HQF BXD Striatum Illumina Mouse-6.1 November 2007 Rank Invariant Data Set

HQF BXD Striatum Illumina Mouse-6.1 November 2007 Rank Invariant Data Set

Accession number: GN152

NOTE (1): The data from the HQF BXD Striatum Illumina Mouse-6.1 November 2007 Rank Invariant Data Set were corrected for a batch effect due to the hybridization of different strains on different dates. Data were adjusted for individual samples using ANOVA to remove effect of batch (factor = date) in Partek Batch Remover. The first 3 principal components capture 19% of the variance in the entire data set after this correction.

NOTE (2): The data from the HQF BXD Striatum Illumina Mouse-6.1 November 2007 Rank Invariant Data Set were corrected for a batch effect due to the hybridization of different strains on different dates. This data was adjusted to correct for batch effects due to date, slide, and position (see table below). Data from individual samples was adjusted using ANOVA to remove effect of batch (factor = date, factor= slide, factor = position) in Partek Batch Remover. Batch effects were corrected by sequentially removing the effect of (1) date, (2) slide, and (3) position. The first 3 principal components capture 15-16% of the variance in the entire data set after this correction.

INFO file to be provided by Rob Williams and Lu Lu. This data set that is still being error-checked and annotated. Data quality appear to be excellent. There do not appear to be any errors in strain assignment of the BXD lines. Conventional inbred strain (the Mouse Diversity Panel) have not been error checked for genotype.

Illumina Mouse-6.1 array (second generation of the Illumina Mouse 6 platform)
This Rank Invariant Illumina data set yields 1567 probes associated with LOD values of great than 10 using data from 54 BXD strains. This is the second large data set Dr. Lu and colleagues have generated and the first to use the slightly modified Illumina array (6.1) and to use the new slide holder for processing. This data set is of high quality. Our first Illumina array data set (LXS hippocampus May07 Rank Invariant using the first generation Mouse-6 array) yielded 1183 probes with LOD>10 using 75 LXS strains.
Figure 1: Sex balance illustrated by the expression of Xist (Illumina probe 104280446). Strains represented by a single male sample have low expression (BXD44, 65, 66, 69, 70, 85, 86, 87, 89, 90, and 97). Strains represents by one or more female samples have high expression (KK, BXD43, 68, 77, and 100). All other strains are represented by one male and one female sample. Note that the Xist signal intensity in females of the wild strains (PWK, PWD, MOLF, CAST and WSB) is lower than in standard mouse strains.

Useful links

A movie of the dissection of the brain, including the striatum, by Dr. Glenn Rosen.
Notes for Dr. Lu on the RNA cleanup (Jan 22, 2008)
We purify RNA by using Na4OAc before running arrays. Here is the detailed method:
Final RNA purification protocol

Add 1/10th volume of 3M Na4OAc , PH5.2. If the sample was eluted with 100 µl nuclease-free Water as suggested, this will be 10 µl of 3M Na4OAc.
Add 2.5 volumes of 100% ethanol (250 µl if the RNA was eluted in100 µl). Mix well and incubate at –20°C for 2hrs.
Centrifuge at speed of 1,3000 rpm for 20 min at 4°C,Carefully remove and discard the supernatant.
Wash the pellet with 800 µl 75% cold ethanol, centrifuge at speed of 8600 rpm for 5 min, and remove the 75% ethanol. Wash again.
To remove the last traces of ethanol, quickly respin the tube, and aspirate any residual fluid.
Air dry the pellet.
Resuspend pellet in nuclease-free water.

Index Slide Position Strain Tissue Age Sex Date

1 1736925204 D C57BL/6J Striatum 58 F 6.7.07

2 1736925140 D C57BL/6J Striatum 61 M 6.12.07

3 1736925204 E DBA/2J Striatum 58 F 6.7.07

4 1736925140 E DBA/2J Striatum 60 M 6.12.07

5 1736925140 A B6D2F1/J Striatum 59 F 6.12.07

6 1736925204 A B6D2F1/J Striatum 59 M 6.7.07

7 1736925225 A BXD1 Striatum 59 F 6.21.07

8 1716756015 A BXD1 Striatum 59 M 6.22.07

9 1736925169 A BXD2 Striatum 61 F 6.21.07

10 1716756027 A BXD2 Striatum 61 M 6.22.07

11 1716756004 C BXD5 Striatum 58 F 6.22.07

12 1716756036 C BXD5 Striatum 58 M 6.28.07

13 1716756004 D BXD6 Striatum 59 F 6.22.07

14 1716756036 D BXD6 Striatum 59 M 6.28.07

15 1716756004 E BXD8 Striatum 61 F 6.22.07

16 1716756036 E BXD8 Striatum 61 M 6.28.07

17 1716756004 F BXD9 Striatum 60 F 6.22.07

18 1716756036 F BXD9 Striatum 60 M 6.28.07

19 1736925139 C BXD11 Striatum 59 F 6.12.07

20 1716756045 B BXD11 Striatum 59 M 6.28.07

21 1736925225 B BXD12 Striatum 62 F 6.21.07

22 1716756015 B BXD12 Striatum 59 M 6.22.07

23 1736925225 C BXD13 Striatum 60 F 6.21.07

24 1716756015 C BXD13 Striatum 60 M 6.22.07

25 1716756045 C BXD14 Striatum 59 F 6.28.07

26 1736925351 C BXD14 Striatum 60 M 6.15.07

27 1736925225 D BXD15 Striatum 60 F 6.21.07

28 1716756015 D BXD15 Striatum 60 M 6.22.07

29 1736925140 B BXD16 Striatum 58 F 6.12.07

30 1736925204 B BXD16 Striatum 60 M 6.7.07

31 1736925225 E BXD18 Striatum 59 F 6.21.07

32 1716756015 E BXD18 Striatum 59 M 6.22.07

33 1736925225 F BXD19 Striatum 60 F 6.21.07

34 1716756015 F BXD19 Striatum 60 M 6.22.07

35 1716756045 D BXD20 Striatum 60 F 6.28.07

36 1736925139 D BXD20 Striatum 60 M 6.12.07

37 1736925169 B BXD21 Striatum 48 F 6.21.07

38 1716756027 B BXD21 Striatum 48 M 6.22.07

39 1736925351 D BXD22 Striatum 60 F 6.15.07

40 1716756045 E BXD22 Striatum 60 M 6.28.07

41 1736925169 C BXD23 Striatum 60 F 6.21.07

42 1716756027 C BXD23 Striatum 60 M 6.22.07

43 1736925140 C BXD24b Striatum 58 F 6.12.07

44 1736925204 C BXD24b Striatum 58 M 6.7.07

45 1736925169 D BXD27 Striatum 60 F 6.21.07

46 1716756027 D BXD27 Striatum 60 M 6.22.07

47 1736925169 E BXD28 Striatum 60 F 6.21.07

48 1716756027 E BXD28 Striatum 60 M 6.22.07

49 1736925169 F BXD29 Striatum 58 F 6.21.07

50 1716756027 F BXD29 Striatum 58 M 6.22.07

51 1736925171 A BxD31 Striatum 60 F 6.21.07

52 1716756034 A BxD31 Striatum 60 M 6.28.07

53 1736925171 B BXD32 Striatum 57 F 6.21.07

54 1716756034 B BXD32 Striatum 57 M 6.28.07

55 1736925171 C BXD33 Striatum 59 F 6.21.07

56 1716756034 C BXD33 Striatum 59 M 6.28.07

57 1736925171 D BXD34 Striatum 60 F 6.21.07

58 1716756034 D BXD34 Striatum 60 M 6.28.07

59 1736925171 E BXD36 Striatum 57 F 6.21.07

60 1716756034 E BXD36 Striatum 57 M 6.28.07

61 1736925171 F BXD38 Striatum 60 F 6.21.07

62 1716756034 F BXD38 Striatum 60 M 6.28.07

63 1716756004 A BXD40 Striatum 60 F 6.22.07

64 1716756036 A BXD40 Striatum 60 M 6.28.07

65 1716756004 B BXD42 Striatum 58 F 6.22.07

66 1716756036 B BXD42 Striatum 58 M 6.28.07

67 1736925339 E BXD43 Striatum 53 F 7.3.07

68 1736925339 F BXD44 Striatum 56 M 7.3.07

69 1736925300 A BXD45 Striatum 60 F 7.6.07

70 1825397020 D BXD45 Striatum 63 M 7.10.07

71 1736925300 B BXD51 Striatum 66 F 7.6.07

72 1825397020 E BXD51 Striatum 64 M 7.10.07

73 1825397020 F BXD55 Striatum 55 F 7.10.07

74 1736925300 C BXD55 Striatum 55 M 7.6.07

75 1736925300 D BXD60 Striatum 61 F 7.6.07

76 1825397021 A BXD60 Striatum 61 M 7.10.07

77 1736925300 E BXD61 Striatum 62 F 7.6.07

78 1825397021 B BXD61 Striatum 62 M 7.10.07

79 1736925300 F BXD62 Striatum 62 F 7.6.07

80 1825397021 C BXD62 Striatum 63 M 7.10.07

81 1825397021 E BXD65 Striatum 62 M 7.10.07

82 1736925245 B BXD66 Striatum 59 M 7.3.07

83 1736925245 C BXD68 Striatum 56 F 7.3.07

84 1736925245 D BXD69 Striatum 65 M 7.3.07

85 1736925245 E BXD70 Striatum 61 M 7.3.07

86 1736925339 A BXD73 Striatum 62 F 7.3.07

87 1736925292 A BXD73 Striatum 50 M 7.6.07

88 1736925292 D BXD77 Striatum 50 F 7.6.07

89 1736925339 B BXD84 Striatum 55 F 7.3.07

90 1736925292 B BXD84 Striatum 55 M 7.6.07

91 1736925292 E BXD85 Striatum 57 M 7.6.07

92 1736925292 F BXD86 Striatum 58 M 7.6.07

93 1736925299 A BXD87 Striatum 31 M 7.6.07

94 1736925299 B BXD89 Striatum 63 M 7.6.07

95 1736925299 C BXD90 Striatum 66 M 7.6.07

96 1736925292 C BXD96 Striatum 61 F 7.6.07

97 1736925339 C BXD96 Striatum 61 M 7.3.07

98 1736925299 D BXD97 Striatum 61 M 7.6.07

99 1736925339 D BXD100 Striatum 61 F 7.3.07

100 1736925140 F 129S1/SvImJ Striatum 60 F 6.12.07

101 1736925204 F 129S1/SvImJ Striatum 59 M 6.7.07

102 1736925129 A A/J Striatum 59 F 6.7.07

103 1736925241 A A/J Striatum 59 M 6.12.07

104 1736925129 B AKR/J Striatum 59 F 6.7.07

105 1736925241 B AKR/J Striatum 59 M 6.12.07

106 1736925241 C BALB/CByJ Striatum 59 F 6.12.07

107 1736925129 C BALB/CByJ Striatum 59 M 6.7.07

108 1716756045 A BTBRT+tf/J Striatum 59 F 6.28.07

109 1736925139 E BTBRT+tf/J Striatum 60 M 6.12.07

110 1716756045 F BXSB/MpJ Striatum 61 F 6.28.07

111 1736925351 E BXSB/MpJ Striatum 61 M 6.15.07

112 1736925129 D C3H/HeJ Striatum 60 F 6.7.07

113 1736925241 D C3H/HeJ Striatum 60 M 6.12.07

114 1736925129 E CAST/Ei Striatum 57 F 6.7.07

115 1736925241 E CAST/Ei Striatum 61 M 6.12.07

116 1736925129 F FVB/NJ Striatum 60 F 6.7.07

117 1736925241 F FVB/NJ Striatum 60 M 6.12.07

118 1716756057 A KK/HiJ Striatum 62 F 6.7.07

119 1736925303 A KK/HiJ Striatum 62 F 6.15.07

120 1716756057 B MOLF/EiJ Striatum 60 F 6.7.07

121 1736925303 B MOLF/EiJ Striatum 60 M 6.15.07

122 1716756057 D NOD/LtJ Striatum 58 F 6.7.07

123 1736925303 C NOD/LtJ Striatum 58 M 6.15.07

124 1736925303 D NZB/BlnJ Striatum 61 F 6.15.07

125 1716756057 E NZB/BlnJ Striatum 58 M 6.7.07

126 1736925303 E NZO/HiltJ Striatum 61 F 6.15.07

127 1716756057 F NZO/HiltJ Striatum 61 M 6.7.07

128 1736925139 F NZW/LacJ Striatum 65 F 6.12.07

129 1825397021 D NZW/LacJ Striatum 70 M 7.10.07

130 1736925303 F PWD/PhJ Striatum 70 F 6.15.07

131 1716756057 C PWD/PhJ Striatum 70 M 6.7.07

132 1736925139 A PWK/PhJ Striatum 59 F 6.12.07

133 1736925351 A PWK/PhJ Striatum 60 M 6.15.07

134 1736925351 B WSB/EiJ` Striatum 71 F 6.15.07

135 1736925139 B WSB/EiJ Striatum 71 M 6.12.07