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Next generation sequencing facilities quantitative analysis of ASAP2 knockout or wild-type Panc1 and MiaPaCa2 cells

ABSTRACT: To assess potential gene expression changes by ASAP2 individual knockout in Panc1 and MiaPaCa2 cells, we performed a transcriptomic analysis using high throughput RNA sequencing (RNA-seq).

ORGANISM(S): Homo sapiens

PROVIDER: GSE149359 | GEO | 2020/04/27

REPOSITORIES: GEO

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Next generation sequencing facilities quantitative analysis of ASAP2 knockout or wild-type Panc1 and MiaPaCa2 cells

Project description:Next generation sequencing facilities quantitative analysis of ASAP2 knockout or wild-type Panc1 and MiaPaCa2 cells

| PRJNA628186 | ENA

Transcriptome profiling of human pancreatic cancer cell line Panc1, MiaPaCa2, AsPC1 transfected with NFATc1-siRNA against siRNA of scrambled sequence

Project description:Genome-wide studies on pancreatic adenocarcinoma (PDAC) have indicated that numerous genes involved in carcinogenesis are highly methylated in their promoter regions but nevertheless strongly transcribed. It has been proposed that transcription factors may specifically bind to methylated promoters and up-regulate transcription. Screening a protein microarray presenting 658 transcription factors, we found that molecules of the NFAT (Nuclear Factor of Activated T-Cells) family preferentially bound to methylated promoter sequences. One family member – NFATc1 – was also strongly expressed in PDAC compared to control samples. To further identify targets of NFATc1 and study involved pathways, we have used siRNA to knockdown NFATc1 in three pancreatic cancer cell lines (Panc1, MiaPaCa2, AsPC1) with the help of the illumina beadchip arrays and we compared the transcriptional profiles of the cell lines under different knockdown conditions. We identify ALDH1A3 as direct targets of NFATc1, that NFATc1 binds the methylated promoter of ALDH1A3 and accelerate PDAC progression.

2021-11-05 | E-MTAB-10122 | biostudies-arrayexpress

Next generation sequencing facilities quantitative analysis of SHARPIN knockout or non-target LoVo cells

Project description:Colorectal cancer (CRC) is one of the most common cancers and a major cause of cancer mortality worldwide. Further improvements are needed for the treatment of CRC. The E3 ubiquitin ligase is an enzyme that plays an important role in regulating protein expression levels via posttranslational ubiquitin-mediated proteolysis, and it is reportedly involved in the progression of various cancers, making it a target of recent interest in anticancer therapy. In this study, using comprehensive expression analysis involving spatial transcriptomic analysis with single-cell RNA sequencing in clinical CRC datasets, we identified the ubiquitin-associated protein Shank-associated RH domain interactor (SHARPIN) as a putative driver gene located on amplified chromosome 8q. SHARPIN was overexpressed in tumor cells, and high expression of SHARPIN in tumor tissues was positively correlated with lymphatic invasion and was independently predictive of a poor prognosis in CRC patients. In vitro and in vivo analyses using SHARPIN-overexpressing or -knockout CRC cells revealed that SHARPIN upregulated MDM2, resulting in subsequent downregulation of p53, which inhibits tumor cell apoptosis and promotes tumor growth in CRC. Furthermore, SHARPIN overexpression and significant effects on survival were observed in various cancers. In conclusion, SHARPIN is a novel driver gene that potentially promotes tumor growth following apoptosis inhibition in part by inhibiting p53 expression via MDM2 upregulation; therefore, SHARPIN represents a potential therapeutic target for CRC.

2024-02-14 | GSE255286 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Nrl-/- Retinal Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) will be used to quantify whole transcriptome changes during genetic perturbations and viral infections Methods: RNA was harvested in Trizol 488 (Thermo Fisher). RNA was extracted using the manufacturer’s protocol and quantified by nanodrop. PANC1 wild-type or ARID1A knockout total RNA was sequenced by The Centre for Applied Genomics (TCAG) at The Hospital for Sick Children (Toronto, Canada) using the Illumina HiSeq2500 platform to generate single-end 100 bp reads. Adapters were trimmed using Trimmomatic and adapter-free reads were mapped to the human genome (hg19). Results: We have identified ARID1A KO to make cells more suceptible to viral infection due to decreased basal level of expression of ISGs Conclusions: Our study represents the first look at the role of ARID1A in the context of viral infection.

2021-12-16 | GSE189281 | GEO

Next Generation Sequencing Facilities Quantitative Analysis of Wild type iNKT cells at stage2 and stage3 transcriptomes

Project description:Purpose:Next Generation Sequencing applying for compare the iNKT cells at stage2 and stage3 distict transcriptome, included pathway-enrichment analysis and genes expression of interests Methods:iNKT cells at stage2 and stage3 were isolated from thymus in 6 week old wild type mice by cell sorting. RNA was extracted, purified and checked for integrity using an Agilent Bioanalyzer 2100. Libraries were generated for sequencing using the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian. Libraries were sequenced using an Illumina HiSeq X Ten sequencer. Resluts: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to further analyse Conclusions:Our study represents the detailed analysis of iNKT cells at stage2 and stage3 transcriptomes, with biologic replicates

2018-08-10 | GSE107642 | GEO

Transcription profiling of human drug-resistant Panc1/mock cells and Panc1 cells expressing wildtype syk

Project description:We recently identified the nonreceptor tyrosine kinase syk as a tumor suppressor in pancreatic ductal adenocarcinoma cells. Reintroduction of syk into Panc1 cells promoted a more differentiated phenotype and retarded invasion and tumorigenic growth. Gene array analysis identified over 2,000 transcripts differentially expressed at FDR<0.01. Among these were members of the MMP2 axis, which were subsequently shown to regulate Panc1 invasion. Experiment Overall Design: Affymetrix global gene arrays were used to analyse differences in gene expression patterns in Panc1 cells stably reexpressing syk, or vector-only mock controls. RNA was harvested from cells grown under identical conditions in standard culture.

2009-09-18 | E-GEOD-18000 | biostudies-arrayexpress

Expression data from inflamed PANC1 cells

Project description:The effects of mutant p53 on TNFa stimulated PANC1 cells was tested. PANC1 cell harbor endogenous mutation in p53 (R273H). We knocked down this mutp53 (using sirna for p53) and then treated with low doses of TNFa to detect any differential transcription regulation governed by mutp53. A total of 7 samples, 3 of them were duplicated

2013-01-26 | E-GEOD-43738 | biostudies-arrayexpress

Sensitivity of MiaPaCa2 cells to E2F inhibitor Ly101-4B.

Project description:MiaPaCa2 cells where screened with a set of original compounds with anticancer activity available at our laboratory. From these compounds we identified the nucleoside analogue ly101-4B as a strong inhibitor of the E2F activity. We confirmed its activity by studying its effect on MiaPaCa2's cell viability , caspase 3/7 activity and LDH release, to measure cell growth, apoptosis and necrosis after treatment with LY101-4B 25 µM. Then, to investigate the mechanism of action of ly101-4B we performed a transcriptomic analysis by using an Affymetrix approach (Genechip® Human Gene 1.0 ST Arrays).

2019-02-28 | GSE109853 | GEO

Expression data from inflamed PANC1 cells

2013-01-26 | GSE43738 | GEO

Gene expression comparison of drug-resistant Panc1/mock cells and Panc1 cells expressing wildtype syk

Project description:We recently identified the nonreceptor tyrosine kinase syk as a tumor suppressor in pancreatic ductal adenocarcinoma cells. Reintroduction of syk into Panc1 cells promoted a more differentiated phenotype and retarded invasion and tumorigenic growth. Gene array analysis identified over 2,000 transcripts differentially expressed at FDR<0.01. Among these were members of the MMP2 axis, which were subsequently shown to regulate Panc1 invasion. Keywords: Genetic manipulation (stable transgene expression)

2009-09-09 | GSE18000 | GEO

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