Data Set Group2: NCI Mammary mRNA M430 (July04)

Data Set: NCI Mammary mRNA M430 (July04) RMA GN Accession: GN37 GEO Series: No Geo series yet Title: Organism: Mouse (Mus musculus, mm10) Group: AKXD Tissue: Mammary Tumors mRNA Dataset Status: Public Platforms: Affy Mouse Genome 430A, 430B, 430A 2.0 (GPL339,GPL340) Normalization: RMA

Contact Information Kent Hunter U.S. National Institute of Health Building 37, Room 5046C, 37 Convent Drive Bethesda, MD 20892 USA Tel. 301-435-8957 hunterk@mail.nih.gov Website Download datasets and supplementary data files GN37_MeanDataAnnotated_rev081815.txt (N/A) GN37_StdError_rev081815.txt (N/A)

Specifics of this Data Set:

None

Summary:

Used the Affymetrix M430A and M430B pair of arrays (total of 45,137 probe sets). Data available as CEL files from GeneNetwork upon request.

About the cases used to generate this set of data:

The lines of mice used in this NCI-sponsored project consist of 18 groups of isogenic F1 progeny made by crossing females from each of 18 AKXD recombinant inbred strains (AKXD2, 3, 7, 9, 10, 11, 13, 14, 16, 18, 20, 21, 22, 23, 24, 25, 27, and 28) to male FVB/N mice that carry a transgene that consistently leads to the development of mammary tumors in females (e.g. Le Voyer et al., 2001). The formal nomenclature of the male transgenic line is FVB/N-TgN(MMTV-PyMT)634Mul. The genomes of each AKXD x FVB F1 consist of one set of FVB chromosomes (including the transgene) and one set of chromosomes inherited from one of the 18 AKXD RI strain mothers. Only the AKXD chromosomes are "recombinant" across this panel of F1 progeny, and the set therefore has a genetic architecture similar to backcross progeny. It is possible to map modifiers that influence tumor characteristics and expression patterns. It is also possible to study covariance of transcript expression levels in tumor tissue. For further background on this special mapping design please see Hunter and Williams (2002). The ancestral strains from which all AKXD strains are derived are AKR/J (AKR) and DBA/2J (D2 or D). DBA/2J has been partially sequenced (approximately 1.5x coverage by D by Celera Genomics). Significant genomic sequence data for AKR is not currently available. Chromosomes of the two parental strains have recombined in the different AKXD strains. All of these strains are available from The Jackson Laboratory as cryopreserved stocks. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.

About the tissue used to generate this set of data:

Mammary tumors used in this array experiment were derived from 18 sets of AKXD x FVB/N F1 females as described above. After the primary tumor was diagnosed, the animals were aged an additional 40 days to permit metastatic progression. Females were sacrificed and mammary tumors were harvested. Samples were processed and arrayed on Affymetrix M430A and M430B arrays. The majority of the samples were assayed on arrays obtained from the same lot number.

About the array platform:

All samples were processed and arrayed in the Laboratory of Population Genetics at the NCI. The table below lists the arrays by Samples, AKXD strain and Age. Sample AKXD strain Age AKXD2957 2 98 AKXD2959 2 96 AKXD1747 3 84 AKXD3446 3 91 AKXD4225 3 83 AKXD2543 7 82 AKXD2967 7 88 AKXD3336 7 95 AKXD2685 9 113 AKXD2710 9 109 AKXD2949 9 115 AKXD2618 10 99 AKXD2620 10 99 AKXD3023 10 94 AKXD1910 11 87 AKXD2824 11 92 AKXD2825 11 103 AKXD2635 13 83 AKXD2718 13 100 AKXD2721 13 91 AKXD2632 14 99 AKXD2640 14 100 AKXD3444 14 96 AKXD1636 16 112 AKXD3688 16 80 AKXD4152 16 91 AKXD1647 18 91 AKXD2616 18 91 AKXD2804 18 80 AKXD2456 20 100 AKXD2554 20 107 AKXD2829 20 105 AKXD1610 21 98 AKXD2611 21 88 AKXD2918 21 98 AKXD2460 22 107 AKXD2461 22 94 AKXD2463 22 110 AKXD2975 23 82 AKXD2976 23 86 AKXD3955 23 90 AKXD1494 24 103 AKXD1880 24 104 AKXD3030 24 89 AKXD1607 25 110 AKXD2326 25 92 AKXD2328 25 90 AKXD2629 25 96 AKXD1756 27 100 AKXD1757 27 98 AKXD1948 27 99 AKXD1950 27 97 AKXD2968 27 94 AKXD2809 28 88 AKXD2815 28 90 AKXD3432 28 91

About data values and data processing:

Probe (cell) level data from the .CEL file: These .CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell. Step 1: We added an offset of 1.0 to the .CEL expression values for each cell to ensure that all values could be logged without generating negative values. Step 2: We took the log base 2 of each cell. Step 3: We computed the Z scores for each cell. 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. Step 6a: The 430A and 430B GeneChips include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes and probe sets provide a way to calibrate expression of the two GeneChips to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5. Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set. Probe set data from the .CHP file: The expression data were generated using MAS5. The same simple steps described above were also applied to these values. A 1-unit difference represents roughly a two-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 probe sets and gene markers on the 430A and 430B microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.

Notes:

Text originally written by Kent Hunter and Robert W. Williams, July 2004. Updated by RWW, Nov 6, 2004.

Experiment Type:

Contributor:

Citation:

Data source acknowledgment:

All of the NCI mammary mRNA M430A and M430B data sets have been generated by Kent Hunter at the Laboratory of Population Genetics at the National Cancer Institute in Bethesda. For contact and citations and other information on these data sets please review the INFO pages and contact Dr. Hunter regarding use of this data set in publications or projects.

Study Id:

9

• The UT Center for Integrative and Translational Genomics
• NIGMS Systems Genetics and Precision Medicine project (R01 GM123489, 2017-2021)
• NIDA NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022)
• NIA Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
• NIAAA Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
• NIDA, NIMH, and NIAAA (P20-DA 21131, 2001-2012)
• NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)