PSON Data Coordinating Center
Physical Sciences Oncology Network Data Coordinating Center
The National Cancer Institute (NCI) is exploring new and innovative scientific approaches to better understand and control cancer. The Division of Cancer Biology Physical Sciences in Oncology Initiative seeks to establish research projects that bring together cancer biologists and oncologists with scientists from the fields of physics, mathematics, chemistry, and engineering to address some of the major questions and barriers in cancer research.
In 2009, the Physical Sciences – Oncology Centers(PS-OCs) Program was launched, a Network of 12 Centers investigating complex and challenging questions in cancer research from a physical sciences perspective. To explore how the NCI could continue to support the integration of physical sciences and cancer research, a Think Tank and series of Strategic Workshops were held in 2012. The workshops served to update opportunities at the interface of physical sciences and cancer research and guide the development of Program Announcements for a second phase of the PS-OC Program and Physical Science – Oncology Projects (PS-OPs) Program that together will form the Physical Sciences – Oncology Network (PS-ON).
Data generated from the PS-ON:
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's entry for Exome characterization at Synapse.org: https://www.synapse.org/#!Synapse:syn7248584
- The project's entry for mRNA characterization at Synpase.org: https://www.synapse.org/#!Synapse:syn7248583
- The project's entry for miRNA characterization at Synapse.org: https://www.synapse.org/#!Synapse:syn7248581
PSON0002-PSON0005 Physical Characterization of Cell Lines These studies provide physical characterization of 30 cell lines from the Physical Sciences Oncology Center (PS-OC) Network Bioresource Core Facility (PBCF). The goal of the studies are to asses the effect of cell line growth substrate on the physical properties of individual cells from the cell lines.
- PSON0002 Physical Characterization of Cell Lines. Atomic Force Microscopy This study uses atomic force microscopy (AFM) to measure the the deflection of a cantilever upon contact with the cells. In this study, the test samples represent 30 cell lines grown on 7 different substrates. Measurements were done in triplicate. Control samples were not included in this study.
- Download the dataset at ftp://caftpd.nci.nih.gov/psondcc/PhysicalCharacterization/AFM.2/
- The project's entry at Synapse.org: https://www.synapse.org/#!Synapse:syn7248585
- PSON0003 Physical Characterization of Cell Lines: MotilityThis study uses images of cells collected using brightfield microscopy at 10x magnification, with ImageJ software used to track motility. Raw data consists of tif files, while the cell positions and derived motility results are in Excel spreadsheets and text files.
- Download the dataset at ftp://caftpd.nci.nih.gov/psondcc/PhysicalCharacterization/Motility
- The project's entry at Synapse.org: https://www.synapse.org/#!Synapse:syn7248586
- PSON0004 Physical Characterization of Cell Lines: Morphology This study uses images of cells collected using brightfield microscopy at 10x magnification, with ImageJ software used to trace the outline of single cells as well as to report area, circularity and aspect ratio. Raw data consists of tif and jpg files, while the derived data are in Excel spreadsheets and text files.
- Download the dataset at ftp://caftpd.nci.nih.gov/psondcc/PhysicalCharacterization/Morphology/
- The project's entry at Synapse.org: https://www.synapse.org/#!Synapse:syn7248591
PSON0005 Physical Characterization of Cell Lines: Traction force and Volume In this study, live cells were plated on fluorescent beads and fluorescently labeled with CellTracker Green CMFDA (Invitrogen) and DRAQ5 (Cell Signaling Technology) to label cytoplasm and cell nucleus respectively. A 63x, 1.2 NA water immersion objective on a laser scanning confocal microscope (Leica TCS SP5, Wetzlar, Germany) was used for all measurements. Cell contractility is measured as total maximum force (nN) using the traction force microscopy (TFM). Raw data consists of tif and jpg files, while the derived data is provided in Excel spreadsheets. This assay could not be performed for the cell line NCI-PBCF-CRL1740 because it was was weakly adherent to the substrate.
Download the dataset at ftp://caftpd.nci.nih.gov/psondcc/PhysicalCharacterization/Traction_force_and_Volume
The project's entry at Synapse.org: https://www.synapse.org/#!Synapse:syn7248592
PSON0006 A physical sciences network characterization of non-tumorigenic and metastatic cells This dataset is supplemental material for the Nature publication of the Physical Sciences-Oncology Network. Download the dataset at ftp://caftpd.nci.nih.gov/psondcc/SciRep_2013.v3/
PSON0007 The effect of two pre-analytical variables (type of collection tube and time to analysis) on the detection and enumeration of Circulating Tumor Cells (CTCs) This study uses immunohistochemistry to detect candidate circulating tumor cells in 90 blood samples from 61 different cancer patients. Collection protocols differ by type of blood collection tube, time to assay, and detection methodology. The dataset includes jpg files of the images of the cells and text files with the cell size and fluorescence intensity, and total cell count per sample. Low pass sequencing on select cells was done, and sequence reads were aligned to the human genome. Derived data for the sequencing and mapping part of this study consists of defined sections of the genome that appear to have comparable sequence coverage. Download the dataset at ftp://caftpd.nci.nih.gov/psondcc/CTC/
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.
In the case of the study of PSON0007 The effect of pre-analytical variables on Circulating Tumor Cells (CTCs), please include the following statement instead: Data used in this publication were generated by projects sponsored by the NCI Center for Strategic Scientific Initiatives (CSSI).
Questions? Please contact firstname.lastname@example.org.