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SK-N-SH Hi-C

ABSTRACT: Hi-C was performed on SK-N-SH cells to study 3-dimensional chromatin architecture.

ORGANISM(S): Homo sapiens

PROVIDER: GSE71072 | GEO | 2015/09/01

SECONDARY ACCESSION(S): PRJNA290278

REPOSITORIES: GEO

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SK-N-SH Hi-C

Project description:Hi-C was performed on SK-N-SH cells to study 3-dimensional chromatin architecture. Two biological replicates were performed, each with roughly 25x10^7 cells.

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Project description:The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line SK-N-SH. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

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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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ChIP-seq from SK-N-SH (ENCSR000FCS)

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