New GEO Series

GSE334540 Single nucleus multiome (RNAseq and ATACseq) of male and female mouse pituitary

Sun, 07 Jun 2026 00:00:00 -0400

Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing
Organism : Mus musculus

This SuperSeries is composed of the SubSeries listed below.

GSE334479 Whole-genome bisulfite sequencing reveals dynamic DNA methylation changes in Vigna radiata under direct and pre-conditioned salt stress

Sun, 07 Jun 2026 00:00:00 -0400

Series Type : Methylation profiling by high throughput sequencing
Organism : Vigna radiata

DNA methylation is an important epigenetic mechanism regulating gene expression and stress memory in plants. To investigate the role of DNA methylation in salt stress adaptation, we performed whole-genome bisulfite sequencing (WGBS) of mung bean (Vigna radiata cv. Weilv 9) leaves under two treatment regimes: T1 (pre-conditioned with 100 mM NaCl for 24 h, recovered for 48 h, then re-exposed to 100 mM NaCl) and T2 (direct exposure to 100 mM NaCl without preconditioning). Seedlings were grown hydroponically in half-strength Murashige and Skoog medium under controlled environmental conditions. Genomic DNA was extracted from the first fully expanded true leaves at 0, 6, and 48 h after the onset of the final salt treatment, with three biological replicates per condition. Bisulfite-converted DNA was sequenced to generate genome-wide methylation profiles. Comparative analysis revealed dynamic changes in CG, CHG, and CHH contexts, providing insights into the epigenetic basis of salt tolerance and stress priming in legumes.

GSE334478 ATAC-seq profiling of chromatin accessibility in Vigna radiata leaves under direct and pre‑conditioned salt stress

Sun, 07 Jun 2026 00:00:00 -0400

Series Type : Genome binding/occupancy profiling by high throughput sequencing
Organism : Vigna radiata

Salinity is a major environmental constraint limiting crop productivity. Chromatin accessibility plays a crucial role in transcriptional regulation under stress conditions. In this study, we investigated genome-wide chromatin accessibility dynamics in mung bean (Vigna radiata cv. Weilv 9) leaves under salt stress using ATAC-seq. Two treatment groups were established: T1 (pre-conditioned with 100 mM NaCl for 24 h, recovered for 48 h, then re-exposed to 100 mM NaCl) and T2 (direct exposure to 100 mM NaCl without preconditioning). Seedlings were grown hydroponically in half-strength Murashige and Skoog medium under controlled environmental conditions. Nuclei were isolated from the first fully expanded true leaves at 0, 6, and 48 h after the onset of the final salt treatment, with three biological replicates per condition. Comparative ATAC-seq analysis revealed dynamic changes in chromatin accessibility associated with transcriptional reprogramming and stress memory. This dataset provides valuable insights into the epigenetic basis of salt tolerance and acclimation in legumes.

GSE334477 Transcriptome analysis of Vigna radiata leaves in response to direct and pre-conditioned salt stress [RNA-Seq]

Sun, 07 Jun 2026 00:00:00 -0400

Series Type : Expression profiling by high throughput sequencing
Organism : Vigna radiata

We investigated the adaptive responses of mung bean cultivar 'Weilv 9' to salt stress using RNA-seq. Two treatments were applied: T1 (pre-conditioned with 100 mM NaCl for 24 h, recovered for 48 h, then re-exposed to 100 mM NaCl) and T2 (direct exposure to 100 mM NaCl without preconditioning). Samples were collected at 0, 1, 3, 6, 12, 24, and 48 h after the onset of the final salt treatment from the first fully expanded true leaves (n=3 per time point per treatment). Plants were grown under controlled conditions (25°C, 12,000 lux, 16h/8h light/dark, 70% RH) in 1/2 MS nutrient solution. The 0 h time point in T2 represents naive control, while in T1 it reflects residual effects after recovery. Data aim to reveal transcriptional reprogramming under salt stress and preconditioning.

GSE334035 Targeting mitochondrial ROS-CK2-SET-PP2A pathway with ceria nanoparticles to reverse Tau pathology in APOEε4-associated Alzheimer’s disease [scRNA-seq]

Sun, 07 Jun 2026 00:00:00 -0400

Contributors : Jong Won Han ; Yubeen Kim ; June-Hyun Jeong ; Yunjung Lee ; Dakyung Lee ; Suk-Kyung Shin ; Seok Beom Hong ; Keuntae Kim ; Sieun Choi ; Rian Kang ; Jong-Chan Park ; Kangmin Suh ; Jinyoung Chu ; Nohyun Lee ; Sang Ihn Han ; Dong-Sup Lee ; Il-Joo Cho ; Seok Chung ; Jong-Il Kim ; Taeghwan Hyeon ; Inhee Mook-Jung
Series Type : Expression profiling by high throughput sequencing
Organism : Homo sapiens

In this study, we used triphenylphosphonium-conjugated ceria nanoparticles (Ceria-TPP) to target mitochondrial ROS in APOEε4 human iPSC-derived brain organoid, and profiled transcriptional changes via single-cell RNA-seq.

GSE334034 Targeting mitochondrial ROS-CK2-SET-PP2A pathway with ceria nanoparticles to reverse Tau pathology in APOEε4-associated Alzheimer’s disease [RNA-seq]

Sun, 07 Jun 2026 00:00:00 -0400

In this study, we used triphenylphosphonium-conjugated ceria nanoparticles (Ceria-TPP) to target mitochondrial ROS in APOEε4 iPSC-derived neurons, and analyzed transcriptional changes using bulk RNA sequencing.

GSE334026 CUT&Tag of H3K18 lactylation in mouse embryonic stem cells treated with vitamin B6 for 7 days

Sun, 07 Jun 2026 00:00:00 -0400

Contributor : Dengwang Chen
Series Type : Genome binding/occupancy profiling by high throughput sequencing
Organism : Mus musculus

Vitamin B6 (pyridoxine) is widely used as a first-line treatment for nausea and vomiting during pregnancy, yet its safety profile during embryonic development, particularly at supraphysiological doses, remains incompletely understood.

GSE333968 Vitamin B6 Promotes Endoderm Differentiation of Mouse Embryonic Stem Cells via Glycolysis-H3K18 Lactylation Axis

Sun, 07 Jun 2026 00:00:00 -0400

Contributor : Dengwang Chen
Series Type : Expression profiling by high throughput sequencing
Organism : Mus musculus

GSE333543 The lateral septum orchestrates state-dependent modulation of associative threat memory dynamics across the ovarian hormone cycle

Sun, 07 Jun 2026 00:00:00 -0400

Contributor : Elizabeth K Lucas
Series Type : Expression profiling by high throughput sequencing
Organism : Mus musculus

Single-nucleus ATAC- and RNA-sequencing data from adult female proestrus C57Bl/6J mouse brain lateral septum, threat conditioned and naive control animals. This GEO submission contains the processed RNA-seq/single-nucleus RNA-seq data associated with existing SRA records.

GSE330574 Transcriptional changes in Drosophila tbph mutants and inducible neuronal TBPH rescue in adult heads at 60 hours post-eclosion

Sun, 07 Jun 2026 00:00:00 -0400

Contributors : Feiguin Fabian ; Romano Giulia
Series Type : Expression profiling by array
Organism : Drosophila melanogaster

TBPH, the Drosophila ortholog of human TDP-43, is required for normal neuronal function. To identify transcriptional programs altered by loss of TBPH and those restored by neuronal re-expression of TBPH, we performed Affymetrix microarray profiling on adult heads from wild-type (w1118) animals, two independent tbph loss-of-function mutants (tbph^Δ23 and tbph^Δ142), and a tbph mutant line carrying an elav-GeneSwitch-driven UAS-TBPH transgene activated by feeding 5 mM RU-486 for 60 hours post-eclosion (Rescue).
Comparison of mutants vs control identified a shared dysregulated transcriptional signature; comparison of rescue vs mutants identified the subset of these genes whose expression was restored by inducible neuronal TBPH re-expression.

GSE322542 Brain Transcriptomics Across Diverse Sleep-Wake Manipulations Reveals Multiple Homeostatic Pathways in Drosophila

Sun, 07 Jun 2026 00:00:00 -0400

Contributors : Shiju Sisobhan ; Clark Rosensweig ; Ravi Allada ; Aadish Shah ; Tomas Andreani
Series Type : Expression profiling by high throughput sequencing
Organism : Drosophila melanogaster

Sleep is governed by two processes: a circadian process that times sleep and wake and a homeostatic process that drives sleep as a function of prior wake history. Discovered in the fruit fly Drosophila, the period (per) gene is a “universal” cornerstone of the circadian clock, robustly oscillating at the transcript level, in all organs and tissues and in essentially all animals. We hypothesized that there may be a comparable factor (we term “sleeper”) for sleep homeostasis. To identify sleeper, we performed a wide-ranging transcriptomic analysis to identify genes whose expression tracks sleep-wake history in the Drosophila brain. We use a variety of methods to manipulate sleep-wake and subsequent rebound including mechanical, thermogenetic, optogenetic, pharmacological and circadian/baseline across 7 datasets. Using a log2 fold change threshold of 1, we did not identify any gene that was sleep-wake dependent across all datasets, raising the possibility that genes identified with a single method of sleep manipulation are related to the nature of the manipulation and not to sleep. Nonetheless, we identified genes whose expression changed with sleep-wake in a consistent direction across at least 2 datasets. We did observe significant pairwise overlap in regulated genes across many of the datasets. Gene ontology analysis of genes associated with sleep and wake as well as with sleep rebound. These analyses highlight previous processes implicated in sleep homeostasis as well as provide potentially novel pathways. In addition, we also examine genes whose expression correlates with prior sleep-wake history and/or predicted subsequent sleep rebound across these datasets. Among significantly correlated genes we observed some that were correlated with recent (<3h) sleep history while others were correlated with much longer (>6h) time frames suggesting temporally distinct genetic pathways for integrating waking experience. This analysis also highlights specific GO pathways for sleep/wake/rebound. Applying a novel GPT based paper search algorithm, we call fl.ai, we identified several genes with implicated or demonstrated function in sleep regulation consistent with potential homeostatic function. Collectively, these studies inform the future design of studies on the nature of sleep homeostasis as well as provide unique molecular clues across diverse sleep-wake conditions.

GSE316842 Transcriptomic Profiling of Blood-Stage Plasmodium falciparum in Children with Severe Malarial Anemia

Sun, 07 Jun 2026 00:00:00 -0400

Contributors : Douglas J Perkins ; Qiuying Cheng ; Ivy Hurwitz ; Christophe G Lambert ; Philip D Seidenberg ; Kristan A Schneider ; Benjamin H McMahon ; Collins Ouma ; Evans Raballah ; Samuel B Anyona ; Clinton O Onyango ; Anne A Ong'ondo ; Nicholas O Ondiek ; Everlyne Modi ; Joan A Ochieng ; Vincent I Omanje ; Rodney B Mongare ; Sharley A Wasena ; Shamim W Osata
Series Type : Expression profiling by high throughput sequencing
Organism : Plasmodium falciparum

Malaria is a major global health threat, with millions of cases and hundreds of thousands of deaths reported annually, primarily in sub-Saharan Africa. Children under five years of age residing in holoendemic Plasmodium falciparum transmission regions are the most vulnerable to malaria, accounting for vast majority of cases and mortality. The major clinical manifestation of severe malaria in these children is severe malarial anemia [SMA, hemoglobin (Hb)<6.0 g/dL]. The molecular mechanisms underlying SMA pathogenesis, particularly the contribution to this disease process of P. falciparum gene activities at transcriptomic levels, remain largely unexplored. As such, the overall objective of the study was to profile the blood-stage Plasmodium falciparum transcriptome in children with SMA. To achieve this goal, we performed RNAseq on total RNA from peripheral blood samples of 60 pediatric malaria patients (3-36 months) with non-SMA (Hb≥6.0 g/dL, n=40) and SMA (n=20) at enrollment. The RNA reads were mapped to the P. falciparum reference genome (PfKE01). Diffentially expressed genes (DEGs) in SMA relative to non-SMA and relevant biological pathways in P. falciparum were identified. In addition, the performance of the expressed parasite genes in predicting SMA was assesed. These findings promote the identification of potential parasite-derived biomarkers and therapeutic targets for improving SMA management.

GSE310989 Bispecific Antibody Engineered Extracellular Vesicles Redirect T Cells to Prevent Postoperative Epidural Fibrosis [scRNA-seq]

Sun, 07 Jun 2026 00:00:00 -0400

Contributors : Zheng Zhang ; Wei Xiong ; Liang Huang ; Shanwei Ye ; Qian Xu
Series Type : Expression profiling by high throughput sequencing
Organism : Mus musculus

Epidural fibrosis (EF) is a frequent and debilitating complication that impairs recovery following spinal surgery, yet effective targeted therapies are lacking. Here we observe enrichment of FAP⁺ fibroblasts at surgical sites in patients after laminectomy. To therapeutically target this subset, we develop bispecific antibody–decorated extracellular vesicles (BsAb EVs), which redirect endogenous T cells to eliminate FAP⁺ fibroblasts in situ. In a preclinical model, BsAb EVs selectively eliminate pathogenic fibroblasts, reduce fibrotic collagen accumulation, and prevent the development of postoperative epidural fibrosis without detectable systemic toxicity under the tested conditions. Single-cell RNA sequencing reveals that FAP⁺ fibroblasts represent a transcriptionally distinct subset from α-SMA⁺ myofibroblasts, characterized by enhanced extracellular matrix remodeling and TGF-β production. Together, these findings highlight a critical stromal subset in EF pathogenesis and position BsAb EVs as a promising immunotherapeutic strategy for targeting pathogenic stromal cells in fibrotic and tissue-remodeling disorders.

GSE310366 Targeted Elimination of FAP⁺ Fibroblasts by BiTE-Engineered Extracellular Vesicles Prevents Epidural Fibrosis

Sun, 07 Jun 2026 00:00:00 -0400

Contributors : Zheng Zhang ; Wei Xiong ; Liang Huang ; Shanwei Ye ; Qian Xu
Series Type : Expression profiling by high throughput sequencing
Organism : Mus musculus

GSE299535 Gene expression analysis of early Barrett's adenocarcinoma, Barrett's esophagus, normal gastric mucosa, and esophageal mucosa

Sun, 07 Jun 2026 00:00:00 -0400

Contributors : Dai Kubota ; Yu Takahashi
Series Type : Expression profiling by array
Organism : Homo sapiens

The objective of this study was to identify genes and pathways early Barrett's adenocarcinoma through comprehensive gene expression analysis.

GSE299273 Relationship between environmental pollutant TBOEP and renal metabolism

Sun, 07 Jun 2026 00:00:00 -0400

Series Type : Expression profiling by high throughput sequencing
Organism : Homo sapiens

Tris(2-butoxyethyl) phosphate (TBOEP) is a common organophosphorus compound widely used in industrial production as a plasticizer and flame retardant. In recent years, studies have shown that TBOEP may pose potential threats to human health, particularly its association with kidney metabolic function has attracted widespread attention. The kidneys, as the most important metabolic organ in the human body, play a crucial role in detoxification, synthesis, and decomposition of various biomolecules. After entering the human body, TBOEP is mainly metabolized and detoxified by the kidneys. However, TBOEP and its metabolites may interfere with the normal function of the kidneys, leading to metabolic disorders. Studies have shown that TBOEP exposure may affect the activity of enzymes in the kidneys, such as cytochrome P450 enzyme systems, which are involved in the metabolism of various endogenous and exogenous substances. In addition, TBOEP may also affect kidney metabolism by influencing gene expression. For example, TBOEP exposure may activate or inhibit genes related to lipid metabolism, glucose metabolism, and oxidative stress, thereby altering the metabolic state of the kidneys. These changes not only affect the function of the kidneys themselves but may also have a chain reaction on the health of other organs and systems through the interaction of the systemic metabolic network. Furthermore, TBOEP exposure may lead to kidney damage and dysfunction, which can further exacerbate metabolic disorders. For example, kidney damage can impair the excretion of metabolic waste products, leading to their accumulation in the body and further disrupting metabolic balance. In summary, as an environmental pollutant, the potential impact of TBOEP on kidney metabolic function cannot be ignored. Future research needs to further explore the toxicological mechanisms of TBOEP and its long-term effects on human health in order to develop effective prevention and intervention measures to protect public health.

GSE288137 Single cell multiomics unravel the transcription networks controlling the different EMT tumor states

Sun, 07 Jun 2026 00:00:00 -0400

Contributors : Andrea Pérez González ; Gabriel Solvi Windels ; Kevin Bévant ; Justine Lengrand ; Sophie Lemaire ; Virginie Moers ; Samuel Scozzaro ; Ulysse Debroux ; Christine Dubois ; Sebastiaan Vanuytven ; Cédric Blanpain
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing
Organism : Homo sapiens ; Mus musculus

Epithelial-to-mesenchymal transition (EMT) is a process by which cells lose their epithelial characteristics and acquire mesenchymal traits. In cancer, EMT is associated with tumor initiation, progression, invasion, metastasis and resistance to therapy. Recent studies demonstrated that EMT is not a binary switch, but presents intermediate states associated with different tumor functions. The gene regulatory networks (GRNs) controlling the different EMT states remain elusive. Here, using multi-OMIC approaches combining single cell RNA-seq and single cell ATAC-seq, we define the transcriptomic and chromatin landscape associated with the distinct EMT states in mouse skin squamous cell carcinoma (SCC) exhibiting EMT. Using CRISPR/Cas9-mediated loss of function studies combined with functional characterization in vitro and in vivo, we unravel the cellular and molecular mechanisms regulated by Pitx1, Klf5, Nfatc1 and Creb3l1, transcription factors (TFs) controlling specific EMT states. Altogether, our results identify the transcriptional and chromatin landscape of the distinct EMT tumor states and uncover novel key TFs controlling these states and their transition, providing potential novel targets for anti-cancer therapy.

GSE269386 Oxidative and glycolytic skeletal muscle-derived exosomes selectively coated miRNAs and participate in regulating myoblast proliferation and differentiation mediated by miR-4331-3p

Sun, 07 Jun 2026 00:00:00 -0400

Contributors : Jia Luo ; Daiyu Zhang ; Zhenhao Wen ; Qiang Pu ; Taorun Luo ; Xiaoqian Wu ; Jie Chai ; Li Chen ; Changfeng Yang ; Yongfu Huang
Series Type : Non-coding RNA profiling by high throughput sequencing
Organism : Sus scrofa

The phenotypic characteristics and meat quality of skeletal muscle are collectively determined by the muscle cells, other cellular groups within it, and their intricate interactions with the extracellular microenvironment. Exosomes have the capacity to influence the development and microenvironment of skeletal muscle, thus playing a crucial role in its differentiation and maturation. In this study, we conducted an initial evaluation of the muscle fiber phenotypes in glycolytic skeletal muscle (Longissimus dorsi, HC-L) and oxidative skeletal muscle (Psoas major, HC-P) of Hechuan black pigs. The results revealed significant differences in terms of muscle fiber diameter, density, and type phenotypes (P<0.05). Subsequently, we isolated and identified exosomes derived from skeletal muscle (SKM-Exos). Co-culture experiments with myoblasts demonstrated that SKM-Exos can promote both myoblast proliferation and differentiation. Furthermore, sequencing analysis confirmed that miRNAs present in SKM-Exos are selectively coated miRNAs. It is noteworthy that the expression of miR-4331-3p was notably higher in SKM-Exos compared to its derived skeletal muscles. It was significantly elevated in the SKM-Exos of HC-L when compared to those of HC-P, and have interactions with the differentially expressed genes between HC-L and HC-P. Interestingly enough, miR-4331-3p has been shown to enhance myoblast proliferation while inhibiting the differentiation process. By investigating the interaction between SKM-Exos, their derived miRNAs, and myoblasts, this study elucidated the molecular mechanism underlying the regulation of muscle fiber differentiation by SKM-Exos and provided valuable insights into the intricate molecular processes involved in meat formation.

GSE259269 Identification of the SARS-CoV-2 genome packaging signal in the nsp12-coding region

Sun, 07 Jun 2026 00:00:00 -0400

Contributors : Youngran Park ; Jongmin Lim ; V Narry Kim ; Young-suk Lee
Series Type : Other
Organism : Chlorocebus aethiops

Selective genome packaging is a critical step for RNA viruses, which must distinguish genomic RNA from other abundant transcripts. For SARS-CoV-2, the cis-acting packaging signal is thought to be recognized by the nucleocapsid (N) protein, but its identity and mechanistic basis for selective recognition remain undefined. Here we identify the packaging signal within the nsp12 polymerase-coding region. CLIP-seq maps N-bound sites and, together with virus-like particle assays, pinpoints a conserved segment with strong packaging activity. An orthogonal defective-interfering RNA approach confirms its role in genome selection. We further delineate two critical subregions, α and β, that engage the N C-terminal domain. Synonymous mutations in either subregion selectively disrupt packaging and reduce viral fitness. Notably, the α subregion encompasses the ribosomal frameshifting element, revealing its dual role in viral translation and assembly. These findings establish the mechanistic basis for SARS-CoV-2 genome packaging and offer a potential antiviral target.

GSE255645 RNA-sequencing results of the human thyroid papillary carcinoma cell TPC-1 with overexpression of the PTCSC3-AS1 gene

Sun, 07 Jun 2026 00:00:00 -0400

Contributors : Yanqiang Wang ; Yutong Zhang
Series Type : Expression profiling by high throughput sequencing
Organism : Homo sapiens

Here we report gene expression profiles of TPC-1 cells treated with PTCSC3-AS1 overexpressed vector (OE) or empty vector (EV). PTCSC3-AS1 gene was cloned from expressed sequence tag (AA632637). And the sequence of PTCSC3-AS1 is included in EST AA632637. A number of dysregulated genes of PTCSC3-AS1 were discovered. This study reveals the role of PTCSC3-AS1 in downstream gene regulation and its function in the tumorigenesis of thyroid cancer.

GSE234339 RIOK3 potentially regulates osteogenesis related pathways in ankylosing spondylitis and the differentiation of bone marrow mesenchymal stem cells

Sun, 07 Jun 2026 00:00:00 -0400

Contributors : Shengqian Xu ; Hexiang Zong ; Yuechen Xu
Series Type : Expression profiling by high throughput sequencing
Organism : Mus musculus

Background: RNA-binding proteins (RBPs) are key effectors of gene expression andplay critical rolesininflammation, immune regulation,andmany rheumatic diseases. This study screened the differentially expressed RBPs between ankylosing spondylitis (AS) patients and the healthy control group through transcriptome sequencing and explored the potential biological function and mechanism of target RBP in AS patients. Methods: The differentially expressed genes (DEGs) in whole blood cells of 5 AS patients and 3 healthy people were obtained by RNA-seq, and the differentially expressed RBPs were obtained by overlapping the DEGs and the summarytable of RBPs. The selected target RBP (RIOK3) was verified by qRT-PCR in the peripheral blood mononuclear cells (PBMCs) of patients with AS and age_x001E_ and sex_x001E_ matched controls. Next, mouse bone marrow mesenchymal stem cells (mBMSCs) were transfected with siRNA targeting RIOK3 usingthelipofectaminetransfectiontechnique, and the molecular functions, biological processes, and signaling pathway enrichment analysis of DEGs regulated by RIOK3 were performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The expression level of the selected genes in siRIOK3 mBMSCs was detected by qRT-PCR to further verify the regulatory role of RIOK3. Then, the RIOK3 stable knockdown transfected cell lines were constructed by lentivirus infection, and calcium deposits were observed byAlizarinredstaining after21daysof osteogenicinduction, and the expression of osteogenic genes ALP, OCN, and OPN were assessed by qRT-PCR. Results: RIOK3 was enriched in interferon-related pathway and innate immune-related pathway, which was an important immune regulatory factor and could effected the function of ribosomes. RIOK3knockdown will inhibited the expression of genes related to transcription and ribosomal function in mBMSCs, especially the transcription factors related to osteogenic differentiation, and will also effected the expression of β-interferon related pathway genes. RIOK3 knockdown effect was mainly co-expressed with HIF-1 signal pathway, MAPK signal pathway, and inflammatory response related pathway genes in the osteogenic differentiation of mBMSCs. The cellularexperimentalresults further confirmedthat RIOK3 knockdown will reduce the osteogenic differentiation ability of mBMSCs. Conclusion: Collectively,RIOK3 may affect the differentiation of mBMSCs and participate in the occurrence and development of AS, especially pathological bone formation. Thisstudymay providenew perspectivefortheresearchofthe mechanism of AS and atheoreticalbasisforRIOK3asapotential target for AS therapy.