SS31 alleviates LPS-induced acute lung injury by inhibiting inflammatory responses through the S100A8/NLRP3/GSDMD signaling pathway by Peiyao Luo, Quankuan Gu, Jianpeng Wang, Xianyong Li, Nana Li, Wei Yang, Xianglin Meng, Mingyan Zhao

“…Methods The study applied transcriptome sequencing, immunofluorescence, PCR, immunofluorescence and other methods to explore the mechanism of SS31 in LPS induced ALI. …”
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Multi-omics investigation of Porphyromonas gingivalis exacerbating acute kidney injury through the gut-kidney axis by Ling Dong, Zhaoxin Ji, Jing Sun, Jiangqi Hu, Qingsong Jiang, Wei Wei

“…In our study, AKI was induced in mice through ischemia-reperfusion injury while administering oral infection with P. gingivalis. …”
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Discovering biomarkers associated with infiltration of CD8+ T cells and tumor-associated fibrosis in colon adenocarcinoma using single-cell RNA sequencing and gene co-expression ne... by Jinning Zhang, Jinning Zhang, Ziquan Sun, Ziquan Sun, Guodong Li, Guodong Li, Lixian Ding, Zitong Wang, Ming Liu, Ming Liu

“…Therefore, it is imperative to identify biomarkers with prognostic value and elucidate the precise role of CD8+ T cells and tumor-associated fibrosis.MethodsWe performed a single-cell transcriptome analysis of COAD samples from the GEO database. …”
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Adverse predictive value of ASPM on lung adenocarcinoma overall survival depended on chemotherapy status by Yan Zheng, Baichen Sun, Zhiling Qu

“…Further, in vitro experiments were conducted to evaluate the effects of ASPM overexpression on cell proliferation and sensitivity to cisplatin.Results Bioinformatics analysis revealed that ASPM’s prognostic significance differed between transcriptomic and proteomic datasets. …”
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Gene networks governing the response of a calcareous sponge to future ocean conditions reveal lineage‐specific XBP1 regulation of the unfolded protein response by Niño Posadas, Cecilia Conaco

“…To describe the gene regulatory networks that govern the stress response of the calcareous sponge, Leucetta chagosensis (class Calcarea, order Clathrinida), individuals were subjected to warming and acidification conditions based on the climate models for 2100. Transcriptome analysis and gene co‐expression network reconstruction revealed that the unfolded protein response (UPR) was activated under thermo‐acidic stress. …”
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Pathogen Recognition and Activation of the Innate Immune Response in Zebrafish by Michiel van der Vaart, Herman P. Spaink, Annemarie H. Meijer

“…Furthermore, we use transcriptome analysis of zebrafish infected with E. tarda, S. typhimurium, and M. marinum to visualize the gene expression profiles resulting from these infections. …”
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Uncovering causal gene-tissue pairs and variants through a multivariate TWAS controlling for infinitesimal effects by Yihe Yang, Noah Lorincz-Comi, Xiaofeng Zhu

“…Abstract Transcriptome-wide association studies (TWAS) are commonly used to prioritize causal genes underlying associations found in genome-wide association studies (GWAS) and have been extended to identify causal genes through multivariate TWAS methods. …”
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Nucleus Pulposus Cells Induce M2 Polarization of RAW264.7 via CX3CL1/CX3CR1 Pathway and M2 Macrophages Promote Proliferation and Anabolism of Nucleus Pulposus Cells by Xiao-Tao Wu, Bo-Wen Wan, Xin-Min Feng, Yu-Ping Tao, Yong-Xiang Wang, Hui-Hui Sun

“…M2 polarized macrophages can further promote NP cell viability, proliferation, and anabolism, while inhibit NP cell apoptosis and catabolism.…”
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Molecular insights into Solanum sisymbriifolium’s resistance against Globodera pallida via RNA-seq by Raquel Varandas, Cristina Barroso, Isabel Luci Conceição, Conceição Egas

“…Results Gene expression profiles were characterized for two S. sisymbriifolium cultivars, Melody and Sis6001, uninfected and infected by G. pallida. The comparative transcriptome analysis revealed a total of 4,087 and 2,043 differentially expressed genes (DEGs) in response to nematode infection in the cultivars Melody and Sis6001, respectively. …”
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Effects of Tannin Supplementation in Diet on the Resistance to Ammonia Stress of Pacific White Shrimp Litopenaeus vannamei by Xiuhong Zhang, Han Gong, Ping Chen, Jiajia Wang, Zhao Chen, Zhiqiang Chang, Jitao Li

“…In this study, we fed a diet containing 800 mg/kg of tannin on Litopenaeus vannamei for 56 days and then subjected to acute ammonia stress for 48 hr to investigate the effect of dietary tannin on the ammonia stress response of L. vannamei through transcriptomic and metabolomic analysis. The transcriptome analysis indicated that ammonia stress-induced differential expression of 4,185 genes, while tannin-fed shrimp only had 964 differentially expressed genes. …”
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Cucurbitacin Profile and Metalloid Stress Response in Cucurbita pepo L. Upon Arsenic Exposure by Gerardo Flores‐Iga, Carlos Lopez‐Ortiz, Purushothaman Natarajan, Padma Nimmakayala, Umesh K. Reddy, Nagamani Balagurusamy, Aldo Almeida

“…To comprehend the effects of As on the root system of C. pepo, we assessed phenotype, cucurbitacin content, and transcriptome under low and high As concentrations. We report that at low dosages, cucurbitacins are decreased, while growth is not significantly affected. …”
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GROWTH-REGULATING FACTOR 9 negatively regulates arabidopsis leaf growth by controlling ORG3 and restricting cell proliferation in leaf primordia. by Mohammad Amin Omidbakhshfard, Ushio Fujikura, Justyna Jadwiga Olas, Gang-Ping Xue, Salma Balazadeh, Bernd Mueller-Roeber

“…Genetic analysis of grf9 org3 and GRF9ox org3 double mutants reveals that both transcription factors act in a regulatory cascade to control the final leaf dimensions by restricting cell number in the developing leaf.…”
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Chondroitin/dermatan sulfate glycosyltransferase genes are essential for craniofacial development. by Judith Habicher, Gaurav K Varshney, Laura Waldmann, Daniel Snitting, Amin Allalou, Hanqing Zhang, Abdurrahman Ghanem, Caroline Öhman Mägi, Tabea Dierker, Lena Kjellén, Shawn M Burgess, Johan Ledin

“…Transcriptome analysis of chsy1-/-, csgalnact1a-/- and csgalnact1a-/-;csgalnact2-/- larvae revealed that the expression had changed in a similar way in the three mutant lines but no differential expression was found in any of fifty GAG biosynthesis enzymes identified. …”
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Large-scale CRISPRi screens link metabolic stress to glioblastoma chemoresistance by Xing Li, Wansong Zhang, Yitong Fang, Tianhu Sun, Jian Chen, Ruilin Tian

“…Molecular mechanisms were investigated through transcriptome analysis, metabolic profiling, and functional assays. …”
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Integration of multi-omics data reveals dysregulated RNA methylation in retinal pigment epithelium drives age-related macular degeneration by Ya-Jun Gong, Zhi-Lin Zou, Kai-Rui Qiu, Qiang Wang, Xiao-Lai Zhou

“…RESULTS: The single-cell transcriptome data analysis revealed massive dysregulation of RNA methylation-related gene expression in the RPE of AMD patients. …”
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The E3 ubiquitin ligase RNF6 facilitates the progression of cervical cancer by inhibiting the Hippo/Yap pathway by Yawen Liu, Juanjuan Zhou, Weiqi Liu, Yi Le, Lingling Zhang, Ziyu Zhang, Ling Zhou, Ling Li

“…Cellular functional experiments demonstrate that RNF6 promotes the proliferation, invasion, and migration of CC cells, while knockdown of RNF6 yields the opposite effect. …”
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Mir-199a-3p aggravates neuroinflammation in an Alzheimer’s disease transgenic mouse model by promoting M1-polarization microglia by Chenyang Wang, Xiaolu Bu, Mengyao Cao, Yunyu Lian, Haocong Ling, Mo You, Junfei Yi, Xiaoya Gao, Duobin Wu, Yang Li

“…In LPS treated BV2 cells, miR-199a-3p mimics promoted M1 polarization, while inhibitors reversed this effect. Transcriptome analysis revealed that miR-199a-3p downregulated WDR76, subsequently suppressing cell cycle-associated pathways, IL-17 signaling, and FOXO pathways, resulting in an increase in the proportion of M1 type microglia. …”
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Damage effect of combined noise and CO exposure on spermatogenesis in male rats by GUO Lulu, ZHANG Zhonghao, LIU Chang

“…Transmission electron microscopy (TEM) was applied to observe the ultrastructural damage in the spermatocytes. Additionally, transcriptome sequencing was performed on testicular tissue, followed by bioinformatics analysis. …”
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Neighbourhood continuity is not required for correct testis gene expression in Drosophila. by Lisa A Meadows, Yuk Sang Chan, John Roote, Steven Russell

“…We compare gene expression in individuals carrying inverted chromosomes with their non-inverted but otherwise identical progenitors using whole-transcriptome microarray analysis, validating these data with specific quantitative real-time PCR assays. …”
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Nurr1 deficiency impairs autophagy-lysosomal function through GBA-dependent transcriptional regulation in Parkinson’s disease pathogenesis by Cheng Cheng, Cheng Cheng, Huijia Yang, Lulu Tian, Yang Ni, Congcong Jia, Weidong Le, Qingshan Wang

“…Transcriptome sequencing and analysis was utilized to confirm the altered pathways and differentially expression genes associated with ALP. …”
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