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SJUT M430 Cerebellum Database (September/03 Freeze) 
About the mice used to map microarray data:
The set of mouse strains used for mapping (a mapping panel) consists of groups of genetically unique BXD recombinant inbred strains. The ancestral strains from which all BXD lines are derived are C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D strains have been almost fully sequence (8x coverage for B6, and 1.5x coverage for D by Celera Genomics). Chromosomes of the two parental strains are recombined randomly in the many different BXD strains. BXD lines 2 through 32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through 42 were also produced by Dr. Taylor, but they were generated in the 1990s. All of these strains are available from The Jackson Laboratory. Lines such as BXD67, BXD68, etc. are BXD Advanced recombinant inbred strains that are part of a large set now being produced by Drs. Lu Lu, Guomin Zhou, Lee Silver, Jeremy Peirce, and Robert Williams. There will eventually be ~45 of these BXDA strains. For additional background on recombinant inbred strains,
please see http://www.nervenet.org/papers/bxn.html.
About the tissue used to generate these data:
The September03 data were processed in two large batches. The first batch (the May03 data set) consisted of samples from 20 samples and 20 strains run on Affymetrix MOE 430A and MOE430B GeneChip pairs (40 arrays total). The second batch of 29 samples, included may biological replicates, 2 technical replicates, and data for 9 new strains. Each individual array experiment involved a pool of brain tissue (intact whole cerebellum) taken from three adult animals usually of the same age. RNA was extracted at UTHSC and all samples were processed at the Hartwell Center (SJCRH, Memphis). We will eventually achieve a sample with good, but not perfect, balance of samples by sex and age. The age range may look broad, but translated into human terms corresponds to a range from about 20 years to 50 years.
| Sample_name |
Tissue_type |
Strain |
Sex |
Age |
| 766-C1 | Cerebellum | B6D2F1 | M | 127 |
| S347-1C1 | cerebellum | B6D2F1 | M | 94 |
| 813-C1 | Cerebellum | BXD1 | F | 57 |
| S200-1C1 | cerebellum | BXD11 | F | 441 |
| 790-C1 | Cerebellum | BXD11 | M | 92 |
| 776-C1 | Cerebellum | BXD12 | F | 130 |
| 756-C1 | Cerebellum | BXD12 | M | 64 |
| 794-C1 | Cerebellum | BXD14 | F | 190 |
| 758-C1 | Cerebellum | BXD14 | M | 91 |
| 750-C1 | Cerebellum | BXD16 | F | 163 |
| 772-C1 | Cerebellum | BXD19 | F | 61 |
| 751-C1 | Cerebellum | BXD2 | F | 142 |
| 774-C1 | Cerebellum | BXD2 | F | 78 |
| 711-C1 | Cerebellum | BXD21 | F | 116 |
| 803-C1 | Cerebellum | BXD21 | M | 64 |
| S174-1C1 | cerebellum | BXD22 | F | 65 |
| 814-C1 | Cerebellum | BXD23 | F | 88 |
| 805-C1 | Cerebellum | BXD24 | F | 71 |
| 759-C1 | Cerebellum | BXD24 | M | 71 |
| S429-1C1 | cerebellum | BXD25 | M | 90 |
| 785-C1 | Cerebellum | BXD28 | F | 113 |
| S203-1C1 | cerebellum | BXD28 | F | 427 |
| 777-C1 | Cerebellum | BXD29 | F | 82 |
| 714-C1 | Cerebellum | BXD29 | M | 76 |
| 714-C1 | Cerebellum | BXD29 | M | 76 |
| 816-C1 | Cerebellum | BXD31 | F | 142 |
| 778-C1 | Cerebellum | BXD32 | F | 62 |
| 786-C1 | Cerebellum | BXD32 | M | 218 |
| 793-C1 | Cerebellum | BXD33 | F | 184 |
| 715-C1 | Cerebellum | BXD33 | M | 124 |
| 725-C1 | Cerebellum | BXD34 | F | 56 |
| 789-C1 | Cerebellum | BXD34 | M | 91 |
| 781-C1 | Cerebellum | BXD38 | F | 55 |
| 761-C1 | Cerebellum | BXD38 | M | 65 |
| 723-C1 | Cerebellum | BXD39 | M | 165 |
| 718-C1 | Cerebellum | BXD40 | F | 56 |
| 718-C1 | Cerebellum | BXD40 | F | 56 |
| 812-C1 | Cerebellum | BXD40 | M | 73 |
| 799-C1 | Cerebellum | BXD42 | F | 100 |
| 709-C1 | Cerebellum | BXD42 | M | 97 |
| 802-C1 | Cerebellum | BXD5 | F | 56 |
| 752-C1 | Cerebellum | BXD5 | M | 71 |
| 719-C1 | Cerebellum | BXD6 | F | 92 |
| S173-1C1 | cerebellum | BXD8 | F | 72 |
| 737-C1 | Cerebellum | BXD9 | M | 86 |
| 773-C1 | Cerebellum | C57BL/6J | F | 116 |
| S054-1C2 | cerebellum | C57BL/6J | M | 109 |
| S175-1C1 | cerebellum | DBA/2J | F | 71 |
| 782-C1 | Cerebellum | DBA/2J | F | 91 |
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About 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-score 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 values 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.
- Step 7: Finally, we compute the arithmetic mean of the values for the set of microarrays for each strain. In this September03 data set we have relatively modest numbers of replicates and for this reason we do not yet provide error terms for transcripts or probes. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, array batch, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the .CEL file. We expect to add statistical controls and adjustments for these variables in a subsequent versions of WebQTL.
Probe set data from the .TXT file: These .TXT files were generated using the MAS 5.0. 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 Feb 2002 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.
Data source acknowledgment:
Data were generated with funds contributed equally by The UTHSC-SJCRH Cerebellum Transcriptome Profiling Consortium. Our members include:
- Tom Curran
- Dan Goldowitz
- Kristin Hamre
- Lu Lu
- Peter McKinnon
- Jim Morgan
- Clayton Naeve
- Richard Smeyne
- Robert Williams
- The Center of Genomics and Bioinformatics at UTHSC
- The Hartwell Center at SJCRH
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