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Epigenetic subtypes of neuroblastoma [scRNA-seq SK-N-SH]

ABSTRACT: Epigenetic subtypes of neuroblastoma [scRNA-seq SK-N-SH]

PROVIDER: PRJNA664098 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12660100_1.fastq.gz	Fastqsanger.gz
	SRR12660100_2.fastq.gz	Fastqsanger.gz
	SRR12660101_1.fastq.gz	Fastqsanger.gz
	SRR12660101_2.fastq.gz	Fastqsanger.gz
	SRR12660102_1.fastq.gz	Fastqsanger.gz

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Epigenetic subtypes of neuroblastoma [scRNA-seq SK-N-SH]

Project description:In the absence of recurrent gene mutations, evidence accumulates that epigenetic deregulation plays a prominent role in neuroblastoma biology. Here we provide single cell expression profiles (scRNA-seq MARS-seq) of SK-N-SH cells (n=1176)

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SNP array of human neuroblastoma cell lines SH-SY5Y, SH-EP and SK-N-SH

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SNP array of human neuroblastoma cell lines SH-SY5Y, SH-EP and SK-N-SH

Project description:TERT promoter muatations occur frequently in tumors of various origin. We here accessed the frequency of TERT pomoter mutations in 131 human primary neuroblastomas and 20 human neuroblastoma cell lines. No TERT promoter mutations were found in the 131 primary neuroblastomas. However, in the three cell lines SH-SY5Y, SH-EP and SK-N-SH a TERT promoter mutation was detected. Sanger sequencing indicated a homozygous mutation. To confirm loss of heterozygosity (LOH) we performed Affymetrix CytoScanHD SNP arrays. Indeed LOH could be confirmed. SNP arry experiments were performed according to the standard protocol for Affymetrix CytoScanHD arrays (Affymetrix, Santa Clara). Briefly, a 250 ng sample of genomic DNA was digested with NspI, ligated to adaptors, amplified by PCR, fragmented and biotin-labeled. The labeled samples were hybridized to Affymetrix CytoscanHD arrays, followed by washing, staining and scanning in the Affymetrix GeneChip Scanner 3000. Analysis was performed using the Affymetrix Chromosome Analysis Suite v2.1.

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Transcriptome analysis of SH-SY5Y and SK-N-AS neuroblastoma cells with KIT gene knockdown

Project description:The goal of this study was to identify dynamic changes in signaling pathway activities after KIT knockdown by RNAi in neuroblastoma with relatively high KIT expression (SH-SY5Y) and low expression (SK-N-AS).

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Project description:Neuroblastoma is a pediatric tumor of the developing sympathetic nervous system. We investigate the developmental origin of neuroblastoma, the role of oncogenic MYCN in blocking normal differentiation and evaluate therapeutic interventions to overcome differentiation blocks. Here, we provide single cell expression profiles (scRNA-seq MARS-seq) of SK-N-AS cells (n=603).

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Project description:Analysis of varied biologic pathways in neuroblastoma SK-N-SH cells grown in doxorubicin and/or SAHA. The hypothesis was that SK-N-SH cells undergo a mesenchymal change through mesenchymal change resulting in a more invasive as well as drug resistant phenotype, and that the mechanism of SAHAs effect on drug resistance may be revealed through this analysis. Total RNA was isolated from wild type, SAHA treated wild type cells, doxorubicin resistant, and SAHA treated doxorubicin resistant SK-N-SH cell lines in triplicate.

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