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

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.

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.

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.

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.