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RNAseq of two mouse LUSC cell lines derived from NTCU-induced model

ABSTRACT: RNAseq of two mouse LUSC cell lines derived from NTCU-induced model

PROVIDER: PRJNA767537 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16122972.fastq.gz	Fastqsanger.gz
	SRR16122973.fastq.gz	Fastqsanger.gz
	SRR16122974.fastq.gz	Fastqsanger.gz
	SRR16122975.fastq.gz	Fastqsanger.gz
	SRR16122976.fastq.gz	Fastqsanger.gz

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RNAseq of two mouse LUSC cell lines derived from NTCU-induced model

Project description:We report RNAseq data form two independent mouse syngeneic LUSC cell lines UN-SCC679 and UN-SCC680 Carcinogenesis and cell line generation: LUSC tumors were induced by N-nitroso-tris-chloroethylurea (NTCU) (Toronto Research Chemicals) treatment applying 0.04 M NTCU by skin painting twice a week for 20 weeks to 8-week-old A/J mice. Lungs of euthanized mice were excised and tumor cell lines UN-SCC679 and UN-SCC680 were derived and cultured for 25 passes to ensure they were immortalized, subcutaneously injected into 6-week-old female Rag2-/-IL2Rg-/- immunodeficient mice flanks subcutaneously and finally engrafted in syngeneic 8-week-old A/J mice. These cell lines were cultured in RPMI 1640 supplemented with 10% Fetalclone (Thermo Fisher Scientific) and 100 U/mL penicillin-100 µg/mL streptomycin (Thermo Fisher Scientific). All cells were grown in a humidified incubator containing 5% CO2 at 37°C. Cell lines were routinely tested for mycoplasma.

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caArray_EXP-598: TCGA (LUSC): Analysis of DNA Methylation for LUSC using Illumina Infinium HumanMethylation450 platform (jhu-usc)

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Project description:TCGA Analysis of DNA Methylation for LUSC using Illumina Infinium HumanMethylation450 platform EXP-598 Assay Type: Methylation Provider: Illumina Array Designs: jhu-usc.edu_TCGA_HumanMethylation450 Organism: Homo sapiens (ncbitax) Tissue Sites: Lung Material Types: Control Analyte, Solid normal_tissue, organism_part, Primary solid_tumor Disease States: Lung Squamous Cell Carcinoma, NOT SPECIFIED

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ChIP-Seq of BCL11A and SOX2 in lung squamous cell carcinoma (LUSC) LK-2 cell line with or without BCL11A knockdown

Project description:BCL11A is upregulated in lung squamous cell carcinoma (LUSC) but not in lung adenocarcinoma (LUAD). BCL11A interacts with SOX2 at protein level. ChIP-Seq experiment was performed for BCL11A and SOX2 in LUSC LK-2 control or BCL11A-KD cell line in order to identify their role in LUSC pathology.

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DNA methylation features of LUSC in promoter and enhancer region [methylation]

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Genome-wide maps of histone modifications in mouse tumor-derived cell lines

Project description:Amplification of chromosomal region 8p11-12 is a frequent genetic alteration implicated in the etiology of lung squamous cell carcinoma (LUSC). Here we identify the H3K36 methyltransferase NSD3 (nuclear receptor binding SET domain protein 3), an 8p11-12-localized gene, as a key regulator of LUSC tumorigenesis. We identify NSD3T1232A as an LUSC-associated variant that increases H3K36 dimethylation (H3K36me2) catalytic activity in vitro and in vivo. NSD3T1232A expression in vivo in LUSC mouse models accelerates tumorigenesis and decreases overall survival. Pathologic generation of H3K36me2 by NSD3T1232A rewires the chromatin landscape to promote oncogenic gene expression programming. Together, our work identifies NSD3 as a principal 8p11-12 amplicon-associated oncogenic driver in LUSC and suggests that NSD3-dependency renders LUSC therapeutically vulnerable to BETi. Here we report the application of Cut and Run technology for high-throughput prolifiling of histone modiifcations in mouse tumor-derived cell lines. We found NSD3 loss leads to decrase of histone H3 lysine 36 dimethylation over gene body regions and intergenic regions, while histone H3 lysine 27 trimethylation is increased over these regions. We also reported that NSD3 depletion mainly down-regulates the expression of genes in PI3K-Akt-mTORC1 pathway and Myc targets through total RNA-seq.

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