GPL18573[RGSE] - GEO DataSets

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Select item 2002995531.

SPIDR enables multiplexed mapping of RNA-protein interactions and uncovers a mechanism for selective translational suppression upon cell stress

(Submitter supplied) RNA-binding proteins (RBPs) regulate all stages of the mRNA life cycle, yet current methods generally map RNA targets of RBPs one protein at a time. To overcome this limitation, we developed SPIDR (Split Pool Identification of RBP targets), a highly multiplexed split-pool method that profiles the binding sites of dozens of RBPs simultaneously. SPIDR identifies precise, single-nucleotide binding sites for diverse classes of RBPs. more...

Organism:: Homo sapiens

Type:: Other

Platforms:: GPL18573 GPL24676 GPL34295
4 Samples

Download data: BW, TXT

Series

Accession:: GSE299553

ID:: 200299553

Select item 2002947332.

Replicative and irradiation-induced senescence of endothelial cells

(Submitter supplied) This research investigates cellular senescence in human umbilical vein endothelial cells (HUVECs), focusing on their implications for cardiovascular diseases. We employed RNA sequencing to analyze gene expression changes in HUVECs subjected to replicative- or stress-induced senescence via ionizing radiation. Our findings reveal that both senescence types exhibit significant upregulation of genes associated with epithelial-mesenchymal transition (EMT) and inflammatory pathways, indicating a shared molecular response. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
9 Samples

Download data: TSV

Series

Accession:: GSE294733

ID:: 200294733

PubMed

Select item 2002940023.

Transcriptomic analyses of ovarian clear cell carcinoma sphe-roids reveal distinct proliferative phenotypes and therapeutic vulnerabilities

(Submitter supplied) Cancer cell spheroids autonomously form in the ascites fluid and are considered a conduit for epithelial ovarian cancer metastasis within the peritoneal cavity. Spheroids are homotypic, avascular, 3D structures that acquire resistance to anoikis to remain viable after cellular detachment. We used in vitro spheroid model systems to interrogate pathways critical for spheroid cell proliferation, distinct from those driving monolayer cancer cell proliferation. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
8 Samples

Download data: CSV

Series

Accession:: GSE294002

ID:: 200294002

PubMed

Select item 2002801204.

PCK1 loss contributes to kidney disease progression by altering mitochondrial fitness through its cataplerotic function [snRNA-seq_Human]

(Submitter supplied) Metabolic alterations are recognized as key features of kidney injury, but their causal role in kidney repair remains a topic of debate. We investigate the role of PCK1, an enzyme involved in gluconeogenesis and cataplerosis, i.e. the removal of TCA intermediates from the mitochondrial matrix, in kidney disease. We demonstrate that PCK1 loss leads to injured mitochondria with decreased respiration and TCA metabolites accumulation. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
6 Samples

Download data: RDS

Series

Accession:: GSE280120

ID:: 200280120

Select item 2002791615.

p63 and ZNF148 cooperate to regulate head and neck squamous cell carcinoma

(Submitter supplied) Head and neck squamous cell carcinoma (HNSCC) is a common and aggressive malignancy. While significant advances have been made in the management of low-grade cancer, treatment of advanced HNSCC remains challenging. Here, we used a proteomic approach to discover novel binding partners of the oncogene p63, the most frequently amplified transcription factor in HNSCC. We identified a zinc finger protein, ZNF148, which is coexpressed and physically binds p63 in carcinoma cells. more...

Organism:: Homo sapiens

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

Platform:: GPL18573
3 Samples

Download data: BW, NARROWPEAK

Series

Accession:: GSE279161

ID:: 200279161

Select item 2002703206.

Profiling of Circulating extracellular vesicles microRNAs Reveals Diagnostic Potential and Pathways in Non-Obstructive and Obstructive Azoospermia

(Submitter supplied) The accurate diagnosis of non-obstructive azoospermia (NOA) and obstructive azoospermia (OA) is crucial for selecting appropriate clinical treatments. This study aimed to investigate the pivotal role of miRNAs in circulating plasma exosomes in distinguishing between NOA and OA, as well as uncovering the signaling pathways involved in azoospermia pathogenesis. In this study, differential expression of extracellular vesicles (EVs) miR-513c-5p and miR-202-5p was observed between NOA and OA patients, while the selenocompound metabolism pathway was identified as relevant to azoospermia pathogenesis through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. more...

Organism:: Homo sapiens

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL18573
9 Samples

Download data: TXT, XLSX

Series

Accession:: GSE270320

ID:: 200270320

Select item 2002702547.

The quantitative impact of 3′UTRs on gene expression

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

Organism:: Escherichia coli; Homo sapiens

Type:: Other; Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

4 related Platforms
118 Samples

Download data

Series

Accession:: GSE270254

ID:: 200270254

Select item 2002702528.

The quantitative impact of 3′UTRs on gene expression [amplicon-seq]

(Submitter supplied) Control of gene expression is fundamental to biology, and post transcriptional regulation is an important component of this process. In mammals, the 3′UTR in particular serves as a major source of regulatory information within the transcript. Here, we developed an accurate, high throughput, reporter based system to evaluate the impact of >1,400 full length human 3′UTRs on RNA stability, translational regulation, and total protein output. more...

Organism:: Homo sapiens

Type:: Other

Platforms:: GPL18573 GPL24676
99 Samples

Download data: TSV

Series

Accession:: GSE270252

ID:: 200270252

Select item 2002702499.

The quantitative impact of 3′UTRs on gene expression [miRNA-seq]

Organism:: Homo sapiens

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL18573
4 Samples

Download data: TSV

Series

Accession:: GSE270249

ID:: 200270249

Select item 20027024710.

The quantitative impact of 3′UTRs on gene expression [PRO-seq]

Organism:: Homo sapiens

Type:: Other

Platform:: GPL18573
5 Samples

Download data: TSV

Series

Accession:: GSE270247

ID:: 200270247

Select item 20028381211.

Epigenetic coordination of transcriptional and translational programs in hypoxia. [RNA-Seq, 2]

(Submitter supplied) Stress adaptation entails perturbations in transcriptional and post-transcriptional mechanisms of regulation of gene expression, but how these programs are coordinated remains largely unknown. To address this, we systematically interrogated the effects of hypoxia on transcriptomes, epigenomes and translatomes of T47D breast cancer cells and H9 human embryonic stem cells. This revealed that hypoxia-induced alterations in H3K4me3 exert unexpectedly minimal effects on transcript abundances. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
8 Samples

Download data: TXT

Series

Accession:: GSE283812

ID:: 200283812

Select item 20026864612.

Functional phenotyping of genomic variants using multiomic scDNA-scRNA-seq

(Submitter supplied) Genomic variation ranging from single nucleotide polymorphisms to structural variants in both coding and non-coding regions can impact gene function and expression, contributing to disease mechanisms such as cancer progression. Current precision editing tools to study variants systematically have limited efficiency and variable outcomes in mammalian cells. Additionally, assessing heterogenous variants in primary tumor samples at scale is challenging with current single-cell technologies. more...

Organism:: Homo sapiens; Mus musculus

Type:: Expression profiling by high throughput sequencing; Other

4 related Platforms
17 Samples

Download data: MTX, TSV

Series

Accession:: GSE268646

ID:: 200268646

Select item 20026422713.

Effect of pharmacological inhibition of SMYD3 on gene expression in patient-derived CRC-SCs

(Submitter supplied) Cancer stem cells (CSC) are responsible for colorectal cancer (CRC) chemoresistance, recurrence, and metastasis. Therefore, it has become crucial finding critical molecular stemness targets that are essential for tumor growth. Here, we performed an extensive in vitro and in vivo molecular and functional characterization revealing the pivotal role of SMYD3 in CSC biology. Specifically, SMYD3 interacts with and methylates c-MYC at K158 and K163, modulating its transcriptional activity implicated in stemness and colorectal malignancy. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
42 Samples

Download data: TXT

Series

Accession:: GSE264227

ID:: 200264227

Select item 20026415714.

Effect of stable genetic ablation and pharmacological inhibition of SMYD3 on gene expression in CRC cell line (HCT-116)

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
12 Samples

Download data: TXT

Series

Accession:: GSE264157

ID:: 200264157

Select item 20024341815.

Epigenetic coordination of transcriptional and translational programs in hypoxia.

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

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other

Platforms:: GPL24676 GPL16791 GPL18573
115 Samples

Download data: CDF, NARROWPEAK, TXT

Series

Accession:: GSE243418

ID:: 200243418

Select item 20029966316.

Effects of alcohol on the transcriptome, methylome, and metabolome of in vitro gastrulating human embryonic cells

(Submitter supplied) Prenatal alcohol exposure (PAE) affects embryonic development, causing a variable fetal alcohol spectrum disorder (FASD) phenotype with neurodevelopmental disorders and birth defects. To explore the effects of PAE on gastrulation, we used an in vitro model with subchronic moderate (20 mM) and severe (70 mM) ethanol exposures during the differentiation of human embryonic stem cells into germ layer cells. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
2 Samples

Download data: TXT, XLSX

Series

Accession:: GSE299663

ID:: 200299663

Select item 20028360017.

LINE-1 transposable elements regulate the exit of human pluripotency and early brain development

(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; Other

Platforms:: GPL18573 GPL26167 GPL24676
83 Samples

Download data: BW, CSV, MTX, TSV

Series

Accession:: GSE283600

ID:: 200283600

Select item 20028323518.

Inducible re-epithelialization of cancer cells increases autophagy and DNA damage: implications for breast cancer dormancy

(Submitter supplied) Epithelial lineage differentiation is pivotal to mammary gland development and it can pause metastasis of breast cancer (BC) by inducing tumor dormancy. To simulate this, we expressed epithelial genes in mesenchymal BC cells. Inducible expression of the epithelial OVOL genes in metastatic BC cells suppressed proliferation and migration. We found that C1ORF116, an OVOL’s target, is susceptible to genetic and epigenetic aberrations in BC. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
8 Samples

Download data: XLSX

Series

Accession:: GSE283235

ID:: 200283235

PubMed

Select item 20028146219.

Dissecting Non-Coding GWAS Loci with High-Resolution 3D Chromatin Interactions Reveals Causal Genes with Relevance to Heart Failure [ATAC-seq]

(Submitter supplied) Heart failure is caused in part by cardiac remodeling processes that include the death of cardiac myocytes and their replacement by cardiac fibroblasts. We hypothesized that these two cell types may harbor epigenetic contexts in which heart disease-associated non-coding SNPs perturb gene expression relevant to disease. Accordingly, we generated high-resolution Hi-C data layered with functional genomic information to annotate and link putative distal regulatory elements in heart disease-associated loci to gene promoters. more...