomic and cellular transcriptome structures across 40 human brain diseases. by Yashar Zeighami, Trygve E Bakken, Thomas Nickl-Jockschat, Zeru Peterson, Anil G Jegga, Jeremy A Miller, Jay Schulkin, Alan C Evans, Ed S Lein, Michael Hawrylycz

“…Through mapping of homologous cell types between mouse and human, most disease risk genes are found to act in common cell types, while having species-specific expression in those types and preserving similar phenotypic classification within species. …”
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ICARus: a pipeline to extract robust gene expression signatures from transcriptome datasets by Zhaorong Li, Juan I. Fuxman Bass, Juan I. Fuxman Bass, Juan I. Fuxman Bass, Juan I. Fuxman Bass

“…The ICARus package offers a robust pipeline to perform ICA on transcriptome datasets. While other packages perform ICA using one value of the main parameter (i.e., the number of signatures), ICARus identifies a range of near-optimal parameter values, iterates through these values, and assesses the robustness and reproducibility of the signature components identified. …”
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Transcriptomics profiling of Parkinson’s disease progression subtypes reveals distinctive patterns of gene expression by Carlo Fabrizio, Andrea Termine, Carlo Caltagirone

“…Background Parkinson’s Disease (PD) varies widely among individuals, and Artificial Intelligence (AI) has recently helped to identify three disease progression subtypes. While their clinical features are already known, their gene expression profiles remain unexplored. …”
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Single-nucleus transcriptomics of wing sexual dimorphism and scale cell specialization in sulphur butterflies. by Ling S Loh, Joseph J Hanly, Alexander Carter, Martik Chatterjee, Martina Tsimba, Donya N Shodja, Luca Livraghi, Christopher R Day, Robert D Reed, W Owen McMillan, Gregory A Wray, Arnaud Martin

“…We show that Doublesex (Dsx) expression is itself dimorphic and required to repress the UVI cell state in females, while unexpectedly, UVI activation in males is independent from Dsx. …”
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Microbiota transplantation for cotton leaf curl disease suppression—core microbiome and transcriptome dynamics by Ayesha Badar, Rhea Aqueel, Ali Nawaz, Umer Zeeshan Ijaz, Kauser Abdulla Malik

“…It is seen that rhizospheric microbiota transplantation from G. arboreum FDH228 significantly suppresses CLCuD in G. hirsutum varieties, outperforming exogenous salicylic acid application. While phyllospheric transplants also reduce disease incidence, they are less effective than rhizospheric transplants. …”
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Transcriptomic profile induced by calcitriol in CaSki human cervical cancer cell line. by Euclides Avila, Luis David Hernández-Monterde, Alberto Cedro-Tanda, Tomas Misael Lizardi-Aguilera, David Barrera, Francisco Vladimir Villegas-Rodriguez, Janice García-Quiroz, Lorenza Díaz, Fernando Larrea

“…Calcitriol decreased EPHA2 and RARA expression while inducing KLK6 and CYP4F3 expression in CaSki cells, as validated by qPCR and Western blot. …”
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Identification of molecular characteristics in polycystic ovary syndrome using single-cell and transcriptome analysis by Xiaolin Zhu, Yanhua Han, Yuenan Feng, Yuanli Shan, Chang Liu, Kexin Wang, Xiaoke Li, Shidi Zhang, Yaguang Han

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Developmental transcriptomics reveals stage-specific immune gene expression profiles in Spodoptera frugiperda by Guangmin Wang, Jia Ran, Chen Jia, Amr Mohamed, Jorge R. Paredes-Montero, Rasha Khalifah Al-Akeel, Liansheng Zang, Wei Zhang, Nemat O. Keyhani, Ioannis Eleftherianos

“…In contrast, cellular immunity indices were highest in pupae and adult females, while the sixth instar (L6) and adult males exhibited the lowest immune capacity. …”
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Exploring Migraine Pathogenesis: Transcriptomic Insights and Pathway Analysis in Nitroglycerin-Induced Rat Model by Qiao-Wen Chen, Run-Tian Meng, Chih-Yuan Ko

“…The control group received saline, while the migraine model group received nitroglycerin (NTG) to induce migraines over four weeks. …”
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Genetic background and oncogenic driver determines the genomic evolution and transcriptomics of mammary tumor metastasis by Christina R. Ross, Karol Szczepanek, Jack Sanford, Gabriel Needle, Tinghu Qiu, Larry Pearce, Maxwell P. Lee, Kent W. Hunter

“…Furthermore, analyzing a cohort with varying genetic backgrounds while maintaining a constant oncogenic driver (PyMT) revealed that genetic background profoundly impacts MSCNVs. …”
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Distinct platelet transcriptomic heterogeneity in respiratory illnesses and modulation by corticosteroids and immune antibody treatments by Wenjun Song, Kaifeng Jin, Qingqing Wang

“…Post-tocilizumab treatment, the instructive interaction from platelets to IFN-activated CD8+ T cells is reduced, while communications from memory B cells, CD4+ T cells, plasmacytoid dendritic cells, and natural killer cells to platelets are enhanced. …”
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Liver transcriptome analysis reveals PSC-attributed gene set associated with fibrosis progression by Alena Laschtowitz, Eric L. Lindberg, Anna-Maria Liebhoff, Laura Anne Liebig, Christian Casar, Silja Steinmann, Adrien Guillot, Jun Xu, Dorothee Schwinge, Michael Trauner, Ansgar Wilhelm Lohse, Stefan Bonn, Norbert Hübner, Christoph Schramm

“…For validation, we compared an external transcriptome data set of liver biopsies from people with PSC (n = 73) with different fibrosis stages (baseline samples from NCT01672853). …”
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Metabolomic and Transcriptomic Analysis of the Mechanism of the Apple Coloration Change After Uncovering Fruit Bag by Pengwei Duan, Xiaojian Ma, Haiqiang Shi, Lizhe Qin, Jizhuang Du, Sumiao Yang, Jianjun Zhang

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Dermal fibroblast transcriptome indicates contribution of WNT signaling pathways in the pathogenesis of Apert syndrome by Arda Çetinkaya, Ekim Taşkıran, Tutku Soyer, Pelin Özlem Şimşek-Kiper, Gülen Eda Utine, Gökhan Tunçbilek, Koray Boduroğlu, Mehmet Alikaşifoğlu

“…COL11A1, COMP, CPXM2, ITGA8, MGF and TNC are differentially expressed genes that have GO terms associated with extracellular matrix (ECM) organization, while FRZB, SFRP2 and WNT2 are involved in WNT signaling pathway. …”
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A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics by Amitabh C. Pandey, Jon Bezney, Dante DeAscanis, Ethan B. Kirsch, Farin Ahmed, Austin Crinklaw, Kumari Sonal Choudhary, Tony Mandala, Jeffrey Deason, Jasmin S. Hamidi, Azeem Siddique, Sridhar Ranganathan, Keith Brown, Jon Armstrong, Steven Head, Phillip Ordoukhanian, Lars M. Steinmetz, Eric J. Topol

“…To address this challenge, here we introduce single-cell CRISPRclean (scCLEAN), a molecular method that globally recomposes scRNAseq libraries, providing a benefit that cannot be recapitulated with deeper sequencing. scCLEAN utilizes the programmability of CRISPR/Cas9 to target and remove less than 1% of the transcriptome while redistributing approximately half of reads, shifting the focus toward less abundant transcripts. …”
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PIT-1/SF-1-positive pituitary tumors in patients with acromegaly: transcriptomic perspective by Julia Rymuza, Qilin Zhang, Mateusz Bujko

“…Somatrotroph PitNETs co-expressing PIT-1 and SF-1 TFs were identified in each of the analyzed RNAseq dataset. Their transcriptomic profile and pituitary TF activity closely resembled those of other somatotroph tumors, while differing substantially from gonadotroph PitNETs, though they retained NR5A1 (SF-1) activity and expressed some SF-1-regulated genes (e.g., LHB and GNHRH). …”
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