OHSU/VA B6D2F2 Striatum M430v2 PDNN Database (September/05 Freeze)
Accession number: GN85
PROVISIONAL DRAFT (NOT APPROVED): This September 2005 data freeze provides estimates of mRNA expression in dorsal striatum of 60 adult brains of F2 intercross mice (C57BL/6J x DBA/2J F2, 30 males and 30 females) measured using Affymetrix M430v2 microarrays. In addition, data were acquired from 5 male and 5 females from both C57BL/6J and DBA/2J parental strains. Data were generated at The Oregon Health Sciences University (OHSU) in Portland, Oregon, by Robert Hitzemann and colleagues. Data were processed using the Position-Dependent Nearest Neighbor (PDNN) method of Zhang and colleagues (2003. To simplify comparison among transforms, PDNN values of each array have been adjusted to an average of 8 units and a variance of 2 units.
This data set was run as a single large batch balanced by sex.
About the cases used to generate this set of data:
Eighty samples, each taken from a single brain hemisphere from an individual mouse, were assayed using M430v2 Affymetrix short oligomer microarrays. All F2 were experimentally naive, born within a 3-day period from second litters of each dam, and housed at weaning (20- to 24-days-of-age) in like-sex groups of 3 to 4 mice for females and 2 to 3 mice for males in standard mouse shoebox cages within Thoren racks. All 60 F2 mice were killed at 77 to 79 days-of-age by cervical dislocation. The brains were immediately split at the midline and then quickly frozen on dry ice. The brains were stored for about two weeks at -80 degrees C until further use.
The F2 was derived as follows: C57BL/6J (B6) and DBA/2J (D2) breeders were obtained from The Jackson Laboratory, and two generations later their progeny were crossed to produce B6D2F1 and D2B6F1 hybrid at the Portland VA Veterinary Medical Unit (AAALAC approved). The reciprocal F1s were mated to create an F2 population with both progenitor X and Y chromosomes about equally represented.
About the tissue used to generate these data:
Brain samples were from 40 male and 40 females. The dorsal striatum was dissected. Total RNA was isolated with TRIZOL Reagent (Life Technologies Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer’s protocol. The extracted RNA was then purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for purity; only samples with an A260/280 ratio greater than 1.8 were used. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. Samples containing at least 10 micrograms of total RNA were sent to the OHSU Gene Microarray Shared Resource facility for analysis. The procedures used at the facility precisely follow the manufacturer’s specifications. Details can be found at http://www.ohsu.edu/gmsr/amc. Following labeling, all samples were hybridized to the GeneChip Test3 array for quality control. If target performance did not meet recommended thresholds, the sample would have been discarded. All labeled samples passed the threshold and were hybridized to the 430A array.
About the arrays:
All 430v2 arrays used in this project were purchased at one time and had the same Affymetrix lot number.
The table below lists the arrays by Case ID, Array ID.
About the marker set:
The 56 mice were each genotyped at 309 MIT microsatellite markers distributed across the genome, including the Y chromosome. The genotyping error check routine (Lincoln and Lander, 1992) implemented within R/qtl (Broman et al., 2003) showed no likely errors at p <.01 probability. Initial genotypes were generated at OHSU. Approximately 200 genotypes were generated at UTHSC by Jing Gu and Shuhua Qi.
About data processing:
Probe (cell) level data from the CEL file: These CEL values produced by GCOS are the 75% quantiles from a set of 91 pixel values per cell. Probe values were processed as follows:
- Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- Step 2: We took the log base 2 of each probe signal.
- Step 3: We computed the Z scores for each probe signal.
- Step 4: We multiplied all Z scores by 2.
- Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
Probe set data: The uncorrected, untransformed CEL files were subject to probe (low) level processing using both the RMA (Robust Multiarray Average; Irizarry et al. 2003) and PDNN (Position Dependent Nearest Neighbor; Zhang et al. 2003) methods because these two performed the best of four methods tested in a recent four inbred strain comparison using the M430A chip on whole brain samples (Hitzemann et al, submitted). RMA was implemented by the Affy package (11/24/03 version) within Bioconductor (http://www.bioconductor.org) and PDNN by the PerfectMatch v. 2.3 program from Li Zhang (PDNN ). For sake of comparison with other data sets, MAS 5 files have also been generated.
To better compare data sets, the same simple steps (1 through 6 above) were applied to PDNN and RMA values. Every microarray data set therefore has a mean expression of 8 units with a standard deviation of 2 units. A 1-unit difference therefore represents roughly a 2-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
About the chromosome and megabase position values:
The chromosomal locations of M430v2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium March 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
Data source acknowledgment:
This project was supported by two Department of Veterans Affairs Merit Review Awards (to JK Belknap and R Hitzemann, respectively), AA10760 (Portland Alcohol Research Center), AA06243, AA13484, AA11034, DA05228 and MH51372.
Please contact either John Belknap or Robert Hitzemann at the Dept. of Behavioral Neuroscience, Oregon Health & Science University (L470), or Research Service (R&D5), Portland VA Medical Ctr., Portland, OR 97239 USA.
Hitzemann, R, McWeeney, S, Harrington, S, Malmanger, B, Lawler, M, Belknap, JK (2004) Brain gene expression among four inbred mouse strains: The development of an analysis strategy for the integration of QTL and gene expression data. Submitted.
Irizarry, RA, Bolstad, BM, Collin, F, Cope, LM, Hobbs, B, Speed, TP (2003) Summaries of Affymetrix GeneChip probe level data. Nuc Acids Res 31:1-15.
Lincoln, SE, Lander, ES (1992) Systematic detection of errors in genetic linkage data. Genomics 14:604-610.
Zhang, L, Miles, MF, Aldape, KD (2003) A model of molecular interactions on short oligonucleotide microarrays. Nat Biotech 21:818-821.
Information about this text file:
This text file was originally generated by John Belknap, March 2004. Updated by RWW, October 31, 2004.