GEO DataSets

(Submitter supplied) The integrated analysis of histone modifier enzymes in solid tumor, especially in esophageal squamous cell carcinoma (ESCC) is still inadequate. Here, we investigate the expression levels of histone modifier enzymes in ESCC tissues. Notably, KAT8 is identified as a prognostic and therapeutic biomarker in ESCC. Esophageal tissue-specific deletion of KAT8 mice exhibite less tumor burden after induction of tumorigenesis via 4NQO treatment compared with wild-type mice. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34284

2 Samples

Download data: TXT

(Submitter supplied) Herpesviruses, including the oncogenic Epstein-Barr Virus (EBV), must bypass host DNA sensing mechanisms to drive infection and pathogenesis. The first viral latency protein expressed, EBNA-LP, is essential for the transformation of naïve B cells, yet its role in evading host defenses remains unclear. Using single-cell RNA sequencing of EBNA-LP-Knockout (LPKO)-infected B cells, we reveal an antiviral response landscape implicating the ‘speckled proteins’ as key restriction factors countered by EBNA-LP. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34284

8 Samples

Download data: CSV

(Submitter supplied) Herpesviruses, including the oncogenic Epstein-Barr Virus (EBV), must bypass host DNA sensing mechanisms to drive infection and pathogenesis. The first viral latency protein expressed, EBNA-LP, is essential for the transformation of naïve B cells, yet its role in evading host defenses remains unclear. Using single-cell RNA sequencing of EBNA-LP-Knockout (LPKO)-infected B cells, we reveal an antiviral response landscape implicating the ‘speckled proteins’ as key restriction factors countered by EBNA-LP. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34284

4 Samples

Download data: CSV

(Submitter supplied) Metabolic stress elicits functional changes in pancreatic islets, contributing to the pathogenesis of type 2 diabetes. However, the molecular mechanisms underlying overnutrition stress in islet cells is not well understood. In our study, we subjected human islets to overnutrition with 25 mM glucose and 0.5 mM palmitic acid or a control culture condition with 5.1 mM glucose. We utilized single-cell RNA sequencing to comprehensively characterize the gene expression changes between these two conditions in a cell-type specific manner. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL34284

14 Samples

Download data: RDS

(Submitter supplied) C.TNC-CAR.Zip18R CAR-T cell of 2 donors were used for 2 in vitro experiments. In the first experiment, we did scRNA-seq for activated CAR-T cells. In the second experiment, the CAR-T cells of each donor were cocultured with tumor cells for 12 hrs, 24 hrs and 48 hrs. The CAR-T cells for each timepoints were extracted for scRNA-seq. Multiplexed 10x Genomics scRNA-seq were performed with a hashtag to label each sample.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34284

8 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) Natural killer (NK) cell function is markedly impaired in acute leukemia patients, weakening their antitumor immune response; however, the specific mechanisms underlying these functional deficits remain incompletely understood. Here, we reveal the critical role of glutathione (GSH) metabolism in maintaining NK cell homeostasis and function. Compared with healthy individuals, NK cells from acute leukemia patients exhibit markedly reduced GSH levels. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34284 GPL24676

14 Samples

Download data: XLSX

(Submitter supplied) Chromosomal rearrangements on the short arm of chromosome 8 cause 8p syndrome, a rare developmentaldisorder characterized by neurodevelopmental delays, epilepsy, and cardiacabnormalities.While significantprogress has been made in managing the symptoms of 8p syndrome and otherconditionscaused by large-scalechromosomalaneuploidies, no therapeutic approach has yet been demonstrated to target the underlyingdisease-causingchromosome.Here, we establish a two-step approachto eliminate theabnormalcopy ofchromosome 8and restore euploidy in cells derived from an individual with a complex rearrangement ofchromosome 8p.Transcriptomic analysis revealed 361 differentially expressed genes between the proband andthe euploid revertant, highlighting genes both within and outside the 8p region that may contribute to 8psyndrome pathology. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34284

12 Samples

Download data: TXT

(Submitter supplied) The regulation of RNA 5-methylcytosine (m5C) modification during the differentiation process of hPSC to the derived cardiomyocytes remains unclear, and the RNA m5C have been shown to enhance innate immune response and associated with tumor progression. The purpose of this study was to provide the RNA m5Cs profiles in human pluripotent stem cells and its derived cardiomyocytes by bsRNA-seq, which provides the positions and methylation levels for future studies.

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL18573 GPL34284

38 Samples

Download data: TXT, XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL34284 GPL24676

16 Samples

Download data: BIGWIG

(Submitter supplied) Human pluripotent stem cells (hPSCs) serve as powerful in vitro models to elucidate the molecular underpinnings of embryonic cell fate transitions. hPSCs can be maintained in two distinct states: a naïve state, corresponding to the pre-implantation epiblast, and a primed state, mirroring the post-implantation epiblast. Our research demonstrates that transposable elements act as sensitive indicators of these pluripotency states. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL34284

4 Samples

Download data: BIGWIG

(Submitter supplied) Glioblastoma (GBM) is defined by heterogenous and resilient cell populations that closely reflect neurodevelopmental cell types. While it is clear that GBM echoes early and immature cell states, identifying the specific developmental programs disrupted in these tumors has been hindered by a lack of high-resolution trajectories of glial and neuronal lineages. Here, we delineate the course of human astrocyte maturation to uncover discrete developmental stages and attributes mirrored by GBM. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL34284

101 Samples

Download data: XLSX

(Submitter supplied) The development of human induced pluripotent stem cell (iPSC)–based regenerative therapies is challenged by the lack of specific cell markers to isolate differentiated cell types and improve differentiation protocols. This issue is particularly critical for notochordal-like cells and chondrocytes, which are crucial in treating back pain and osteoarthritis, respectively. Both cell types produce abundant proteoglycan aggrecan (ACAN), crucial for the extracellular matrix. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34284

8 Samples

Download data: TSV

(Submitter supplied) Hypoxia is closely linked to chemotherapy resistance and accelerates breast cancer progression. However, the underlying mechanism of resistance to hypoxic chemotherapy remains uncertain. ZNF207 was identified as a differentially expressed gene involved in hypoxia and chemotherapy resistance by RNA-sequencing array. ZNF207 expression was elevated in lung, breast, liver, colon, and ovarian cancers, and its positive expression was correlated significantly with advanced TNM stage, lymph node metastasis, and poor prognosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34284

6 Samples

Download data: TXT

(Submitter supplied) Detachment of cancer cells from tumor, anchorage-independent survival, and maintenance of proliferative capacity upon reattachment are crucial steps in metastases formation. Better understanding of the underlying molecular mechanisms could help to improve targeted cancer therapies. We show reversible detachment of cancer cells using N-glycosylation inhibitors 2-deoxy-D-glucose (2DG) and tunicamycin, with re-attached cells retaining their proliferating capacity. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34284

30 Samples

Download data: TXT

(Submitter supplied) Natural products have a long history of providing potent probes into protein biosynthesis, with numerous molecules serving as valuable therapeutics. The marine natural product girolline has been described as an inhibitor of protein synthesis. Here, we demonstrate that it is not a general translation inhibitor but represents a sequence-specific modulator of translation factor eIF5A. Girolline interferes with ribosome-eIF5A interaction and induces ribosome stalling, primarily on AAA-encoded lysine. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL34284

12 Samples

Download data: TXT

(Submitter supplied) We found that RARG fusions selectively upregulated BCL2 and ATF3 in HSPCs, driving uncontrolled proliferation and disrupting the differentiation of RARG-AML cells.To investigate the mechanism how RARG fusions mediate activation of their downstream targets such as BCL2 and ATF3, we defined the chromatin accessibility using ATAC-seq assay in human CD34+ (hCD34+) cells with or without CPSF6::RARG or NUP98::RARG overexpression.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL34284

6 Samples

Download data: BW

(Submitter supplied) To understand how RARG fusion proteins regulate their target genes in the hematopoietic system, we overexpressed fusions or PML-RARA in hCD34+ cells and identified target genes that are regulated by RARG fusions. We found that RARG fusions selectively upregulated BCL2 and ATF3 in HSPCs, driving uncontrolled proliferation and disrupting the differentiation of RARG-AML cells.To investigate the mechanism how RARG fusions mediate activation of their downstream targets such as BCL2 and ATF3, we dected the epigenetic changes (H3K27ac, H3K4me1, and H3K4me3) associated with RARG fusions binding in hCD34+ cells overexpressing CPSF6::RARG and NUP98::RARG.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL34284

34 Samples

Download data: BW

(Submitter supplied) In this study, we isolated RNA from the whole blood of 19 patients who developed myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) following acute SARS-CoV-2 infection. We also isolated RNA from the whole blood of 17 healthy controls (HCs). We analyzed the genes that had differential expression between patients with ME/CFS and HCs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34284

36 Samples

Download data: TSV

(Submitter supplied) Perfluorooctanoic sulfonate (PFOS) is difficult to degrade and tends to accumulate in the body, which causes widespread concern. The expression of genes related to endometrial receptivity and the differentiation of human endometrial stromal cells (hESCs) were assessed in this study concerning PFOS. In this study, we investigated the effect of PFOS exposure on endometrial tolerance by cell and animal experiments. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34284

6 Samples

Download data: XLS

(Submitter supplied) The combination of CDK4/6 inhibitors (CDK4/6i) and endocrine therapy (ET) has significantly improved outcomes for patients with hormone receptor-positive (HR+) metastatic breast cancer. However, most patients eventually develop resistance, leading to treatment discontinuation. The therapeutic benefits of maintaining CDK4/6i or transitioning to CDK2 inhibitors (CDK2i) beyond disease progression remain unclear. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34284

8 Samples

Download data: TXT