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Data for submission "Collagen organization of renal cell carcinoma differs between low and high grade tumors"

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Abel, E.Jason; Huang, Wei; Eliceiri, Kevin W.; Woo, Kaitlin M.; Mehta, Guneet S.; Houlihan, Matthew; Bredfeldt, Jeremy S.; Altwegg, Marie; Thimm, Terra N.; Liu, Yuming; Keikhosravi, Adib; Best, Sara L.; Drifka, Cole R.
Jan 22, 2018
collagen organization; renal cell carcinoma; tumor grading; second harmonic generation imaging; tissue microarray
This repository contains datasets generated and/or analysed in the RCC project.
Sample: A human RCC tissue microarray (TMA) block was constructed by the Translational Research Initiatives in Pathology (TRIP) lab at the University of Wisconsin-Madison (UW-Madison). A section of 5um thickness was cut from the TMA block containing ~600um diameter tissue TMA cores. The section was then placed on a glass slide, stained with standard hematoxylin and eosin (H&E), and mounted under a #1.5 glass coverslip. Different tissue cores were from different patients. HE imaging: A bright field image of the entire H&E slide was collected with an Aperio CS2 Digital Pathology Scanner (Leica Biosystems) at 20x magnification. Each core of grade 1 and grade 4 was cropped to the size of 1520 pixels by 1520 pixels using Aperio ImageScope viewing software (Leica Biosystems). In total, 75 TMA cores were verified and annotated as grade 1 and 55 TMA cores as grade 4. Each core represents an individual patient. SHG imaging: All cores in this study were imaged with a custom built forward detection SHG microscope (Bredfeldt et al., 2014a). A MIRA 900 Ti: Sapphire laser (Coherent, Santa Clara, CA) was used to deliver 780 nm light to the sample using a 40x/1.25NA water immersion objective (Nikon, Melville, NY). No SHG signal was observed for five grade 1 cores and four grade 4 cores after navigating the system to at least 3 different fields of view on each core. Hence, in total, 70 TMA cores have SHG singal and annotated as grade1, 51 TMA cores as grade 4. To be noted, HE image and SHG image provided here are all original images and not co-registered.
This study was supported by the UW Department of Urology with additional funding from the UW Laboratory for Optical and Computational Instrumentation. We acknowledge funding support from the UW Institute for Clinical and Translational Research (ICTR) under award #UL1TR000427. We also acknowledge funding from NIH under grants R01 CA179556 (KWE) and U54DK104310 (KWE). The authors thank the UW Translational Research Initiatives in Pathology Laboratory, in part supported by the UW Department of Pathology and Laboratory Medicine and UWCCC grant P30 CA014520, for use of its facilities and services.
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