Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of depletion of NUP153 on gene expression in esophageal squamous cell carcinoma cell line TE5 cells [RNA-seq]

ABSTRACT: To investigate the function NUP153 in the regulation of cancer cell biology, we established TE5 cell lines in which NUP153 gene has been knocked down by shRNA.

ORGANISM(S): Homo sapiens

PROVIDER: GSE200714 | GEO | 2023/04/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Effect of depletion of NUP153 on gene expression in esophageal squamous cell carcinoma cell line TE5 cells [RNA-seq]

Project description:Effect of depletion of NUP153 on gene expression in esophageal squamous cell carcinoma cell line TE5 cells [RNA-seq]

| PRJNA826343 | ENA

Effect of depletion of USP36 on gene expression of ECA109 cells, esophageal squamous cell carcinoma cell line.

Project description:To investigate the function of USP36 in the regulation of cell proliferation and escc progression, we established eca109 cell lines in which each target gene has been knocked down by siRNA.We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different cells at same time points.

2023-01-04 | GSE206845 | GEO

Transcriptional profiling of Drosophila melanogaster cell lines S2 and Kc with Nup153 RNAi-mediated depletion.

Project description:Expression profiling of Nup153 RNAi-mediated depletion in Drosophila S2 and Kc cells. This experiment is related to experiment E-MEXP-2525.

2010-02-12 | E-MEXP-2523 | biostudies-arrayexpress

Nucleoporin Nup153 Regulates Stem Cell Pluripotency through Gene Silencing

Project description:Nucleoporins (Nups) are a family of proteins best known as the constituent building blocks of nuclear pore complexes (NPCs), the transport channels that mediate nuclear transport. Recent evidence suggest that several Nups have additional roles in controlling the activation and silencing of developmental genes, however, the mechanistic details of these functions remain poorly understood. Here, we show that depletion of Nup153 in mouse embryonic stem cells (mESCs) causes the de-repression of developmental genes and induction of early differentiation. This loss of pluripotency is not associated with defects in global nucleo-cytoplasmic transport activity. Instead, Nup153 binds to the transcriptional start site (TSS) of developmental genes and mediates the recruitment of the polycomb repressive complex 1 (PRC1) to its target loci. Our results reveal a nuclear transport-independent role of Nup153 in maintaining stem cell pluripotency and introduce a role of NPC proteins in mammalian epigenetic gene silencing. RNA-seq, ChIP-Seq, and DamID-Seq for Nup153, Oct4, and key chromatin regulators in mouse ES cells and neural progenitors

2015-06-19 | E-GEOD-64008 | biostudies-arrayexpress

Genomic characterization of a newly established esophageal squamous cell carcinoma cell line from China and published esophageal squamous cell carcinoma cell lines.

Project description:Background:Esophageal squamous cell carcinoma (ESCC) is one of the most prevalent malignancies and a major cause of cancer related death worldwide, especially in China. Cell lines are widely used disease models for basic medical research, however, well characterized ESCC cell models from China were seldom reported. Misidentifying and cross-contaminations of cell lines also hamper the way of producing solid and reproductive data. Methods:CSEC216 was originated from a 45-year-old male ESCC patient from Chaoshan littoral, China. Specimens were minced into fragments and seeded in T-25 flask for primary culture. Immunoflourescence staining was performed for identifying the origination and proliferation activity. In vitro migration and invasion abilities was tested by transwell assay. DNA Short Tandem Repeats profiling was implemented for cell authorization. Karyotype was investigated by spectrum karyotyping. Whole genome sequencing was utilized to investigate genomic alterations. Background information and genomic mutation data of published ESCC cell lines were obtained from online databases. Results:CSEC216 was an uncontaminated cell line, exhibited epithelial cell features with polygonal morphology and adherent growth as monolayer. Immuno staining demonstrated its epithelial origination and high proliferation rate. The Population Doubling time was 29.7 h. The karyotype demonstrated tumor cell patterns with aneuploidy and complex chromosomal aberrations. Mutation signatures, genes with SNA or CNA of CSEC216 and published ESCC cell lines were similar with the mutation spectrum of original ESCC tumors. Conclusions:ESCC cell line CSEC216 from high incidence region in China was established with no cross-contamination. Biological features were studied. Genomic mutation features of CSEC216 and 28 ESCC cell lines were characterized which provided thorough cytogenetic background that facilitated future usage.

| S-EPMC7247234 | biostudies-literature

Nup153 defines neural identity through cooperative transcriptional control with Sox2

Project description:Through RNA interference and genome-wide Nup153 binding studies, we found that Nup153 and Sox2 bind and co-regulate hundreds of genes. Furthermore, we found that Nup153 exhibits binding location dependent spatially distinct transcriptional control by differentially regulating expression when bound to the promoter region or to the transcription end site (TES). These results establish Nup153 not only as a novel transcriptional co-regulator of Sox2 but also as a key player in the regulation of cell fate by directly modulating gene expression.

2017-09-14 | GSE99783 | GEO

Nucleoporin Nup153 Regulates Stem Cell Pluripotency through Gene Silencing

2015-06-19 | GSE64008 | GEO

Effect of depletion of RBM4 on gene expression of esophageal squamous cell carcinoma cell KYSE150

Project description:To explore the role of RBM4 in esophageal squamous cell carcinoma cell,we performed high-throughput mRNA sequencing (mRNA-seq) in KYSE150 with stable knockdown of RBM4 by shRNA . We then performed gene expression profiling analysis using data obtained from RNA-seq of KYSE150 cells,three replicates were sequenced.

2023-04-26 | GSE220613 | GEO

Gene expression profile of human esophageal squamous carcinoma cell line TE-1.

Project description:Esophageal squamous cell carcinoma (ESCC) is one of the most common and deadly causes of cancer worldwide. However, to date, the mechanisms underlying its pathogenesis remain unclear. The present study investigated the gene expression profile of human esophageal cancer cell line TE-1, a cell model for ESCC, to gain insight to the genetic regulation of this disease. Human esophageal cancer TE-1 cells and normal esophageal HET-1A cells were cultured for isolation of total RNA. Differential expression of RNA transcripts was assessed using the Agilent 4×44 K microarray, combined with real-time PCR (qRT-PCR) for validation. Classification and function of the differential genes were illustrated by bioinformatics processing including hierarchical clustering and gene ontology (GO) analysis. We identified 4,986 transcripts with differential expression (fold-change ≥1.5, P<0.05), including 2,368 up-regulated and 2,618 down-regulated transcripts. GO analysis showed that the dysregulated transcripts were associated with biological process, cellular component, and molecular function. After bioinformatic analysis of significantly regulated signaling pathways, we found these transcripts may target 35 gene pathways, including p53 signaling, glioma, ubiquitin-mediated proteolysis, insulin signaling, cell cycle, inositol phosphate metabolism, mTOR signaling, and MAPK signaling. The differentially expressed transcripts were screened between the esophageal cancer cell line TE-1 and normal esophageal cell line HET-1A, as well as their target gene pathways. Further data mining is related to prevention and treatment of esophageal cancer.

| S-EPMC4613095 | biostudies-literature