txid9443[Organism] - GEO DataSets

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Select item 2002807671.

Adenine base editors induce off-target structure variations in mouse embryos and primary human T cells

(Submitter supplied) Background The safety of CRISPR-based gene editing methods is of the utmost priority in clinical applications. Previous studies have reported that Cas9 cleavage induced frequent aneuploidy in primary human T cells, but whether cleavage-mediated editing of base editors would generate off-target structure variations remains unknown. Here, we investigated the potential off-target structural variations associated with CRISPR/Cas9, ABE and CBE editing in mouse embryos and primary human T cells by whole-genome sequencing and single-cell RNA-seq analyses. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
2 Samples

Download data: MTX, TSV

Series

Accession:: GSE280767

ID:: 200280767

Select item 2002804492.

CoREST Complex Inhibition Alters RNA Splicing to Promote Neoantigen Expression and Enhance Tumor Immunity [RNA-seq]

(Submitter supplied) Epigenetic macromolecular enzyme complexes tightly regulate gene expression at the chromatin level and have recently been found to colocalize with RNA splicing machinery during active transcription1; however, the precise functional consequences of these interactions are uncertain. Here, we identify unique interactions of the CoREST repressor complex (LSD1-HDAC1-CoREST) with components of the RNA splicing machinery and their functional consequences in tumorigenesis. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL20301
24 Samples

Download data: TXT

Series

Accession:: GSE280449

ID:: 200280449

Select item 2002804483.

CoREST Complex Inhibition Alters RNA Splicing to Promote Neoantigen Expression and Enhance Tumor Immunity [PRO-seq]

Organism:: Homo sapiens

Type:: Other

Platform:: GPL24676
4 Samples

Download data: BEDGRAPH

Series

Accession:: GSE280448

ID:: 200280448

Select item 2002804474.

Gene expression of exosomes from human umbilical cord mesenchymal stem cells

(Submitter supplied) To determine the gene expression of exosomes in human umbilical cord mesenchymal stem cells

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
3 Samples

Download data: CSV

Series

Accession:: GSE280447

ID:: 200280447

Select item 2002802525.

Genome-wide mapping of human SMYD3 and H3K4me3 in the HN-6 (control) and 5-3 (SMYD3 KO) HPV-negative head and neck squamous cell carcinoma cell line.

(Submitter supplied) We used CUT&RUN to evaluate the genome-wide mapping of human SMYD3 and H3K4me3 in HN-6 and 5-3 (SMYD3 KO) cells.

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL30173
9 Samples

Download data: BED, BIGWIG

Series

Accession:: GSE280252

ID:: 200280252

Select item 2002802516.

RNA-seq of HN-6 (control) and 5-3 (SMYD3 KO) cell lines.

(Submitter supplied) We used RNA-seq to evaluate the transcriptomic changes induced by permanent SMYD3 KO in the HPV-negative head and neck squamous cell carcinoma cell lines HN-6.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
6 Samples

Download data: CSV

Series

Accession:: GSE280251

ID:: 200280251

Select item 2002800487.

Preconditioning With Electrical Stimulation Promotes Flap Survival by Improving Blood Supply Via ROS/Nrf2/HO1 Pathway

(Submitter supplied) We have previously demonstrated that preconditioning flap donor with electrical stimulation (ES) could increase the survival area of pedicled perforator flaps in a rat model. However, the detailed molecular mechanisms remain unclear. In this study, we first verified the effects of ES through in vivo and in vitro experiments. Then we explored the underlying mechanisms in vitro. The results indicated that preconditioning with ES could not only increase the flap survival area but mitigate human umbilical vein endothelial cells (HUVECs) dysfunction. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
6 Samples

Download data: TXT

Series

Accession:: GSE280048

ID:: 200280048

Select item 2002799828.

DNA Methylation Biomarkers for Cervical Cancer Risk Prediction in HIV-Positive Nigerian Women

(Submitter supplied) Cervical cancer (CC) remains a significant public health issue in low- and middle-income countries (LMICs), especially in Western sub-Saharan Africa and Nigeria. While global CC incidence and mortality have declined, these regions continue to face high rates due to inadequate screening and the high prevalence of HIV, which increases CC risk by promoting persistent HPV infections. This study aimed to identify DNA methylation (DNAm) biomarkers for cervical intraepithelial neoplasia (CIN) and CC in HIV-positive Nigerian women and to assess their potential for clinical risk prediction. more...

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL21145
576 Samples

Download data: IDAT, TXT

Series

Accession:: GSE279982

ID:: 200279982

Select item 2002799039.

α4 Blockade Reduces CD8 TEM Cells in the Brain and Elevates CNS Viral Loads

(Submitter supplied) Background. The blood-brain barrier (BBB) regulates immune cell entry into the CNS, and various strategies have been developed to target this barrier in efforts to alleviate neuroinflammation in neurodegenerative diseases. α4β1 is crucial for T cell influx into the CNS. In the context of HIV, CD4 T cells drive viral infiltration, while CD8 T cells are essential for viral clearance. This dual role complicates strategies aimed at targeting T cell entry during HIV infection, yet it remains an area that has not been thoroughly explored. more...

Organism:: Macaca mulatta; blank sample

Type:: Other

Platforms:: GPL29487 GPL27943
288 Samples

Download data: DCC, PKC, TIFF

Series

Accession:: GSE279903

ID:: 200279903

Select item 20027946410.

Cytotoxic and Molecular Effects of Soil Extracts from the Agbogbloshie Electronic-Waste Site on Fish and Human Cell Lines.

(Submitter supplied) Effect-based methods (EBM) are of growing interest in environmental monitoring programs. Few EBM have incorporated transcriptomics even though these provide a wealth of biological information and can be modeled to yield transcriptomic points of departure (tPODs). The study objectives were to: A) characterize cytotoxic effects of soil extracts on the rainbow trout RTgill-W1 and the human Caco-2 cell lines; B) measure gene expression changes and calculate tPODs; and C) compare in vitro responses to available measures of plastic-related compounds and metals. more...

Organism:: Oncorhynchus mykiss; Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL29994 GPL24676
552 Samples

Download data: TXT

Series

Accession:: GSE279464

ID:: 200279464

Select item 20027928911.

Mast cell heterogeneity in human nasal polyps

(Submitter supplied) Mast cells (MCs) expressing a distinctive protease phenotype (MCTs) selectively expand within the epithelium of human mucosal tissues during type 2 (T2) inflammation. While MCTs are phenotypically distinct from subepithelial MCs (MCTCs), signals driving human MCT differentiation and this subset’s contribution to inflammation remain unexplored. Here, we identify TGF-b as a key driver of the MCT transcriptome in nasal polyps. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
4 Samples

Download data: H5, RDS

Series

Accession:: GSE279289

ID:: 200279289

Select item 20027875712.

Tumor-intrinsic kinome landscape of pancreatic cancer reveals new therapeutic approaches

(Submitter supplied) Effective therapies for pancreatic ductal adenocarcinoma (PDAC) have been largely elusive. Prior proteogenomic studies of PDAC have been limited to bulk samples limiting the ability to define tumor-intrinsic targets and understanding tumor heterogeneity. Here, we perform Multiplexed kinase Inhibitor Beads and Mass Spectrometry (MIB-MS) on 102 patient derived xenografts (PDX) derived from 14 unique primary PDAC to define the tumor-intrinsic kinome landscape. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL24676 GPL18573
88 Samples

Download data: CSV

Series

Accession:: GSE278757

ID:: 200278757

Select item 20027683913.

Connecting Transcriptomics with Computational Modeling to Reveal Developmental Adaptations in Pediatric Human Atrial Tissue

(Submitter supplied) Nearly 1% of babies are born with congenital heart disease (CHD) – many of whom will require heart surgery within the first few years of life. A detailed understanding of cardiac maturation can help to expand our knowledge on cardiac diseases that develop during gestation, identify age-appropriate drug therapies, and inform clinical care decisions related to surgical repair and postoperative management. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL23159
117 Samples

Download data: CEL

Series

Accession:: GSE276839

ID:: 200276839

Select item 20027683714.

Type III interferons induce pyroptosis in gut epithelial cells and impair tissue repair upon intestinal injury.

(Submitter supplied) Tissue damage and repair are hallmarks of the inflammatory process. Despite a wealth of information on the mechanisms that govern tissue damage, mechanistic insight on how inflammatory mediators affect repair is lacking. Here, we investigated how interferons influence tissue repair after damage to the intestinal mucosa driven by inflammation or genotoxicity. We found that type III, but not type I or II, interferons delay epithelial cell regeneration by inducing the upregulation of Z-DNA-binding protein 1 (ZBP1). more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL23934
15 Samples

Download data: CHP, CSV

Series

Accession:: GSE276837

ID:: 200276837

Select item 20027647915.

ZNF350 gene polymorphisms promote the response to Peg-IFNα therapy through JAK-STAT signaling pathway in patients with chronic hepatitis B

(Submitter supplied) The varying individual responses to Peg-IFNα in patients with CHB pose significant hurdles in treatment optimization, and the underlying mechanisms remain unclear. We aimed to identify genetic polymorphisms influencing the efficacy of Peg-IFNα in patients with HBeAg-positive CHB，with the goal to predict Peg-IFNα response before treatment.

Organism:: Homo sapiens

Type:: Genome variation profiling by array

Platform:: GPL33106
124 Samples

Download data: XLSX

Series

Accession:: GSE276479

ID:: 200276479

Select item 20027632216.

Spatial tumor immune heterogeneity facilitates subtype co-existence and therapy response via AP1 dichotomy in pancreatic cancer [ChIP-seq]

(Submitter supplied) Pancreatic ductal adenocarcinoma (PDAC) displays a high degree of spatial subtype heterogeneity. This intratumoral co-existence of classical and basal-like programs is evident in multi-scale transcriptomic and spatial analyses of resected, advanced-stage and chemotherapy-treated specimens and reciprocally linked to a diverse stromal immune microenvironment as well as worse clinical outcome. However, the underlying mechanisms of intratumoral subtype heterogeneity remain largely unclear. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL28038
11 Samples

Download data: NARROWPEAK

Series

Accession:: GSE276322

ID:: 200276322

Select item 20027593617.

BACH2 Controls Seeding and Establishment of Long-Lived HIV-1 Reservoir in CD4+ T cells

(Submitter supplied) Despite antiretroviral therapy, HIV mainly persists in memory CD4+ T cells in people living with HIV. Most long-lived viral reservoir cells are infected near the time of therapy initiation. A better understanding of the early events in reservoir seeding presents opportunities for preventing latent reservoir formation. Here, we demonstrated that CD4+ T cells expressing CCR5, permissive to HIV-1 infection, are effector or terminally differentiated cells. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
8 Samples

Download data: TXT

Series

Accession:: GSE275936

ID:: 200275936

Select item 20027476118.

MiR-335-5p escaped from circKIAA0586 adsorption contributes to mechanical overloading-induced cartilage degeneration by targeting HELLS (circRNA-Seq)

(Submitter supplied) Mechanical overload is essential to cartilage degeneration during osteoarthritis (OA) development. Recent studies have confirmed that circular RNAs (circRNAs) are mechanically sensitive and that the circRNA-associated competitive endogenous RNA (ceRNA) network regulates cartilage degeneration and OA development. However, the involvement of the circRNA-associated ceRNA network in chondrocyte senescence induced by mechanical overloading remains unestablished.Here,we examined the circRNA, miRNA and mRNA expression of chondrocytes subjected to mechanical overloading.