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}NCBI GEO2026 · RNA sequencing
Analysis of aged and young Rat OPC data (bulk RNA-seq; Re-analysis)We compared gene expression of aged and young oligodendrocyte progenitor cells (OPC) and identified differentially expressed genes.
NCBI GEO2026 · RNA sequencing
Transcriptomics reveals orchestration of larval and juvenile development and metamorphosis in Southern Flounder Paralichthys lethostigma (reanalysis of GSE307589)Developmental transitions involve changes in the genetic programs governing molecular processes. Characterizing these genetic programs gives us insight into how genes work to orchestrate developmental transitions in morphology, physiology, or even behavior. One fascinating developmental transition, metamorphosis, bridges larval and juvenile periods. Southern Flounder, a flatfish, is an ideal model
NCBI GEO2026 · RNA sequencing · 30 samples
Contrasting epigenetic dynamics in chromosome arms and pericentromeres during ROS1-induced plant immune memory [RNA-seq]Induced resistance against (hemi-)biotrophic pathogens can be triggered in Arabidopsis by 17β-estradiol (E2)-dependent activation of ROS1 in plants carrying the XVE:ROS1-YFP transgene. Here, we use ribosome-depleted RNA-seq to characterise the transcriptional changes associated with the estbalishment of this ROS1-mediated resistance.
NCBI GEO2026 · Table · TSV · 4 samples
Contrasting epigenetic dynamics in chromosome arms and pericentromeres during ROS1-induced plant immune memory [ONT-seq]Induced resistance against (hemi-)biotrophic pathogens can be triggered in Arabidopsis by 17β-estradiol (E2)-dependent activation of ROS1 in plants carrying the XVE:ROS1-YFP transgene. Here, we use long-read Oxford Nanopore Technologies sequencing (ONT-seq) and the centromere-complete Arabidopsis genome assembly Col-CEN to characterise genome-wide changes in DNA methylation associated with the est
NCBI GEO2026 · Excel spreadsheet · 42 samples
Contrasting epigenetic dynamics in chromosome arms and pericentromeres during ROS1-induced plant immune memory [BiSulfite-seq]Induced resistance against (hemi-)biotrophic pathogens can be triggered in Arabidopsis by 17β-estradiol (E2)-dependent activation of ROS1 in plants carrying the XVE:ROS1-YFP transgene. Here, we characterise the genome-wide cytosine DNA methylation changes associated with the estbalishment of this ROS1-mediated resistance.
NCBI GEO2026 · RNA sequencing
Rete ridges form through evolutionarily distinct mechanisms from other appendages during mammalian skin development [1]The loss of fur during human evolution has long mystified scientists and the public. This loss coincides with the acquisition of epidermal rete ridges, whose developmental timing and molecular mechanisms are poorly understood despite their prominence in humans. Examination of human and pig skin development revealed that rete ridges form through an independent mechanism from hair follicles and swea
NCBI GEO2026 · RNA sequencing · 28 samples
RNA-sequencing analysis of gene expression evolution in mole ratsUnderstanding the genetic basis of phenotypic adaptation poses a significant challenge in evolutionary genomics. Mutations in regulatory sequences that influence gene expression, such as tissue-specific enhancers, are widely recognised as key drivers of phenotypic evolution. However, because cis-regulatory elements evolve rapidly, linking changes in their activity to corresponding changes in gene
NCBI GEO2026 · Excel spreadsheet
Intermittent Fasting Rewires Tissue-Specific Gene-Transposable Element Regulatory NetworksIntermittent fasting (IF) is a dietary intervention known to promote systemic health benefits, yet its impact on genome-wide transcriptional regulatory networks, particularly those involving transposable elements (TEs), remains poorly understood. This study investigates the multi-tissue transcriptomic response to chronic IF in mice, focusing on TE regulation and its integration with host gene netw
NCBI GEO2026 · RNA sequencing · 21 samples
Widespread transmission of DNA supercoiling and selective topoisomerase utilization regulates torsional stress within the neuronal genomeThis SuperSeries is composed of the SubSeries listed below.
NCBI GEO2026 · RNA sequencing · 3 samples
Widespread transmission of DNA supercoiling and selective topoisomerase utilization regulates torsional stress within the neuronal genome [RNA-Seq]DNA supercoiling has the potential to alter gene transcription and chromatin topology, yet how its distribution is regulated on a genome-wide level is poorly understood. Here we utilized psoralen crosslinking and sequencing (TMP-seq) to assess the distribution of underwound DNA at high resolution in postmitotic neurons. We report that supercoiling propagates widely (> 200 kb) from the sites of act
NCBI GEO2026 · Excel spreadsheet · 9 samples
Exercise training does not mitigate high-phosphate diet induced mitochondrial dysfunction in skeletal muscleInorganic phosphate (Pi) consumption is two-to-three-fold higher than the recommended daily allowance for adults due to its use as a preservative and flavor enhancer in processed foods. We reported previously that mice fed high-Pi diet (HPD) for 12 weeks exhibited reduced VO2max, altered metabolic gene expression, and mitochondrial dysfunction in skeletal muscle. Exercise is a common intervention
NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 103 samples
Degenerate long-range interactions drive phase transition of heterochromatin [ChIP-Seq]Despite intensive efforts, the molecular mechanisms that organize genomes into A and B compartments are still not understood. This is largely due to experimental challenges in targeted manipulation of the molecular components involved. We made use of C. elegans as elementary model system to unveil fundamental concepts of genome compartmentalization. Simultaneous deletion of the H3 lysine 9 methyla
NCBI GEO2026 · RNA sequencing · 58 samples
Cardiac Fibrosis in Dilated Cardiomyopathy: Transcriptomics Insights, Histological Correlations, and Organoid Model Verifications [RNA-seq I]Dilated cardiomyopathy (DCM) represents a leading cause of heart failure among younger adults. Despite endomyocardial biopsy (EMB) transcriptome enriching our understanding of DCM, the link between its gene expression and phenotype remains unclear. RNA-seq analysis of 58 DCM samples and 12 publicly available control samples unveiled about 25,000 transcripts. A principal component analysis highligh
NCBI GEO2026 · Excel spreadsheet
A single-cell and spatial immune atlas of chronic antibody-mediated rejection reveals autoimmune-shared immune states and a CXCL12-CXCR4 fibroblast-immune nicheChronic antibody-mediated rejection (CAMR) is a leading cause of late kidney allograft failure and shares features of chronic immune activation with systemic autoimmune diseases, but how circulating immune states connect to spatially organized graft injury and whether related immune features recur in autoimmune inflammation remain unclear. Here, we integrated single-cell profiles from peripheral b
NCBI GEO2026 · Excel spreadsheet
Expression quantification from the AmarylOmicBase study (multiple species)To facilitate new studies in the Amaryllidoideae subfamily, we present AmarylOmicBase, a unified transcriptomic database that integrates assemblies, annotations, and expression profiles from 39 studies, covering 27 Amaryllidoideae species and 4 hybrid cultivars across 13 genera of Amaryllidoideae. The AmarylOmicBase (v2, https://doi.org/10.5281/zenodo.20349158) includes de novo assemblies generate
NCBI GEO2026 · Excel spreadsheet · 6 samples
Whole-transcriptome RNA sequencing-based biomarker screening and human-rat cross-species conserved target analysis for cerebral palsy_Homo sapiens_miRNAseqCerebral Palsy (CP) is a group of neurodevelopmental disorders characterized by persistent motor and posture impairments. Its molecular mechanisms remain poorly understood, and there is a lack of reliable blood-based biomarkers.
NCBI GEO2026 · RNA sequencing
SARS-CoV-2 infection in Peromyscus leucopus [re-analysis of GSE154104]Novel coronavirus causing Covid-19 identified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused pandemic in 2020. Although the virus and disease in humans has been thoroughly researched, so far there has not been animal model comparable to humans – genetically diverse species able to get infected and sick from Covid-19. The white-footed deermouse Peromyscus leucopus is a long-
NCBI GEO2026 · RNA sequencing
Ductal Epithelial MXD3 Promotes Disease Progression in Acute Pancreatitis through Wnt/b-catenin-Mediated Inflammation and InjuryAcute pancreatitis (AP) is a severe inflammatory disease where epithelial injury and dysregulated repair are central to pathogenesis, yet the underlying transcriptional mechanisms remain poorly understood. This study employed an integrated approach to identify and characterize the transcription factor MXD3 as a master regulator of AP progression. Using single-cell RNA sequencing in a cerulein-indu
NCBI GEO2026 · Excel spreadsheet · 8 samples
Cross-platform Hi-C meta-analysis identifies functional insulators that actively block enhancer-promoter interactionsInsulator protein CTCF controls genome architecture through forming thousands of cohesin-dependent structural loops. However, genome-wide studies only found mild transcriptional consequences upon acute CTCF-depletion, raising confusions about how CTCF regulates enhancer-promoter (E-P) interactions and gene expression. Here we reanalyze independent Hi-C, in situ Hi-C, and micro-C data in mouse embr
NCBI GEO2026 · RNA sequencing · 7 samples
AMPK-p38 axis converts human pluripotent stem cells to naïve stateThis SuperSeries is composed of the SubSeries listed below.
NCBI GEO2026 · Excel spreadsheet · 6 samples
AMPK-p38 axis converts human pluripotent stem cells to naïve state [RNA-Seq]Pluripotent stem cells (PSCs) have been reported to exhibit two stages of pluripotency, ‘primed’ and ‘naïve’ states. Typical human PSCs (hPSCs) are in the primed state. Though several methods for conversion from primed to naive state have been reported, the mechanism of the process is not fully understood. Here, we report that 5' adenosine monophosphate-activated protein kinase (AMPK) and its down
NCBI GEO2026 · Excel spreadsheet
Epigenomic Aberrations in Brains of Humans with Mild Cognitive Impairment and Alzheimer’s Disease [re-analysis]Epigenetic mechanisms, particularly histone modifications at gene promoters, are crucial for controlling gene transcription. During the progression of neurodegenerative disorders, epigenomic aberrations may contribute to gene dysregulation, leading to manifestation of symptoms. To test this, we employed a multifaceted approach to investigate how the two key histone methylation marks, H3K4me3 (link
NCBI GEO2026 · Excel spreadsheet
Reanalysis of ChIP-Seq of PRJEB5782In this reanalysis, 20 ERR series were reanalyzed for ChIp-Seq data.
NCBI GEO2026 · Methylation profiling by genome tiling array · 61 samples
Intracranial mesenchymal tumor, FET-CREB fusion-positive: an integrative analysis of 81 casesIntracranial mesenchymal tumors, FET-CREB fusion-positive (ICMT ) show fusions involving FET RNA-binding protein family gene (EWSR1 or FUS) and CREB family of transcription factors (ATF1, CREB1 or CREM). The methylation characteristics and clinical behavior of this important tumor type require further characterization. We study the methylation profiles of 81 ICMT cases (61 newly profiled cases and
NCBI GEO2026 · Excel spreadsheet
Re-analysis of PRO-cap data from HCT116 cells (GSE219977)This submission provides processed PRO-cap coverage tracks (bigWig files) from the re-analysis of public data (GSE219977, samples GSM6783554 and GSM6783555) from Homo sapiens HCT116 genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, (insertion) using CRISPR targeting H. sapiens SUPT16H. Data were aligned to the hg38 reference genome (GENCODE release 33; https://www.genco