Data Set Group: SJUT Cerebellum mRNA M430 (Mar05)

Contact Information 
Robert Williams
University of Tennessee Health Science Center
71 S Manassas St, Room 405 TSRB
Memphis, TN 38163 USA
Tel. 901 4487050
rwilliams@uthsc.edu
Website

Download datasets and supplementary data files 



Specifics of this Data Set: 
None

Summary: 
This March 2005 data freeze provides estimates of mRNA expression in adult cerebellum of 48 lines of mice including 45 BXD recombinant inbred strains, C57BL/6J, DBA/2J, and F1 hybrids. Data were generated by a consortium of investigators at St. Jude Children's Research Hospital (SJ) and the University of Tennessee Health Science Center (UT). Cerebellar samples were hybridized in small pools (n = 3) to Affymetrix M430A and B arrays. This particular data set was processed using the Microarray Suite 5 (<a datackesavedhref="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" _blank"="" class="fs14">MAS 5) protocol. To simplify comparisons among transforms, MAS5 values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.

About the cases used to generate this set of data: 
We have exploited a set of BXD recombinant inbred strains. All BXD lines are derived crossed between C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D parental strains have been almost fully sequenced (8x coverage for B6 by a public consortium and approximately 1.5x coverage for D by Celera Discovery Systems) and data for 1.75 millioin B vs D SNPs are incorporated into WebQTLs genetic maps for the BXDs. BXD2 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were also produced by Taylor, but they were generated in the 1990s. These strains are all available from The Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004).
Most BXD animals were generated inhouse at the University of Tennessee Health Science Center by Lu Lu and Robert Williams using stock obtained from The Jackson Laboratory between 1999 and 2004. All BXD strains with numbers above 42 are new advanced intecross type BXDs (Peirce et al. 2004) that are current available from UTHSC. Additional cases were provided by Glenn Rosen, John Mountz, and HuiChen Hsu. These cases were bred either at The Jackson Laboratory (GR) or at the University of Alabama (JM and HCH).

About the tissue used to generate this set of data: 
The March 2005 data set consists of a total of 102 array pairs (Affymetrix 430A and 430B) from 49 different genotypes. Each sample consists of whole cerebellum taken from three adult animals of the same age and sex. Two sets of technical replicates (BXD14 n = 2; BXD29 n = 3) were combined before generating group means; giving a total of 101 biologically independent data sets. The two reciprocal F1s (D2B6F1 and B6D2F1) were combined to give a single F1 mean estimate of gene expression. 430A and 430B arrays were processed in three large batches. The first batch (May03 data) consists of 17 samples from 17 strains balanced by sex (8M and 9F). The second batch consists of 29 samples, and includes biological replicates, 2 technical replicates, and data for 9 new strains. The third batch consists of 56 samples, and also includes biological replicates, 2 technical replicates, and data for 15 additional strains.
Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from both sexes for each strain. Six of 48 genotypes are still represented by single samples: BXD5, BXD13, BXD20, BXD23, BXD27 are femaleonly strains, whereas BXD25, BXD77, BXD90 are maleonly. Ten strains are represented by three independent samples with the following breakdown by sex: C57BL/6J (1F 2M), DBA/2J (2F 1M), B6D2F1 (1F 2M), BXD2 (2F 1M), BXD11 (2F 1M), BXD28 (2F 1M), BXD40 (2F 1M), BXD51 (1F 2M), BXD60 (1F 2M), BXD92 (2F 1M).
The age range of samples is relatively narrow. Only 18 samples were taken from animals older than 99 days and only two samples are older than 7 months of age. BXD11 includes an extra (third) 441dayold female sample and the BXD28 includes an extra 427dayold sample.
RNA was extracted at UTHSC by Lu Lu, Zhiping Jia, and Hongtao Zhai.
All samples were subsequently processed at the Hartwell Center Affymetrix laboratory at SJCRH by Jay Morris.
The table below summarizes information on strain, sex, age, sample name, and batch number.
Id 
Strain 
Sex 
Age 
SampleName

BatchID

Source 
1 
C57BL/6J 
F 
116 
R0773C

2

UAB 
2 
C57BL/6J 
M 
109 
R0054C

1

JAX 
3 
C57BL/6J 
M 
71 
R1450C

3

UTM DG 
4 
DBA/2J 
F 
71 
R0175C

1

UAB 
5 
DBA/2J 
F 
91 
R0782C

2

UAB 
6 
DBA/2J 
M 
62 
R1121C

3

UTM RW 
7 
B6D2F1 
F 
60 
R1115C

3

UTM RW 
8 
B6D2F1 
M 
94 
R0347C

1

JAX 
9 
B6D2F1 
M 
127 
R0766C

2

UTM JB 
10 
D2B6F1 
F 
57 
R1067C

3

UTM RW 
11 
D2B6F1 
M 
60 
R1387C

3

UTM RW 
12 
BXD1 
F 
57 
R0813C

2

UAB 
13 
BXD1 
M 
181 
R1151C

3

UTM JB 
14 
BXD2 
F 
142 
R0751C

1

UAB 
15 
BXD2 
F 
78 
R0774C

2

UAB 
16 
BXD2 
M 
61 
R1503C

3

HarvardU GR 
17 
BXD5 
F 
56 
R0802C

2

UMemphis 
18 
BXD6 
F 
92 
R0719C

1

UMemphis 
19 
BXD6 
M 
92 
R0720C

3

UMemphis 
20 
BXD8 
F 
72 
R0173C

1

UAB 
21 
BXD8 
M 
59 
R1484C

3

HarvardU GR 
22 
BXD9 
F 
86 
R0736C

3

UMemphis 
23 
BXD9 
M 
86 
R0737C

1

UMemphis 
24 
BXD11 
F 
441 
R0200C

1

UAB 
25 
BXD11 
F 
97 
R0791C

3

UAB 
26 
BXD11 
M 
92 
R0790C

2

UMemphis 
27 
BXD12 
F 
130 
R0776C

2

UAB 
28 
BXD12 
M 
64 
R0756C

2

UMemphis 
29 
BXD13 
F 
86 
R1144C

3

UMemphis 
30 
BXD14 
F 
190 
R0794C

2

UAB 
31 
BXD14 
F 
190 
R0794C

3

UAB 
32 
BXD14 
M 
91 
R0758C

2

UMemphis 
33 
BXD14 
M 
65 
R1130C

3

UTM RW 
34 
BXD15 
F 
60 
R1491C

3

HarvardU GR 
35 
BXD15 
M 
61 
R1499C

3

HarvardU GR 
36 
BXD16 
F 
163 
R0750C

1

UAB 
37 
BXD16 
M 
61 
R1572C

3

HarvardU GR 
38 
BXD19 
F 
61 
R0772C

2

UAB 
39 
BXD19 
M 
157 
R1230C

3

UTM JB 
40 
BXD20 
F 
59 
R1488C

3

HarvardU GR 
41 
BXD21 
F 
116 
R0711C

1

UAB 
42 
BXD21 
M 
64 
R0803C

2

UMemphis 
43 
BXD22 
F 
65 
R0174C

1

UAB 
44 
BXD22 
M 
59 
R1489C

3

HarvardU GR 
45 
BXD23 
F 
88 
R0814C

2

UAB 
46 
BXD24 
F 
71 
R0805C

2

UMemphis 
47 
BXD24 
M 
71 
R0759C

2

UMemphis 
48 
BXD25 
M 
90 
R0429C

1

UTM RW 
49 
BXD27 
F 
60 
R1496C

3

HarvardU GR 
50 
BXD28 
F 
113 
R0785C

2

UTM RW 
51 
BXD28 
M 
79 
R0739C

3

UMemphis 
52 
BXD29 
F 
82 
R0777C

2

UAB 
53 
BXD29 
M 
76 
R0714C

1

UMemphis 
54 
BXD29 
M 
76 
R0714C

2

UMemphis 
55 
BXD29 
M 
76 
R0714C

3

UMemphis 
56 
BXD31 
F 
142 
R0816C

2

UAB 
57 
BXD31 
M 
61 
R1142C

3

UTM RW 
58 
BXD32 
F 
62 
R0778C

2

UAB 
59 
BXD32 
M 
218 
R0786C

2

UAB 
60 
BXD33 
F 
184 
R0793C

2

UAB 
61 
BXD33 
M 
124 
R0715C

1

UAB 
62 
BXD34 
F 
56 
R0725C

1

UMemphis 
63 
BXD34 
M 
91 
R0789C

2

UMemphis 
64 
BXD36 
F 
64 
R1667C

3

UTM RW 
65 
BXD36 
M 
61 
R1212C

3

UMemphis 
66 
BXD38 
F 
55 
R0781C

2

UAB 
67 
BXD38 
M 
65 
R0761C

2

UMemphis 
68 
BXD39 
F 
59 
R1490C

3

HarvardU GR 
69 
BXD39 
M 
165 
R0723C

1

UAB 
70 
BXD40 
F 
56 
R0718C

2

UMemphis 
71 
BXD40 
M 
73 
R0812C

2

UMemphis 
72 
BXD42 
F 
100 
R0799C

2

UAB 
73 
BXD42 
M 
97 
R0709C

1

UMemphis 
74 
BXD43 
F 
61 
R1200C

3

UTM RW 
75 
BXD43 
M 
63 
R1182C

3

UTM RW 
76 
BXD44 
F 
61 
R1188C

3

UTM RW 
77 
BXD44 
M 
58 
R1073C

3

UTM RW 
78 
BXD45 
F 
63 
R1404C

3

UTM RW 
79 
BXD45 
M 
93 
R1506C

3

UTM RW 
80 
BXD48 
F 
64 
R1158C

3

UTM RW 
81 
BXD48 
M 
65 
R1165C

3

UTM RW 
82 
BXD51 
F 
66 
R1666C

3

UTM RW 
83 
BXD51 
M 
62 
R1180C

3

UTM RW 
84 
BXD51 
M 
79 
R1671C

3

UTM RW 
85 
BXD60 
F 
64 
R1160C

3

UTM RW 
86 
BXD60 
M 
61 
R1103C

3

UTM RW 
87 
BXD60 
M 
99 
R1669C

3

UTM RW 
88 
BXD62 
M 
61 
R1149C

3

UTM RW 
89 
BXD62 
M 
60 
R1668C

3

UTM RW 
90 
BXD69 
F 
60 
R1440C

3

UTM RW 
91 
BXD69 
M 
64 
R1197C

3

UTM RW 
92 
BXD73 
F 
60 
R1276C

3

UTM RW 
93 
BXD73 
M 
77 
R1665C

3

UTM RW 
94 
BXD77 
M 
62 
R1424C

3

UTM RW 
95 
BXD85 
F 
79 
R1486C

3

UTM RW 
96 
BXD85 
M 
79 
R1487C

3

UTM RW 
97 
BXD86 
F 
58 
R1408C

3

UTM RW 
98 
BXD86 
M 
58 
R1412C

3

UTM RW 
99 
BXD90 
M 
74 
R1664C

3

UTM RW 
100 
BXD92 
F 
62 
R1391C

3

UTM RW 
101 
BXD92 
F 
63 
R1670C

3

UTM RW 
102 
BXD92 
M 
59 
R1308C

3

UTM RW 


About the array platform: 
Affymetrix Mouse Genome 430A and B array pairs: The 430A and B array pairs consist of 992936 25nucleotide probes that collectively estimate the expression of approximately 39,000 transcripts. The array sequences were selected late in 2002 using Unigene Build 107. The arrays nominally contain the same probe sequences as the 430 2.0 series. However, we have found that roughy 75000 probes differ from those on A and B arrays and those on the 430 2.0

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 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 performed a quantile normalization for the log base 2 values for the total set of 104 arrays (all three batches) using the same initial steps used by the RMA transform.
 Step 3: We computed the Z scores for each cell value.
 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 twofold difference in expression level corresponds approximately to a 1 unit difference.
 Step 6: We corrected for technical variance introduced by three large batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all three batches and used this as a single multiplicative probespecific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the three batches is the same.
 Step 7a: The 430A and 430B arrays include a set of 100 shared probe sets (a total of 2200 probes) that have identical sequences. These probes and probe sets provide a way to calibrate expression of the 430A and 430B arrays to a common scale. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression correction 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 small offset. The result of this step is that the mean of the 430A expression is fixed at a value of 8, whereas that of the 430B chip is typically reduced to 7. The average of the merged 430A and 430B array data set is approximately 7.5.
 Step 7b: We recentered the merged 430A and 430B data sets to a mean of 8 and a standard deviation of 2. This involved reapplying Steps 3 through 5.
 Step 8: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
Probe set data: The expression data were processed by Yanhua Qu (UTHSC). Probe set data were generated from the fully normalized CEL files (quantile and batch corrected) using the standard MAS 5 Tukey biweight procedure. A 1unit difference represents roughly a twofold difference in expression level. Expression levels below 5 are usually close to background noise levels.

Notes: 
About the chromosome and megabase position values:
The chromosomal locations of probe sets included on the microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium March 2005 Assembly (see http://genome.ucsc.edu/cgibin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
This text file originally generated by RWW and YHQ, March 21, 2005. Updated by RWW, March 23, 2005; RWW April 8.

Experiment Type: 

Contributor: 

Citation: 

Data source acknowledgment: 
Data were generated with funds contributed by members of the UTHSCSJCRH 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

Study Id: 
12




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