PSON0001 Genomic Characterization of Cell Lines This study provides genomic characterization of 39 cell lines from Physical Sciences Oncology Center (PS-OC) Network Bioresource Core Facility (PBCF) through the sequencing of mRNA (TruSeq Stranded RNA Sample Preparation Kit), miRNA (TruSeq Small Total RNA Sample Prep Kit ) and exome ( Agilent SureSelectXT2 Human All Exon V5 kit) and aligning to a reference genome (HG19/37 ). Software for the mRNA characterizations included: cufflinks, cuffdecoder, fastcqReports, mapsplice, tophat, transdecoder, for miRNA included: bowtie2, miRanalyzer, miTools. and for exome included bowtie2. Datasets include the output specific to these software packages, as well as more widely used bioinformatics formats: bam, bed, fasta, fastq, vcf (4.1).

Download the dataset at ftp://caftpd.nci.nih.gov/psondcc/CellLineGenomics/

The project entries at NCBI’s BioProject database, with links to their entries at NCBI’s Short Read Archive (SRA) and BioSample databases:

• miRNA sequencing BioProject PRJNA325939 http://www.ncbi.nlm.nih.gov/bioproject/325939
• mRNA sequencing BioProject PRJNA325938 http://www.ncbi.nlm.nih.gov/bioproject/325938
• Exome sequencing BioProject PRJNA325935 http://www.ncbi.nlm.nih.gov/bioproject/325935

The project entries at Synapse:

• Exome characterization https://www.synapse.org/#!Synapse:syn7248584
• mRNA characterization https://www.synapse.org/#!Synapse:syn7248583
• miRNA characterization https://www.synapse.org/#!Synapse:syn7248581

Table 1. 39 Cell lines used in PSON0001 Genomic Characterization of Cell Lines

Data usage policy

The data contained within the PS-ON DCC is based on several research projects and is intended to be rapidly and constantly updated for the research community to access and use. The NCI requests that any data users:

• Inform the data submitters about the intention to submit a publication that uses PS-ON DCC data.
  • Include the following statement in any publications resulting from the use of PS-ON DCC data: Data used in this publication were generated by projects sponsored by the NCI Physical Sciences in Oncology Initiative.

Created on 06 Apr 2016, Last modified on 26 Sep 2016