8 An Overview of National Toxicology Program’s Toxicogenomic …
145
Fig. 8.2 Rat in vivo experimental protocol used for DrugMatrix data generation
niehs.nih.gov/ntp-cebs/datatype/Drug_Matrix/DrugMatrix_Histopathology.xlsx).
In order understand the temporal aspects of toxicity, samples were collected with
durations of exposure ranging from 0.25 days to 14 or more days (dose administered
daily). For expression studies in rat hepatocytes, a single dose reflective of 24-h
“toxic concentration 20” (dose where there is a 20% reduction in cell viability) was
dispensed. Hepatocyte gene expression was measured 16 and 24-h post dose delivery.
NTP has retained a collection of biological samples from the in vivo studies including
snap-frozen liver, heart, kidney, thigh muscle, whole blood and/or plasma that are
available upon request for further investigation. A complete list of the available tissue
and RNA samples can be found elsewhere (ftp://anonftp.niehs.nih.gov/ntp-cebs/
datatype/Drug_Matrix/DrugMatrix_Aliquot%20Information.xlsx and ftp://anonftp.
niehs.nih.gov/ntp-cebs/datatype/Drug_Matrix/DrugMatrix_RNAMicroarray.xlsx).
Initially, GE Codelink microarrays representing approximately 10,000 genes
were used to quantify gene expression. In this first phase, >12,000 arrays were
run. Due to the evolution of array technology platforms, and ubiquitous usage in
the research community, a subset of the RNA samples (>5000) that provided the
most informative data were re-analyzed using Affymetrix 230 2.0 microarrays.
All raw microarray data is available in the Gene Expression Omnibus database
(GEO Data Sets: GSE59913, GSE59923, GSE59894, GSE59895, GSE59905,
GSE59906, GSE59907, GSE59925, GSE59926, GSE57800, GSE57805,
GSE57811, GSE57815, GSE57816). Data from both platforms are systematically integrated and available through the DrugMatrix Database. All individual
treatment transcriptomic signatures, i.e., single dose/duration) from the database
are available in CEBS (ftp://anonftp.niehs.nih.gov/ntp-cebs/datatype/Drug_Matrix/
Differential%20Gene%20Expression%20Data/).
145
Fig. 8.2 Rat in vivo experimental protocol used for DrugMatrix data generation
niehs.nih.gov/ntp-cebs/datatype/Drug_Matrix/DrugMatrix_Histopathology.xlsx).
In order understand the temporal aspects of toxicity, samples were collected with
durations of exposure ranging from 0.25 days to 14 or more days (dose administered
daily). For expression studies in rat hepatocytes, a single dose reflective of 24-h
“toxic concentration 20” (dose where there is a 20% reduction in cell viability) was
dispensed. Hepatocyte gene expression was measured 16 and 24-h post dose delivery.
NTP has retained a collection of biological samples from the in vivo studies including
snap-frozen liver, heart, kidney, thigh muscle, whole blood and/or plasma that are
available upon request for further investigation. A complete list of the available tissue
and RNA samples can be found elsewhere (ftp://anonftp.niehs.nih.gov/ntp-cebs/
datatype/Drug_Matrix/DrugMatrix_Aliquot%20Information.xlsx and ftp://anonftp.
niehs.nih.gov/ntp-cebs/datatype/Drug_Matrix/DrugMatrix_RNAMicroarray.xlsx).
Initially, GE Codelink microarrays representing approximately 10,000 genes
were used to quantify gene expression. In this first phase, >12,000 arrays were
run. Due to the evolution of array technology platforms, and ubiquitous usage in
the research community, a subset of the RNA samples (>5000) that provided the
most informative data were re-analyzed using Affymetrix 230 2.0 microarrays.
All raw microarray data is available in the Gene Expression Omnibus database
(GEO Data Sets: GSE59913, GSE59923, GSE59894, GSE59895, GSE59905,
GSE59906, GSE59907, GSE59925, GSE59926, GSE57800, GSE57805,
GSE57811, GSE57815, GSE57816). Data from both platforms are systematically integrated and available through the DrugMatrix Database. All individual
treatment transcriptomic signatures, i.e., single dose/duration) from the database
are available in CEBS (ftp://anonftp.niehs.nih.gov/ntp-cebs/datatype/Drug_Matrix/
Differential%20Gene%20Expression%20Data/).