skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Examining microarray slide quality for the EPA using SNL's hyperspectral microarray scanner.

Abstract

This report summarizes research performed at Sandia National Laboratories (SNL) in collaboration with the Environmental Protection Agency (EPA) to assess microarray quality on arrays from two platforms of interest to the EPA. Custom microarrays from two novel, commercially produced array platforms were imaged with SNL's unique hyperspectral imaging technology and multivariate data analysis was performed to investigate sources of emission on the arrays. No extraneous sources of emission were evident in any of the array areas scanned. This led to the conclusions that either of these array platforms could produce high quality, reliable microarray data for the EPA toxicology programs. Hyperspectral imaging results are presented and recommendations for microarray analyses using these platforms are detailed within the report.

Authors:
;
Publication Date:
Research Org.:
Sandia National Laboratories
Sponsoring Org.:
USDOE
OSTI Identifier:
875988
Report Number(s):
SAND2005-7536
TRN: US200604%%219
DOE Contract Number:
AC04-94AL85000
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; 54 ENVIRONMENTAL SCIENCES; IMAGES; QUALITY ASSURANCE; DATA ANALYSIS; SANDIA NATIONAL LABORATORIES; US EPA; MULTIVARIATE ANALYSIS; EMISSION; TOXIC MATERIALS; Imaging systems.; Spectral data.; Spectroscopic imaging.; Microstructure.

Citation Formats

Rohde, Rachel M., and Timlin, Jerilyn Ann. Examining microarray slide quality for the EPA using SNL's hyperspectral microarray scanner.. United States: N. p., 2005. Web. doi:10.2172/875988.
Rohde, Rachel M., & Timlin, Jerilyn Ann. Examining microarray slide quality for the EPA using SNL's hyperspectral microarray scanner.. United States. doi:10.2172/875988.
Rohde, Rachel M., and Timlin, Jerilyn Ann. Tue . "Examining microarray slide quality for the EPA using SNL's hyperspectral microarray scanner.". United States. doi:10.2172/875988. https://www.osti.gov/servlets/purl/875988.
@article{osti_875988,
title = {Examining microarray slide quality for the EPA using SNL's hyperspectral microarray scanner.},
author = {Rohde, Rachel M. and Timlin, Jerilyn Ann},
abstractNote = {This report summarizes research performed at Sandia National Laboratories (SNL) in collaboration with the Environmental Protection Agency (EPA) to assess microarray quality on arrays from two platforms of interest to the EPA. Custom microarrays from two novel, commercially produced array platforms were imaged with SNL's unique hyperspectral imaging technology and multivariate data analysis was performed to investigate sources of emission on the arrays. No extraneous sources of emission were evident in any of the array areas scanned. This led to the conclusions that either of these array platforms could produce high quality, reliable microarray data for the EPA toxicology programs. Hyperspectral imaging results are presented and recommendations for microarray analyses using these platforms are detailed within the report.},
doi = {10.2172/875988},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Tue Nov 01 00:00:00 EST 2005},
month = {Tue Nov 01 00:00:00 EST 2005}
}

Technical Report:

Save / Share:
  • We describe the design, construction, and operation of a hyperspectral microarray scanner for functional genomic research. The hyperspectral instrument operates with spatial resolutions ranging from 3 to 30 {micro}m and records the emission spectrum between 490 and 900 nm with a spectral resolution of 3 nm for each pixel of the microarray. This spectral information, when coupled with multivariate data analysis techniques, allows for identification and elimination of unwanted artifacts and greatly improves the accuracy of microarray experiments. Microarray results presented in this study clearly demonstrate the separation of fluorescent label emission from the spectrally overlapping emission due to themore » underlying glass substrate. We also demonstrate separation of the emission due to green fluorescent protein expressed by yeast cells from the spectrally overlapping autofluorescence of the yeast cells and the growth media.« less
  • The slide rule is used to estimate energy savings for the following types of options: ceiling insulation, wall insulation, floor insulation, infiltration reduction, window characteristics, and equipment efficiency. The modifiers are additional energy conservation options whose savings are estimated using tables contained in this booklet. These options include: heat absorbing and reflective glazing, movable insulation, night setback thermostat, roof color, and whole house fan. (MHR)
  • We have analyzed hyperspectral Airborne Visible-Infrared Imaging System (AVIRIS) imagery taken in September of 1992 in Long Valley Caldera, CA, a geothermally active region expressed surficially by hot springs and fumaroles. Geological and vegetation mapping are attempted through spectral classification of imagery. Particular hot spring areas in the caldera are targeted for analysis. The data is analyzed for unique geobotanical patterns in the vicinity of hot springs as well as gross identification of dominant plant and mineral species. Spectra used for the classifications come from a vegetation spectral library created for plant species found to be associated with geothermal processes.more » This library takes into account the seasonality of vegetation by including spectra for species on a monthly basis. Geological spectra are taken from JPL and USGS mineral libraries. Preliminary classifications of hot spring areas indicate some success in mineral identification and less successful vegetation species identification. The small spatial extent of individual plants demands either sub-pixel analysis or increased spatial resolution of imagery. Future work will also include preliminary analysis of a hyperspectral thermal imagery dataset and a multitemporal air photo dataset. The combination of these remotely sensed datasets for Long Valley will yield a valuable product for geothermal exploration efforts in other regions.« less
  • A series of field experiments were done to determine if ground shock could have induced physiological responses in plants and if the level of the response could be observed. The observation techniques were remote sensing techniques and direct contact physiological measurements developed by Carter for detecting pre-visual plant stress. The remote sensing technique was similar to that used by Pickles to detect what appeared to be ground shock induced plant stress above the 1993 Non Proliferation Experiment`s underground chemical explosion. The experiment was designed to provide direct plant physiological measurements and remote sensing ratio images and from the same plantsmore » at the same time. The simultaneous direct and remote sensing measurements were done to establish a ground truth dataset to compare to the results of the hyperspectral remote sensing measurements. In addition, the experiment was designed to include data on what was thought to be the most probable interfering effect, dehydration. The experimental design included investigating the relative magnitude of the shock induced stress effects compared to dehydration effects.« less