Project description:Chromatin state maps (H3K4me3 and H3K27me3) from partially and fully reprogrammed mouse cell lines obtained by ectopic expression of Oct4, Sox2, Klf4 and c-Myc using constitutive retroviral infection of MEFs (MCV6, MCV8, MCV8.1) or induction of lentivirus in secondary B lymphocytes obtained from iPS-derived chimeric mice (BIV8). Keywords: High-throughput ChIP-sequencing, Illumina, cell type comparison H3K4me3 and H3K27me3 ChIP-Seq in singlicate from three partially reprogrammed cell lines (BIV1, MCV8, MCV6), one iPS cell line (MCV8.1) and MEFs (subsampled from Mikkelsen et al, Nature, 2007)) Raw sequence data files for this study are available for download from the SRA FTP site at ftp://ftp.ncbi.nlm.nih.gov/sra/Studies/SRP000/SRP000215
Project description:Neuroblastoma cell lines are an important and cost-effective model used to study oncogenic drivers of the disease. While many of these cell lines have been previously characterized with SNP, methylation, and/or expression microarrays, there has not been an effort to comprehensively sequence these cell lines. Here, we present raw whole transcriptome data generated by RNA sequencing of 39 commonly-used neuroblastoma cell lines. This data can be used to perform differential expression analysis based on a genetic aberration or phenotype in neuroblastoma (eg: MYCN amplification status, ALK mutation status, 11q status, sensitivity to pharmacological pertubation). Additionally, we designed this experiment to enable structural variant and/or long-noncoding RNA analysis across these cell lines. Finally, as more DNase/ATAC and histone/transcription factor ChIP sequencing is performed in these cell lines, our RNA-Seq data will be an important complement to inform transcriptional targets as well as regulatory (enhancer or repressor) elements in neuroblastoma.
