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RNA-seq of LS180 cells

ABSTRACT: A combination of ribosome profiling and RNA-seq was used to analyze the translatome of LS180 colon adenocarcinoma cells

ORGANISM(S): Homo sapiens

PROVIDER: GSE211535 | GEO | 2024/06/30

REPOSITORIES: GEO

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Ribosome profiling of LS180 cells

Project description:A combination of ribosome profiling and RNA-seq was used to analyze the translatome of LS180 colon adenocarcinoma cells

2024-06-30 | GSE211536 | GEO

Ribosome profiling of LS180 cells

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RNA-seq of LS180 cells treated with Rifampicin or SR12813

Project description:Abstract: SR12813 is an experimental cholesterol-lowering drug that reduces intracellular cholesterol through accelerated proteasomal degradation of 3-hydroxy-3-methylglutaryl-coenzyme A reductase and is also recognized as a prototypical activator of the pregnane X receptor (PXR, NR1I2). Rifampicin, a clinically used antibiotic, likewise functions as a human PXR agonist. Although PXR-mediated induction of drug metabolism genes has been extensively characterized in hepatocytes and humanized mouse liver, comparatively little is known about the transcriptional effects of these ligands in intestinal and colon cancer cells. Here, we employed RNA sequencing in LS180 colon adenocarcinoma cells to compare transcriptional responses elicited by SR12813 and Rifampicin. LS-180 cells were treated for 48 hours with DMSO, Rifampicin or SR12813.

2025-12-29 | E-MTAB-16299 | biostudies-arrayexpress

RNA-seq of LS180 cells

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Transcription profiling of human colon cancer cell lines LS180 (MSI+) and SW480 (MSI-)

Project description:Inhibition of the nonsense mediated decay (NMD) mechanism in cells results in stabilization of transcripts carrying premature translation termination codons. A strategy referred to as gene indentification by NMD inhibition (GINI) has been proposed to identify genes carrying nonsense mutations (Noensie & Dietz, 2001). Genes containing frameshift mutations in colon cancer cell line have been identifying mutatnt genes using GINI, we have now further improved the strategy. In this approach, inhibition of NMD with emetine is complemented with inhibiting NMD by blocking the phosphorylation of the hUpf1 protein with caffeine. In addition, to enhance the GINI strategy, comparing mRNA level alterations produced by inhibiting transcription alone or inhbiiting transcription together with NMD following caffeine pretreatment were used for the efficient identification of false positives produced as a result of stress response to NMD inhibition. To demonstrate the improved efficiency of this approach, we analyzed colon cancer cell lines showing microstellite instability. Bi-allelic inactivating mutations were found in the FXR1, SEC1L1, NCOR1, BAT3, PHD14, ZNF294, C190ORF5 genes as well as genes coding for proteins with yet unknown functions. Experiment Overall Design: Using GINI2 as a method of identifying novel biallelic truncating mutations in MSI+ colon cancer cells, various treatment conditions were applied to cultured colon cancer cell lines LS180 (MSI+) and SW480 (MSI-) and gene expression profiling was measured using Affymetrix GeneChip U133 Plus 2 arrays.

2008-06-13 | E-GEOD-5486 | biostudies-arrayexpress

Cell lines LS180 vs U937

Project description:Dr. Esko's laboratory focuses on the structure, function, and biosynthesis of glycoproteins and proteoglycans. This laboratory also works on the design and synthesis of small molecule inhibitors of glycosylation. We analyzed the expression patterns of glycosyltransferase, growth factors, and receptors in endothelial cells derived from NDST1 deficient and wild-type mice using cancer cell line types U937 and LS180 .

2011-02-17 | E-GEOD-27351 | biostudies-arrayexpress

Alterations in total and in polysomal mRNA fraction in response to expression of RNA binding motif protein 35A

Project description:The gene coding for RNA binding motif protein 35A (RBM35A) is inactivated by frameshift mutations in an LS180 colon carcinoma cell line and in approximately in 50% of colon tumors with microsatellite instability. To get insight into the mechanism of action of these putative tumor suppressor gene we expressed functional copy of the RBM35A cDNA in the LS180 cells. We analyzed alterations in mRNA profiles in total and in polysomal fraction of mRNA in LS180 cells in response to expressing RBM35A gene under Tet off tetracycline inducible promoter.

2008-10-16 | GSE13171 | GEO

RNA-seq of LS180 cells treated with Rifampicin or SR12813

Project description:RNA-seq of LS180 cells treated with Rifampicin or SR12813

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SOX9-BAF multi-omics profiling in human colon cancer cell models

Project description:This study combines matched ATAC-seq, RNA-seq, and CUT&RUN profiling in human colon cancer cell models to track SOX9 degradation/recovery, BAF subunit perturbation, histone-mark occupancy, ARID1A/ARID1B knockdown, and SOX9-variant chromatin accessibility. The main time-course series uses HT29-dTAG cells; the SOX9-variant ATAC-seq subset uses LS180 cells.

2026-06-16 | GSE335210 | GEO

Ribosome profiling of Streptomyces griseus NBRC13350 and Streptomyces venezuelae ATCC15439

Project description:We performed ribosome profiling which is the deep-sequencing of mRNA fragments protected by translating ribosome for two Streptomyces species through different growth phases to provide the translatome data

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