UMUTAffy Hippocampus Exon (Feb09) RMA

Accession number: GN206

Data generated by RW Williams, Lu Lu, Manjunatha Jagalur, and David Kulp. All arrays run at the VA Medical Center, Memphis, by Yan Jiao.

Data entered by Arthur Centeno and Manju Jagalur, Feb 27, 2009. This data set modified data for two BXD strains. Data were added for BXD79 that had been incorrectly included as a striatum sample (this data set was therefore deleted from the Exon 1.0ST striatum data set). We also changed data for BXD39. As expected, this addition and correction improved QTL mapping values. For example, for Kcnj9 probe set 4519178 the LRS values increased from 103.3 in the Aug08 data to 115.7 for these Feb09 data. Rob is concerned about the high error term of BXD39.

1. Strain correction: In this step the strong probe level cis-QTLs were identified and using an expectation maximization (EM)-like method, the genotypes of each marker was re-assigned. This set of reassigned markers was compared to existing list genotypes of BXD strains and the maximal match was identified as the correct strain.
      Results: Three chips were initially found to be strain-mislabeled.
   
2. Sex correction: In this step probes that are highly correlated to sex were identified and using an EM-like method we detected and corrected the sex of single array data sets.
      Results: Two chips were found to be sex-mislabeled
   
3. Data exclusion criteria: In this step individual arrays were evaluated. Arrays were systematically excluded from the data set (drop one out) and the number of cis-QTLs was recomputed. If excluding an array resulted in s significantly higher number of cis-QTLs then that array was considered to be of poor quality and was excluded from the final data set This step was repeated across all arrays in multiple cycles until there was no improvement in number of cis-QTLs
   Results: None of the arrays were dropped.
   
4. Tissue correction: In this step probes that are highly correlated to tissue type were identified and EM-like method was used to identify correct tissue.
     Results: Three arrays were found to have been reverse labeled between hippocampus and striatum data sets. Samples were relabeled and reassigned based upon this analysis.
   
5. Noise Removal: A noise component was calculated using the expression of "unhybridized" probes (those with the lowest signal) and was removed from the data.
      Result: A spurious transband was detected on distal chromosome 12 and removed.

After this procedure we analyzed probe sets (n = 64) with the lowest expression (mean between 4.0 to 4.2). These probe sets had no cis eQTLs, confirming the absence of any significant biological variance in their expression. These background probe sets also did not have any notable transband expression pattern using the QTL heatmap function in GeneNetwork. This confirms that residual noise in this data set does not by chance covary well with any genetic markers. The covariation among this set of probe sets is poor. However, a small subset of probe sets do covary and generate a principal component that in total accounts for 25% the variance among this "noise" set. The first PC does not map well to any region. (RWW June 2010).

Index Original CEL Tube ID Strain Age Sex Source 1 JR3551H.CEL jr3551h C57BL/6J 60 F UTM RW 2 JR3552H.CEL jr3552hre C57BL/6J 60 F UTM RW 3 R0572H.CEL r0572h C57BL/6J 69 F 4 R2137H.CEL r2137h C57BL/6J 55 F JAX 5 R3552H.CEL r3552h C57BL/6J 60 F Glenn 6 JR3549H.CEL jr3549h C57BL/6J 60 M UTM RW 7 JR3550H.CEL jr3550hre C57BL/6J 60 M UTM RW 8 R0574H.CEL r0574h C57BL/6J 69 M 9 R2136H.CEL r2136h C57BL/6J 55 M JAX 10 R3549H.CEL r3549h C57BL/6J 60 M Glenn 11 JR3557H.CEL jr3557h DBA/2J 60 F UTM RW 12 JR3558H.CEL jr3558hre DBA/2J 60 F UTM RW 13 R3558H.CEL r3558h DBA/2J 60 F Glenn 14 JR3555H.CEL jr3555h DBA/2J 60 M UTM RW 15 JR3556H.CEL jr3556h DBA/2J 60 M UTM RW 16 R3555H.CEL r3555h DBA/2J 60 M Glenn 17 R3497H.CEL r3497h B6D2F1 58 F Glenn 18 R3500H.CEL r3500h B6D2F1 58 M Glenn 19 R1374H.CEL r1374h D2B6F1 58 F UTM RW 20 R1382H.CEL r1382h D2B6F1 59 M UTM RW 21 R3532H.CEL r3532h 129S1/SvImJ 60 F Glenn 22 R3512H.CEL r3512h 129S1/SvImJ 59 M Glenn 23 R3520H.CEL r3520h A/J 59 F Glenn 24 R3523H.CEL r3523h A/J 59 M Glenn 25 R3514H.CEL r3514h AKR/J 59 F Glenn 26 R3515H.CEL r3515h AKR/J 59 M Glenn 27 R3508H.CEL r3508h BALB/cByJ 59 F Glenn 28 R3505H.CEL r3505h BALB/cByJ 59 M Glenn 29 R3524H.CEL r3524h BTBR T+ tf/J 60 F Glenn 30 R3509H.CEL r3509h BTBR T+ tf/J 60 M Glenn 31 R1542H.CEL r1542h BXD1 59 F Glenn 32 R1520H.CEL r1520h BXD2 56 F Glenn 33 R1694H.CEL r1694h BXD5 58 M Glenn 34 R3454H.CEL r3454h BXD6 58 M Glenn 35 R3457H.CEL r3457h BXD8 61 F Glenn 36 R3455H.CEL r3455h BXD9 60 M Glenn 37 R3462H.CEL r3462h BXD11 59 M Glenn 38 R3464H.CEL r3464h BXD12 59 F Glenn 39 R2315H.CEL r2315h BXD13 84 M UTM RW 40 R3480H.CEL r3480h BXD14 60 F Glenn 41 R3478H.CEL r3478h BXD15 60 M Glenn 42 R3482H.CEL r3482h BXD16 59 F Glenn 43 R3488H.CEL r3488h BXD18 59 M Glenn 44 R3471H.CEL r3471h BXD19 60 M Glenn 45 R2506H.CEL r2506h BXD20 60 M Glenn 46 R3490H.CEL r3490h BXD21 60 F Glenn 47 R3492H.CEL r3492h BXD22 60 F Glenn 48 R3486H.CEL r3486h BXD23 60 F Glenn 49 R1547H.CEL r1547h BXD24 59 M Glenn 50 R2892H.CEL r2892h BXD25 67 F UTM RW 51 R3485H.CEL r3485h BXD27 60 M Glenn 52 R3477H.CEL r3477h BXD28 60 F Glenn 53 R3475H.CEL r3475h BXD29 60 F Glenn 54 R3456H.CEL r3456h BXD31 60 M Glenn 55 R3570H.CEL r3570h BXD32 66 F 56 R3571H.CEL r3571h BXD32 58 M 57 R3467H.CEL r3467h BXD33 59 M Glenn 58 R3466H.CEL r3466h BXD34 60 F Glenn 59 R3463H.CEL r3463h BXD36 61 F Glenn 60 R3458H.CEL r3458h BXD38 55 M Glenn 61 JR4433H.CEL jr4433sa BXD39 63 F UTM RW 62 R1535H.CEL r1535h BXD39 60 F Glenn 63 R3459H.CEL r3459h BXD40 60 M Glenn 64 R1541H.CEL r1541h BXD42 58 F Glenn 65 R1279H.CEL r1279h BXD43 57 M UTM RW 66 R1472H.CEL r1472h BXD45 65 M UTM RW 67 R1586H.CEL r1586h BXD48 59 F UTM RW 68 R2936H.CEL r2936h BXD50 61 F UTM RW 69 R1313H.CEL r1313h BXD51 62 M UTM RW 70 JR2680H.CEL jr2680h BXD55 65 M UTM RW 71 R1340H.CEL r1340h BXD60 64 F UTM RW 72 R1856H.CEL r1856h BXD61 94 M UTM RW 73 R1317H.CEL r1317h BXD62 59 F UTM RW 74 R1945H.CEL r1945h BXD63 107 F UTM RW 75 R2615H.CEL r2615h BXD64 68 F UTM RW 76 R3567H.CEL r3567h BXD65 60 F UTRW 77 R1949H.CEL r1949h BXD66 96 M UTM RW 78 R2060H.CEL r2060h BXD67 54 F UTM RW 79 R2902H.CEL r2902h BXD68 57 M UTM RW 80 R1466H.CEL r1466h BXD69 59 F UTM RW 81 R2063H.CEL r2063h BXD70 55 M UTM RW 82 R1269H.CEL r1269h BXD73 72 M UTM RW 83 JR2316H.CEL jr2316hre BXD74 193 M UTM RW 84 R1871H.CEL r1871h BXD75 61 F UTM RW 85 JR1948H.CEL jr1948h BXD76 81 F UTM RW 86 R1427H.CEL r1427h BXD77 61 M UTM RW 87 JR4434H.CEL jr4434sare BXD79 63 F UTM RW 88 R3568H.CEL r3568h BXD80 66 M UTRW 89 R2959H.CEL r2959h BXD83 58 F UTM RW 90 R2898H.CEL r2898h BXD84 67 M UTM RW 91 R3566H.CEL r3566h BXD85 65 M UTRW 92 R1556H.CEL r1556h BXD86 57 F UTM RW 93 R1710H.CEL r1710h BXD87 84 M UTM RW 94 JR4079H.CEL jr4079hre BXD89 63 M UTM RW 95 R2058H.CEL r2058h BXD90 61 F UTM RW 96 R1284H.CEL r1284h BXD92 58 M UTM RW 97 JR2057H.CEL jr2057h BXD93 92 F UTM RW 98 JR2313H.CEL jr2313h-re BXD94 59 F UTM RW 99 R1915H.CEL r1915h BXD96 65 F UTM RW 100 R2648H.CEL r2648h BXD97 74 F UTM RW 101 R1942H.CEL r1942h BXD98 62 F UTM RW 102 R1369H.CEL r1369h BXD99 76 M UMemphis 103 R2889H.CEL r2889h BXSB/MpJ 61 F Glenn 104 R2887H.CEL r2887h BXSB/MpJ 61 M Glenn 105 R3501H.CEL r3501h C3H/HeJ 60 F Glenn 106 R3504H.CEL r3504h C3H/HeJ 60 M Glenn 107 R3564H.CEL r3564h CAST/EiJ 57 F Glenn 108 R3565H.CEL r3565h CAST/EiJ 61 M Glenn 109 R3493H.CEL r3493h FVB/NJ 60 F Glenn 110 R3496H.CEL r3496h FVB/NJ 60 M Glenn 111 JR1683H.CEL jr1683h KK/HlJ 72 F UTM RW 112 JR3542H.CEL jr3542hre KK/HlJ 61 M UTM RW 113 JR2046H.CEL jr2046hre LG/J 63 F UTM RW 114 JR2047H.CEL jr2047h LG/J 63 M UTM RW 115 R3541H.CEL r3541h MOLF/EiJ 60 F Glenn 116 R3553H.CEL r3553h MOLF/EiJ 60 M Glenn 117 R3516H.CEL r3516h NOD/LtJ 58 F Glenn 118 R3519H.CEL r3519h NOD/LtJ 58 M Glenn 119 R3554H.CEL r3554h NZB/BlNJ 61 F Glenn 120 R3513H.CEL r3513h NZB/BlNJ 58 M Glenn 121 R3539H.CEL r3539h NZO/HlLtJ 60 F Glenn 122 R3536H.CEL r3536h NZO/HlLtJ 60 M Glenn 123 R3540H.CEL r3540h NZW/LacJ 65 F Glenn 124 R3535H.CEL r3535h NZW/LacJ 60 M Glenn 125 R3527H.CEL r3527h PWD/PhJ 60 F Glenn 126 R3526H.CEL r3526h PWD/PhJ 60 M Glenn 127 R3531H.CEL r3531h PWK/PhJ 60 M Glenn 128 R3561H.CEL r3561h WSB/EiJ 60 F Glenn 129 R3525H.CEL r3525h WSB/EiJ 60 M Glenn

We thank Affymetrix Inc. for their generous support of this project and array data set.

Table updated by Rob with questions for Arthur, Aug 13, 2009.