HEIMED M430 Microarray Eye RMA November05 / WebQTL

From ea46f42ee640928b92947bfb204c41a482d80937 Mon Sep 17 00:00:00 2001 From: root Date: Tue, 8 May 2012 18:39:56 -0500 Subject: Add all the source codes into the github. --- web/dbdoc/EYE_M2_1105_R.html | 329 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 329 insertions(+) create mode 100755 web/dbdoc/EYE_M2_1105_R.html (limited to 'web/dbdoc/EYE_M2_1105_R.html') diff --git a/web/dbdoc/EYE_M2_1105_R.html b/web/dbdoc/EYE_M2_1105_R.html new file mode 100755 index 00000000..25a9369d --- /dev/null +++ b/web/dbdoc/EYE_M2_1105_R.html @@ -0,0 +1,329 @@ + +HEIMED M430 Microarray Eye RMA November05 / WebQTL + + + + + + + + + + + + + + + + + +

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+ +Hamilton Eye Institute Mouse Eye M430v2 (November05) RMA Data Set

Accession number: GN93

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Summary:

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+SUPERCEDED EYE DATASET. The HEIMED November 2005 data set provides estimates of mRNA expression in whole eyes of 63 lines of mice without significant biological replication. Data were generated at UTHSC with support from a grant from Dr. Barrett Haik, Director of the Hamilton Eye Institute (HEI). Pooled RNA samples were hybridized to Affymetrix M430 2.0 arrays. This particular data set was processed using the RMA protocol. To simplify comparison among different transforms, RMA values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units.
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About the cases used to generate this set of data:

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+We have used a set of 14 conventional inbred strains, reciprocal F1s between C57BL/6J (B6 or B) and DBA/2J D2 (or D), and 47 BXD recombinant inbred strains. The BXD strains were generated by crossing C57BL/6J with DBA/2J. The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage of D). Physical maps in WebQTL incorporate approximately 2 million B vs D SNPs from Celera Genomics and from the Perlegen-NIEHS sequencing effort. BXD1 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory. + +
Please note that BXD24/TyJ (JAX stock number 000031) used in this study is also known as BXD24b/TyJ and has complete retinal degeneration. BXD24a/TyJ, a 1988 F80 stock that has now been rederived, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control. + +
BXD43 through BXD99 were bred 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). Many of the 50 new BXD strains are available from Lu Lu and colleagues.
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Mouse Diversity Panel (MDP). In addition to the BXD strains, we have profiled a MDP consisting 14 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons: +
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genetic and phenotypic diversity, including use by the Phenome Project +
their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains +
their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA) +
genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS) +
availability from The Jackson Laboratory +
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All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants. + +
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129S1/SvImJ +
    Collaborative Cross strain sequenced by NIEHS; background for many knockouts (R1 ES cell line); Phenome Project A list. This strain (JAX No 002448, aka 129S1/Sv-++Kitl/+) also carries hypopigmentation mutations (white bellied chinchilla) of the tyrosinase gene on Chr 7 and a mutant allele of the steel (Kitl) gene. + +
A/J +
    Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel. A tyrosinase-negative albino (c) mutant + + +
BALB/cByJ +
     Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list. A tyrosinase-negative albino (c) mutant + + +
C3H/HeJ
    Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list. Important to note for this Eye dataset, C3H/HeJ is a Pdeb6 mutant with near total photoreceptor loss at maturity. + +
C57BL/6J +
    Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list + +
CAST/Ei +
    Collaborative Cross strain sequenced by NIEHS; Phenome Project A list + +
DBA/2J +
    Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list + +
KK/HlJ +
    Sequenced by Perlegen/NIEHS + +
LG/J +
    Paternal parent of the LGXSM panel + +
NOD/LtJ +
    Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic + +
NZO/HILtJ +
    Collaborative Cross strain + +
PWD/PhJ +
    Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues + +
PWK/PhJ +
    Collaborative Cross strain; Phenome Project D list + +
WSB/EiJ
    Collaborative Cross strain sequenced by NIEHS; Phenome Project C list + +
B6D2F1 and D2B6F1, aka F1 in some graphs and tables +
F1 hybrids generated by crossing C57BL/6J with DBA/2J +
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    About the tissue used to generate this set of data:
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Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Eyes were removed immediately and placed in RNAlater at room temperature. Usually six eyes from animals with a common sex, age, and strain were stored in a single tube. + +
Each array was hybridized with a pool of RNA from 4 to 8 eyes from 2 to 4 animals. RNA was extracted at UTHSC by Zhiping Jia. If tissue was saved for RNA extraction at a later time, eyes were placed directly in RNAlater (Ambion, Inc.) and treated per the manufacturer’s directions. If eyes were used for immediate RNA extraction then we proceeded immediately to the next steps.
+ +Dissecting and preparing eyes for RNA extraction +
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Place eyes for RNA extraction in RNA STAT-60 (Tel-Test Inc.) and process per manufacturer’s instructions (in brief form below). +
Store RNA in 75% ethanol at –80 deg. C until use. +
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Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we: +
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homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue) +
allowed the homogenate to stand for 5 min at room temperature +
added 0.2 ml of chloroform per 1 ml RNA STAT-60 +
shook the sample vigorously for 15 sec and let the sample sit at room temperature for 3 min +
centrifuged at 12,000 G for 15 min +
transfered the aqueous phase to a fresh tube +
added 0.5 ml of isopropanol per 1 ml RNA STAT-60 +
vortexed and allowed sample to stand at room temperature for 5-10 min +
centrifuged at 12,000 G for 10-15 min +
removed the supernatant and washed the RNA pellet with 75% ethanol +
stored the pellet in 75% ethanol at -80 deg C until use +
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Sample Processing. Samples were processed in the VA Medical Center, Memphis, Rheumatology Disease Research Core Center lead by Drs. John Stuart and Weikuan Gu. All processing steps were performed by Dr. Yan Jiao. In brief, samples were purified using a standard sodium acetate in alcohol method (recommended by Affymetrix). The RNA quality was checked using a 1% agarose gel. The 18S and 28S bands had to be clear and the 28S band had to be more prominent. RNA concentation was measured using a spectrophotometer. The 260/280 ratios had to be greater than 1.7, and the majority were 1.8 or higher. We used a total of 8 micrograms of RNA as starting amount for cDNA synthesis using a standard Eberwine T7 polymerase method (Superscript II RT, Invitrogen Inc., Affy Part No 900431, GeneChip Expression 3' Amplification One-Cyle cDNA Synthesis Kit). The Affymetrix IVT labeling kit (Affy 900449) was used to generate labeled cRNA. At this point the cRNA was evaluated again using both the 260/280 ratio (values of 2.0 or above were acceptable) and 1% agarose gel inspection of the product (a size range from 200 to 7000 bp is considered suitable for use). We used 45 micrograms of labeled cRNA for fragmentation. Those samples that passed both QC steps (<10% usually fail) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No.900371). After fragmentation, samples were either stored at -80 deg. centrigrade until use (one third roughly) or were immediately used for hybridization. + +
Dealing with Ocular Pigmentation: Variable ocular pigmentation is a potential confound in a study of the whole eye transcriptome. Even the most careful RNA preparations of brown and beige colored mice tend to have faint residual pigmentation that does affect hybridization signal. The key determinant of this interesting effect is the Tyrp1 (brown) locus on Chr 5 at about 80 Mb. Loci on Chr 4 that map at this location should be considered with skepticism and reviewed carefully. To address this problem Yan Jiao purified total RNA a second time using the Qiagen RNeasy MinElute Cleanup Kit (Cat No. 74204). This was done for 8 colored samples (R2534E2, R2578E2, R1441E2, R2537E2, R2536E2, R2589E2, R2539E2), of which 5 were finally included in this data set (cases in which the strain ID is labeled with asterisks in the table). + + +
Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one of sample from each sex for all BXD strains. The current first batch of array data, represents a balanced sample of males and females, but without within-strain replication. We expect to add roughly 100 additional samples inthe next few months. + +
Batch Structure: This data set consists of a single batch. The great majority of arrays are from a single lot. + +
The table below summarizes information on strain, age, sex, original CEL filename, several quality control values, and source of mice. Columns labeled "PDNN 2Z outlier" and "RMA 2Z outlier" list the fraction of probe sets with values that deviated more than 2 z units from the mean. Scale factor, background average, present, absent, marginal and 3'/5' ratios for actin and Gapdh were collated from the Affymetrix Report (RPT) files. +
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Id tube ID group type Strain age sex original CEL filename PDNN 2Z outlier RMA 2Z outlier scale factor background average present absent marginal AFFX-b-ActinMur(3'/5') AFFX-GapdhMur(3'/5') source
1 R2607E1 GDP BXD C57BL/6J 67 F R2605E.CEL 0.005 0.009 2.428 115.12 0.586 0.4 0.014 1.31 0.76 UTM RW
2 R0872E2 GDP BXD C57BL/6J 66 M R0872E.CEL 0.013 0.012 3.128 88.58 0.589 0.396 0.015 1.3 0.79 UTM RW
3 R2572E1 GDP BXD DBA/2J 65 M R2572E.CEL 0.041 0.051 2.406 79.07 0.555 0.429 0.016 1.37 0.79 UTM RW
4 R2601E1 GDP BXD B6D2F1 73 F R2601E.CEL 0.003 0.004 2.545 91.96 0.589 0.396 0.015 1.44 0.78 UTM RW
5 R2602E1 GDP BXD B6D2F1 73 M R2602E.CEL 0.001 0.004 2.599 84.44 0.597 0.388 0.015 1.37 0.78 UTM RW
6 R2600E1 GDP BXD D2B6F1 72 F R2600E.CEL 0.003 0.008 2.47 94.75 0.581 0.402 0.017 1.41 0.78 UTM RW
7 R2604E1 GDP BXD D2B6F1 69 M R2604E.CEL 0.003 0.007 2.657 89.63 0.594 0.392 0.015 1.28 0.79 UTM RW
8 R2597E1 BXD BXD2 61 M R2597E.CEL 0.003 0.007 2.374 93.56 0.603 0.383 0.015 1.34 0.77 Glenn
9 R2591E1 BXD BXD5 60 F R2591E.CEL 0.051 0.009 1.7 136.48 0.585 0.4 0.015 1.33 0.78 Glenn
10 R2570E1 BXD BXD6 65 F R2570E.CEL 0.002 0.006 1.987 86.73 0.585 0.4 0.015 1.46 0.76 UTM RW
11 R2538E1 BXD BXD8 77 F R2538E.CEL 0.037 0.028 1.905 101.98 0.612 0.373 0.015 1.52 0.79 UTM RW
12 R2569E1 BXD BXD9 67 M R2569E.CEL 0.014 0.027 1.753 87.36 0.551 0.434 0.015 2.82 3.14 UTM RW
13 R2581E1 BXD BXD11 65 F R2581E.CEL 0.006 0.012 1.941 88.55 0.621 0.364 0.016 1.55 0.81 UTM RW
14 R2543E1 BXD BXD12 63 M R2543E.CEL 0.036 0.007 1.605 117.69 0.586 0.399 0.016 1.43 0.77 UTM RW
15 R2586E1 BXD BXD13 60 F R2586E.CEL 0.020 0.035 2.006 73.61 0.564 0.42 0.016 2.85 3.81 Glenn
16 R2557E1 BXD BXD14 60 F R2557E.CEL 0.014 0.017 1.83 98.76 0.625 0.361 0.014 1.31 0.78 Glenn
17 R2567E1 BXD BXD16 60 M R2567E.CEL 0.016 0.025 2.239 82.35 0.567 0.416 0.017 1.37 0.75 Glenn
18 R2559E1 BXD BXD18 59 M R2559E.CEL 0.035 0.006 1.654 103.68 0.608 0.377 0.015 1.27 0.78 Glenn
19 R2560E1 BXD BXD19 60 F R2560E.CEL 0.026 0.007 1.792 98.33 0.609 0.375 0.016 1.35 0.8 Glenn
20 R2584E1 BXD BXD20 59 F R2584E.CEL 0.003 0.007 2.07 83.82 0.593 0.391 0.016 1.4 0.76 Glenn
21 R2541E2 BXD BXD21 61 M R2541E2.CEL 0.049 0.036 2.625 125.08 0.56 0.424 0.015 1.29 0.78 UTM RW
22 R2553E1 BXD BXD22 58 F R2553E.CEL 0.003 0.005 1.952 111.3 0.599 0.385 0.015 1.28 0.76 Glenn
23 R2558E1 BXD BXD23 60 F R2558E2.CEL 0.013 0.015 1.908 114.53 0.599 0.388 0.014 1.2 0.82 Glenn
24 R2589E2 BXD BXD24-rd* 59 M R2589E2.CEL 0.098 0.098 2.606 112.19 0.575 0.409 0.016 1.24 0.8 Glenn
25 R2573E1 BXD BXD25 67 F R2573E2.CEL 0.009 0.018 3.153 71.88 0.579 0.407 0.014 1.77 0.97 UAB
26 R2562E1 BXD BXD28 60 F R2562E.CEL 0.003 0.005 1.649 116.35 0.599 0.384 0.017 1.37 0.79 Glenn
27 R2561E1 BXD BXD29 60 F R2561E.CEL 0.019 0.029 1.952 93.32 0.583 0.402 0.015 2.19 1 Glenn
28 R2598E1 BXD BXD31 61 M R2598E.CEL 0.003 0.006 1.989 106.48 0.609 0.376 0.015 1.27 0.78 UTM RW
29 R2563E1 BXD BXD32 63 F R2563E.CEL 0.008 0.011 1.547 101.52 0.619 0.367 0.014 1.5 0.8 UTM RW
30 R2542E1 BXD BXD33 67 F R2542E.CEL 0.010 0.016 2.128 97.08 0.565 0.418 0.016 1.91 0.93 UTM RW
31 R2585E1 BXD BXD34 60 M R2585E.CEL 0.007 0.014 2.64 75.13 0.583 0.4 0.017 1.25 0.77 Glenn
32 R2532E1 BXD BXD38 62 M R2532E.CEL 0.002 0.003 2.038 93.65 0.598 0.387 0.015 1.37 0.8 UTM RW
33 R2574E1 BXD BXD39 70 F R2574E.CEL 0.001 0.004 1.981 90.64 0.612 0.373 0.015 1.39 0.78 UTM RW
34 R2590E1 BXD BXD40 60 M R2590E.CEL 0.004 0.007 2.708 77.3 0.591 0.393 0.015 1.4 0.77 Glenn
35 R2596E1 BXD BXD42 59 M R2596E.CEL 0.013 0.017 2.632 108.46 0.59 0.396 0.015 1.24 0.8 Glenn
36 R2605E1 BXD BXD43 79 M R2607E.CEL 0.003 0.006 1.817 131.22 0.605 0.382 0.013 1.32 0.8 UTM RW
37 R2594E1 BXD BXD44 63 F R2594E.CEL 0.004 0.009 1.766 117.33 0.598 0.388 0.014 1.35 0.85 UTM RW
38 R2592E1 BXD BXD45 62 M R2592E.CEL 0.002 0.004 1.85 106.16 0.601 0.386 0.013 1.43 0.85 UTM RW
39 R2606E1 BXD BXD48 78 M R2606E.CEL 0.003 0.010 2.556 106.16 0.589 0.397 0.014 1.35 0.83 UTM RW
40 R2603E1 BXD BXD51 66 F R2603E.CEL 0.003 0.009 2.488 115.16 0.577 0.408 0.015 1.24 0.79 UTM RW
41 R2534E2 BXD BXD61* 70 F R2534E2.CEL 0.030 0.028 2.473 117.76 0.579 0.406 0.015 1.42 0.79 UTM RW
42 R2611E1 BXD BXD64 68 M R2611E.CEL 0.013 0.022 2.292 91.99 0.58 0.405 0.015 1.57 1.06 UTM RW
43 R2583E1 BXD BXD65 60 M R2583E.CEL 0.005 0.010 2.492 70.43 0.569 0.415 0.016 1.67 1.01 UTM RW
44 R2536E2 BXD BXD66* 64 F R2536E2.CEL 0.039 0.065 2.74 108.62 0.561 0.423 0.017 1.28 0.79 UTM RW
45 R2551E1 BXD BXD68 67 F R2551E.CEL 0.037 0.039 2.493 92.38 0.543 0.441 0.016 2.91 1.55 UTM RW
46 R2593E1 BXD BXD69 59 F R2593E.CEL 0.008 0.013 1.672 127.6 0.592 0.395 0.013 1.47 0.92 UTM RW
47 R2537E2 BXD BXD70* 59 M R2537E2.CEL 0.046 0.044 2.93 98.66 0.58 0.405 0.016 1.29 0.75 UTM RW
48 R2565E1 BXD BXD75 61 F R2565E.CEL 0.009 0.017 1.79 101.68 0.58 0.405 0.015 2.31 3.47 UTM RW
49 R2579E1 BXD BXD80 65 F R2579E.CEL 0.005 0.010 2.419 72.13 0.592 0.394 0.015 1.73 0.82 UTM RW
50 R2540E1 BXD BXD87 63 M R2540E.CEL 0.013 0.016 2.333 93.15 0.611 0.374 0.014 1.22 0.81 UTM RW
51 R2545E1 BXD BXD89 67 M R2546E.CEL 0.046 0.046 1.667 104.76 0.562 0.423 0.015 3.6 9.84 UTM RW
52 R2578E2 BXD BXD90* 61 F R2578E2.CEL 0.033 0.034 2.785 92.27 0.586 0.398 0.016 1.52 0.77 UTM RW
53 R2554E1 BXD BXD96 67 M R2554E.CEL 0.004 0.004 2.177 93.02 0.602 0.383 0.015 1.46 0.77 UTM RW
54 R2577E1 BXD BXD97 55 M R2577E.CEL 0.019 0.016 2.07 76.58 0.595 0.391 0.014 1.87 1.29 UTM RW
55 R2595E1 GDP 129S1/SvImJ 59 F R2595E.CEL 0.017 0.021 1.792 115.39 0.61 0.375 0.015 1.46 0.77 UTM RW
56 R2533E1 GDP 129S1/SvImJ 60 M R2533E.CEL 0.021 0.013 2.107 93.55 0.579 0.405 0.016 1.37 0.78 UTM RW
57 R2546E1 GDP A/J 66 F R2545E.CEL 0.018 0.014 1.989 95.59 0.586 0.397 0.017 1.47 0.78 UTM RW
58 R0754E2 GDP A/J 60 M R0754E.CEL 0.014 0.016 2.718 85.63 0.598 0.387 0.015 1.36 0.76 JAX
59 R1676E1 GDP BALB/cByJ 83 F R1676E.CEL 0.042 0.041 2.685 98.37 0.589 0.396 0.015 1.46 0.74 JAX
60 R1672E1 GDP BALB/cByJ 83 M R1672E.CEL 0.022 0.022 2.216 110.52 0.599 0.386 0.015 1.26 0.8 JAX
61 R1700E1 GDP C3H/HeJ 83 F R1700E.CEL 0.090 0.092 2.978 68.77 0.608 0.379 0.014 1.48 0.78 UTM RW
62 R1704E1 GDP C3H/HeJ 83 M R1704E.CEL 0.086 0.089 2.581 88.29 0.601 0.386 0.013 1.38 0.84 UTM RW
63 R2564E1 GDP CAST/Ei 64 F R2564E.CEL 0.078 0.064 1.937 88.89 0.585 0.399 0.016 1.6 0.77 JAX
64 R2580E1 GDP CAST/Ei 64 M R2580E.CEL 0.076 0.067 2.089 94.64 0.582 0.401 0.017 1.4 0.76 JAX
65 R2636E1 GDP KK/HIJ 64 F R2636E.CEL 0.023 0.026 2.61 93.1 0.589 0.395 0.015 1.39 0.76 UTM RW
66 R2637E1 GDP KK/HIJ 64 M R2637E.CEL 0.039 0.020 2.189 102.78 0.594 0.39 0.015 1.3 0.79 UTM RW
67 R0999E1 GDP LG/J 57 F R0999E.CEL 0.012 0.012 2.448 82.09 0.594 0.391 0.015 1.38 0.79 UTM RW
68 R1004E1 GDP LG/J 65 M R1004E.CEL 0.013 0.015 2.438 91.71 0.587 0.398 0.015 1.38 0.79 UTM RW
69 R1688E1 GDP NOD/LtJ 66 F R1688E.CEL 0.017 0.019 2.664 97.65 0.586 0.399 0.015 1.26 0.8 JAX
70 R2566E1 GDP NOD/LtJ 76 M R2566E2.CEL 0.019 0.025 3.031 69.44 0.598 0.388 0.015 1.38 0.75 UTM RW
71 R2550E1 GDP NZO/HlLtJ 96 M R2550E.CEL 0.023 0.015 1.794 87.16 0.607 0.378 0.015 1.52 0.82 JAX
72 R2535E1 GDP NZO/HlLtJ 62 F R2535E.CEL 0.046 0.025 1.893 85.67 0.604 0.382 0.014 1.41 0.85 JAX
73 R2634E1 GDP PWD/PhJ 62 F R2635E.CEL 0.077 0.069 3.292 89.8 0.559 0.425 0.016 1.57 0.81 JAX
74 R2635E1 GDP PWD/PhJ 62 M R2634E.CEL 0.088 0.081 3.722 80.05 0.542 0.441 0.017 1.53 0.85 JAX
75 R2544E1 GDP PWK/PhJ 63 F R2544E.CEL 0.106 0.100 2.196 107.51 0.549 0.435 0.017 1.36 0.82 JAX
76 R2549E1 GDP PWK/PhJ 83 M R2549E.CEL 0.065 0.048 2.275 83.8 0.573 0.412 0.015 1.57 0.83 JAX
77 R2368E1 GDP WSB/EiJ 67 F R2368E.CEL 0.025 0.028 2.567 85.7 0.595 0.391 0.014 1.29 0.74 UTM RW
78 R2547E1 GDP WSB/EiJ 67 M R2547E.CEL 0.032 0.021 2.135 90.04 0.582 0.401 0.016 1.32 0.77 UTM RW

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    About the array platfrom :
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Affymetrix Mouse Genome 430 2.0 arrays: The 430 2.0 array consists of 992936 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are essentially duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contain the same probe sequence as the old M430A and 430B array pair. However, we have found that roughy 75000 probes differ between those on A and B arrays and those on the new 430 2.0.
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    About data processing:
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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. +
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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 of the log base 2 values for the total set of arrays 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 two-fold difference in expression level corresponds approximately to a 1 unit difference. + +
Step 7: Finally, when appropriate, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. + +
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    Data source acknowledgment:
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+Support for acquisition of microarray data sets was generously provided by Dr. Barrrett Haik, Chair of the Department of Ophthalmology, and director of the Hamilton Eye Institute. Support for the continued development of GeneNetwork was provided by a NIDA/NIMH/NIAAA Human Brain Project grant. All arrays were processed at the VA Medical Center, Memphis by Weikuan Gu. +
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    Information about this text file:
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This text file originally generated by RWW, Nov 4, 2005. Updated by RWW, Nov 5, 2005. Modified Nov 7 with help of Y. Jiao. +
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