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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of human pancreatic cell lines, L3.6pl and BxPC-3, upon knockdown of p63 for 48 hours compared to siControl

ABSTRACT: Investigation of gene expression profile changes upon down regulation of p63 in L3.6pl and BxPC-3 cell lines which are representative of the squamous molecular subtype in pancreatic cancer

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Steven Johnsen

PROVIDER: E-MTAB-7033 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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DeltaNp63-dependent super enhancers define molecular identity in pancreatic cancer by an interconnected transcription factor network.

Hamdan Feda H FH Johnsen Steven A SA

Proceedings of the National Academy of Sciences of the United States of America 20181212 52

Molecular subtyping of cancer offers tremendous promise for the optimization of a precision oncology approach to anticancer therapy. Recent advances in pancreatic cancer research uncovered various molecular subtypes with tumors expressing a squamous/basal-like gene expression signature displaying a worse prognosis. Through unbiased epigenome mapping, we identified deltaNp63 as a major driver of a gene signature in pancreatic cancer cell lines, which we report to faithfully represent the highly a ...[more]

PMID: 30541891

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ChIP seq for p63, H3K27ac and BRD4 in L3.6pl, BxPC-3 pancreatic cancer cell lines and ChIP-seq of H3K27ac and BRD4 in Panc-1 pancreatic cell line

Project description:We investigated the regions that are occupied by deltaNp63 in BxPC-3 and L3.6pl and identification of super enhancers in different pancreatic cancer cell lines. Thereby, we identified a group of 45 super enhancers that are associated with poorer prognosis and are highly dependent on deltaNp63.

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Project description:This experiment describes the differential gene expression between parental gemcitabine-sensitive BxPC-3 cells and their resistant subclones, Bx-GEM. To select for the resistant subclones, parental BxPC-3 cells were treated with increasing concentrations of gemcitabine (10, 25, 50, 100 and 200 nM) for more than one year. Cells resistant at each stage of drug dosing were re-cultured in the subsequent dose, and their resistance confirmed via cell viability assays. Subclones resistant to 200 nM gemcitabine, in additon to the parental cells were used for gene profiling by array. Total RNA was extracted from the cells using the miRNeasy Mini Kit (Qiagen). The Illumina TotalPrep RNA Amplification Kit (life technologie) was used to generate single-stranded cRNA from input amounts of 500ng total RNA. 1,5 ug of cRNA were hybridized for 17 hr at 58Â°C on Illumina human HT12-Microarray using the Standard Illumina Hybridisation Protocol Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide). Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to the Standard Illumina Scanning Protocol Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide).

2017-01-20 | E-MTAB-4901 | biostudies-arrayexpress

RNA-seq of human pancreatic cell lines, L3.6pl and BxPC-3, upon knockdown of p63 for 48 hours compared to siControl

Project description:RNA-seq of human pancreatic cell lines, L3.6pl and BxPC-3, upon knockdown of p63 for 48 hours compared to siControl

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