Author: Editor

Gene Expression Omnibus Announcements & Study Releases

Announcements of updates and changes to the Gene Expression Omnibus (GEO) databases and notifications of newly released functional genomic studies.

• GSE291988 Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization [methyl-seq] December 11, 2025
  Contributors : Shireen Shajahan ; Yann Loe-Mie ; Jack-Christophe CossecSeries Type : Methylation profiling by high throughput sequencingOrganism : Mus musculusA remarkable transition during murine development is the progression from the 1-cell embryo to the 2-cell stage, accompanied by the activation of a specific set of embryonic genes, epigenome reprogramm […]
• GSE165094 Whole genome bisulfite sequencing of peach fruits December 11, 2025
  Contributors : Kai Tang ; Jian-Kang Zhu ; Zhaobo LangSeries Type : Methylation profiling by high throughput sequencingOrganism : Prunus persicaUsing whole genome bisulfite sequencing to provide single-base resulution of DNA methylation status in peach fruits (Prunus persica) in six different stages.
• GSE313368 Dictionary of human intestinal organoid responses to secreted niche factors at single cell resolution December 11, 2025
  Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe intestinal epithelium is often a site of pathology, such as in inflammatory bowel disease (IBD), and its maintenance is highly modulated by interactions with the microenvironment. However, a systematic understanding of how the myriad of niche cues impact distinct epith […]
• GSE270833 Nuclear Phase Separation drives Acute Myeloid Leukemia December 11, 2025
  Contributors : Gandhar K Datar ; Chun-Wei Chen ; Joshua A Riback ; Margaret A GoodellSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensTo investigate how nuclear condensates formed by NPM1c coordinate protein recruitment and promote chromatin binding in leukemia
• GSE263810 Integrated transcriptomic, epigenetic, and TCR clonality analysis of CD4⁺ Tm subsets in liver and lung during chronic GVHD in mice [ATAC-seq] December 11, 2025
  Contributors : Defu Zeng ; Xiwei Wu ; Xiaohui Kong ; Hyejin ChoSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusPathogenic CD4+ T cells perpetuate chronic tissue inflammation, but mechanisms remain largely undefined. Here, with transcriptome, epigenome, and clonal analysis, we compared CD4+Tm subsets among […]
• GSE284076 Post-transcriptional modifications on tRNA fragments confer functional changes to high-density lipoproteins in atherosclerosis [small RNA-seq] December 11, 2025
  Contributors : Elizabeth M. Semler ; Danielle L. Michell ; Kasey C. VickersSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensEpitranscriptomic modifications on RNA play critical roles in stability, processing, and function, partly by influencing interactions with RNA-binding proteins and receptors. The diverse role(s) […]
• GSE283353 Activation of IRF3 impairs mitochondrial function and leads to heart failure. [CMI3OE vs Ctrl] December 11, 2025
  Contributors : Manju Kumari ; Joerg HeerenSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAverting heart failure in ischemic cardiomyopathy is challenging. Heightened inflammatory response and mitochondrial dysfunction drives the pathophysiology of heart failure. However, the transcriptional regulators within cardiomyoc […]
• GSE312833 Single cell RNA sequencing of rat lung after Glenn or sham surgery December 11, 2025
  Contributors : Pan AY ; Spearman ADSeries Type : Expression profiling by high throughput sequencingOrganism : Rattus norvegicusPathogenesis of single ventricle pulmonary arteriovenous malformations is not well understood. We used single cell RNA sequenicng (scRNA-seq) to investigate the molecular changes at single cell resolution early after Glenn or sham su […]
• GSE312476 Heat-Shock Pathway Activation by TRC-051384 Protects Spiral Ganglion Neurons from Noise-Induced Hearing Loss [RNA-Seq] December 11, 2025
  Contributors : Jeffrey N Savas ; Seby Edassery ; Miguel RamirezSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusNoise-induced hearing loss (NIHL) is a major public health problem caused by damage to cochlear hair cells, synapses, and spiral ganglion neurons (SGNs). However, effective treatments are completely lacking. We […]
• GSE313053 APC coordinates GSK3 phosphorylation of SETD8 to suppress colorectal cancer December 11, 2025
  Contributors : Christopher J Lengner ; Mario A Blanco ; Ning Li ; Zvi CramerSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusMutations in the tumor suppressor APC initiate CRC in part by preventing the GSK3 kinase from phosphorylating β-CATENIN, leading to its stabilization and transactivation of mitogenic […]
• GSE312965 Early-life stromal niches orchestrate B lymphopoiesis at the brain’s borders December 11, 2025
  Contributors : Samuel E Marsh ; Alec J Walker ; Beth StevensSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSingle cell RNA sequencing of murine brain border and bone marrow tissues at postnatal day (P)14 to profile early-life immune cells and their stromal/endothelial niches in these organs.
• GSE313177 An Inducible CRISPRi system for phenotypic analysis of essential genes in Pseudomonas aeruginosa December 11, 2025
  Contributors : Sullivan Jaryd ; Warrier Thulasi ; Hung DebSeries Type : Expression profiling by high throughput sequencingOrganism : Pseudomonas aeruginosaPrecise and tunable genetic tools are essential for high throughput functional genomics. To address this need in the important gram-negative pathogen Pseudomonas aeruginosa, we developed and characterized […]
• GSE313282 Differences in mRNA expression in young vs mature adult Drosophila hindguts December 11, 2025
  Contributors : Jessica K Sawyer ; Donald T FoxSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterTissue maintenance in the presence of cell death-promoting insults requires a host of molecular mechanisms. Many studies focus on cell renewal through regeneration, while fewer studies explore mechanisms that promote […]
• GSE313350 Asparagine synthetase and G-protein coupled estrogen receptor are critical responders to nutrient supply in KRAS mutant colorectal cancer December 11, 2025
  Contributors : Lingeng Lu ; Caroline Johnson ; Sajid KhanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSurvival differences exist in colorectal cancer (CRC) patients by sex and disease stage. However, the potential molecular mechanism(s) are not well understood. Here we show that asparagine synthetase (ASNS) and G pro […]
• GSE291983 Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization [Hi-C] December 11, 2025
  Contributors : Shireen Shajahan ; Yann Loe-Mie ; Jack-Christophe CossecSeries Type : OtherOrganism : Mus musculusA remarkable transition during murine development is the progression from the 1-cell embryo to the 2-cell stage, accompanied by the activation of a specific set of embryonic genes, epigenome reprogramming, and nuclear architecture reorganization. […]