diff options
| author | root | 2012-05-08 18:39:56 -0500 |
|---|---|---|
| committer | root | 2012-05-08 18:39:56 -0500 |
| commit | ea46f42ee640928b92947bfb204c41a482d80937 (patch) | |
| tree | 9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/dbdoc/UTHSC_1107_RankInv.html | |
| parent | 056b5253fc3857b0444382aa39944f6344dc1ceb (diff) | |
| download | genenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz | |
Add all the source codes into the github.
Diffstat (limited to 'web/dbdoc/UTHSC_1107_RankInv.html')
| -rwxr-xr-x | web/dbdoc/UTHSC_1107_RankInv.html | 253 |
1 files changed, 253 insertions, 0 deletions
diff --git a/web/dbdoc/UTHSC_1107_RankInv.html b/web/dbdoc/UTHSC_1107_RankInv.html new file mode 100755 index 00000000..bf72cfd5 --- /dev/null +++ b/web/dbdoc/UTHSC_1107_RankInv.html @@ -0,0 +1,253 @@ +<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> +<HTML><HEAD><TITLE>HQF BXD Striatum Illumina Mouse-6.1 November 2007 Rank Invariant Data Set</TITLE> +<META http-equiv=Content-Type content="text/html; charset=iso-8859-1"> +<base href="http://www.genenetwork.org/"> +<LINK REL="stylesheet" TYPE="text/css" HREF='/css/general.css'> +<LINK REL="stylesheet" TYPE="text/css" HREF='/css/menu.css'> +<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT> +</HEAD> +<BODY bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff> +<TABLE cellSpacing=5 cellPadding=4 width="100%" border=0> +<TBODY> +<TR> +<script language="JavaScript" src="/javascript/header.js"></script> +</TR> +<TR> +<TD bgColor=#eeeeee class="solidBorder"> +<Table width= "100%" cellSpacing=0 cellPadding=5><TR> +<!-- Body Start from Here --> + +<TD vAlign=top width="100%" height=200 bgColor=#eeeeee> +<P class="title">HQF BXD Striatum Illumina Mouse-6.1 November 2007 Rank Invariant Data Set <A HREF="/webqtl/main.py?FormID=editHtml"> +<img src="/images/modify.gif" alt="modify this page" border= 0 valign="middle"></A><BR><BR>Accession number: <A HREF="/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=152">GN152</A></P> +<p> +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. +</p> +<p> +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.</p> +<p> +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. +<p> +<table border="0" cellpadding="0" cellspacing="0" bgcolor="#000000" width="60%" align="left"><tr><td> +<table width="100%" border="0" cellpadding="5" cellspacing="1"> +<tr bgcolor="royalblue"><td><font color=#FFFFFF>Index</font></td><td><font color=#FFFFFF>Slide</font></td><td><font color=#FFFFFF>Position</font></td><td><font color=#FFFFFF>Strain</font></td><td><font color=#FFFFFF>Tissue</font></td><td><font color=#FFFFFF>Age</font></td><td><font color=#FFFFFF>Sex</font></td><td><font color=#FFFFFF>Date</font></td></tr> +<tr bgcolor="#eeeeee"><td>1</td><td>1736925204</td><td>D</td><td>C57BL/6J</td><td>Striatum</td><td>58</td><td>F</td><td>6.7.07</td></tr> +<tr bgcolor="#eeeeee"><td>2</td><td>1736925140</td><td>D</td><td>C57BL/6J</td><td>Striatum</td><td>61</td><td>M</td><td>6.12.07</td></tr> +<tr bgcolor="#eeeeee"><td>3</td><td>1736925204</td><td>E</td><td>DBA/2J</td><td>Striatum</td><td>58</td><td>F</td><td>6.7.07</td></tr> +<tr bgcolor="#eeeeee"><td>4</td><td>1736925140</td><td>E</td><td>DBA/2J</td><td>Striatum</td><td>60</td><td>M</td><td>6.12.07</td></tr> +<tr bgcolor="#eeeeee"><td>5</td><td>1736925140</td><td>A</td><td>B6D2F1/J</td><td>Striatum</td><td>59</td><td>F</td><td>6.12.07</td></tr> +<tr bgcolor="#eeeeee"><td>6</td><td>1736925204</td><td>A</td><td>B6D2F1/J</td><td>Striatum</td><td>59</td><td>M</td><td>6.7.07</td></tr> +<tr bgcolor="#eeeeee"><td>7</td><td>1736925225</td><td>A</td><td>BXD1</td><td>Striatum</td><td>59</td><td>F</td><td>6.21.07</td></tr> +<tr bgcolor="#eeeeee"><td>8</td><td>1716756015</td><td>A</td><td>BXD1</td><td>Striatum</td><td>59</td><td>M</td><td>6.22.07</td></tr> +<tr bgcolor="#eeeeee"><td>9</td><td>1736925169</td><td>A</td><td>BXD2</td><td>Striatum</td><td>61</td><td>F</td><td>6.21.07</td></tr> +<tr bgcolor="#eeeeee"><td>10</td><td>1716756027</td><td>A</td><td>BXD2</td><td>Striatum</td><td>61</td><td>M</td><td>6.22.07</td></tr> +<tr bgcolor="#eeeeee"><td>11</td><td>1716756004</td><td>C</td><td>BXD5</td><td>Striatum</td><td>58</td><td>F</td><td>6.22.07</td></tr> +<tr bgcolor="#eeeeee"><td>12</td><td>1716756036</td><td>C</td><td>BXD5</td><td>Striatum</td><td>58</td><td>M</td><td>6.28.07</td></tr> +<tr bgcolor="#eeeeee"><td>13</td><td>1716756004</td><td>D</td><td>BXD6</td><td>Striatum</td><td>59</td><td>F</td><td>6.22.07</td></tr> +<tr bgcolor="#eeeeee"><td>14</td><td>1716756036</td><td>D</td><td>BXD6</td><td>Striatum</td><td>59</td><td>M</td><td>6.28.07</td></tr> +<tr bgcolor="#eeeeee"><td>15</td><td>1716756004</td><td>E</td><td>BXD8</td><td>Striatum</td><td>61</td><td>F</td><td>6.22.07</td></tr> +<tr bgcolor="#eeeeee"><td>16</td><td>1716756036</td><td>E</td><td>BXD8</td><td>Striatum</td><td>61</td><td>M</td><td>6.28.07</td></tr> +<tr bgcolor="#eeeeee"><td>17</td><td>1716756004</td><td>F</td><td>BXD9</td><td>Striatum</td><td>60</td><td>F</td><td>6.22.07</td></tr> +<tr bgcolor="#eeeeee"><td>18</td><td>1716756036</td><td>F</td><td>BXD9</td><td>Striatum</td><td>60</td><td>M</td><td>6.28.07</td></tr> +<tr bgcolor="#eeeeee"><td>19</td><td>1736925139</td><td>C</td><td>BXD11</td><td>Striatum</td><td>59</td><td>F</td><td>6.12.07</td></tr> +<tr bgcolor="#eeeeee"><td>20</td><td>1716756045</td><td>B</td><td>BXD11</td><td>Striatum</td><td>59</td><td>M</td><td>6.28.07</td></tr> +<tr bgcolor="#eeeeee"><td>21</td><td>1736925225</td><td>B</td><td>BXD12</td><td>Striatum</td><td>62</td><td>F</td><td>6.21.07</td></tr> +<tr bgcolor="#eeeeee"><td>22</td><td>1716756015</td><td>B</td><td>BXD12</td><td>Striatum</td><td>59</td><td>M</td><td>6.22.07</td></tr> +<tr bgcolor="#eeeeee"><td>23</td><td>1736925225</td><td>C</td><td>BXD13</td><td>Striatum</td><td>60</td><td>F</td><td>6.21.07</td></tr> +<tr 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bgcolor="#eeeeee"><td>80</td><td>1825397021</td><td>C</td><td>BXD62</td><td>Striatum</td><td>63</td><td>M</td><td>7.10.07</td></tr> +<tr bgcolor="#eeeeee"><td>81</td><td>1825397021</td><td>E</td><td>BXD65</td><td>Striatum</td><td>62</td><td>M</td><td>7.10.07</td></tr> +<tr bgcolor="#eeeeee"><td>82</td><td>1736925245</td><td>B</td><td>BXD66</td><td>Striatum</td><td>59</td><td>M</td><td>7.3.07</td></tr> +<tr bgcolor="#eeeeee"><td>83</td><td>1736925245</td><td>C</td><td>BXD68</td><td>Striatum</td><td>56</td><td>F</td><td>7.3.07</td></tr> +<tr bgcolor="#eeeeee"><td>84</td><td>1736925245</td><td>D</td><td>BXD69</td><td>Striatum</td><td>65</td><td>M</td><td>7.3.07</td></tr> +<tr bgcolor="#eeeeee"><td>85</td><td>1736925245</td><td>E</td><td>BXD70</td><td>Striatum</td><td>61</td><td>M</td><td>7.3.07</td></tr> +<tr bgcolor="#eeeeee"><td>86</td><td>1736925339</td><td>A</td><td>BXD73</td><td>Striatum</td><td>62</td><td>F</td><td>7.3.07</td></tr> +<tr bgcolor="#eeeeee"><td>87</td><td>1736925292</td><td>A</td><td>BXD73</td><td>Striatum</td><td>50</td><td>M</td><td>7.6.07</td></tr> +<tr bgcolor="#eeeeee"><td>88</td><td>1736925292</td><td>D</td><td>BXD77</td><td>Striatum</td><td>50</td><td>F</td><td>7.6.07</td></tr> +<tr bgcolor="#eeeeee"><td>89</td><td>1736925339</td><td>B</td><td>BXD84</td><td>Striatum</td><td>55</td><td>F</td><td>7.3.07</td></tr> +<tr bgcolor="#eeeeee"><td>90</td><td>1736925292</td><td>B</td><td>BXD84</td><td>Striatum</td><td>55</td><td>M</td><td>7.6.07</td></tr> +<tr bgcolor="#eeeeee"><td>91</td><td>1736925292</td><td>E</td><td>BXD85</td><td>Striatum</td><td>57</td><td>M</td><td>7.6.07</td></tr> +<tr bgcolor="#eeeeee"><td>92</td><td>1736925292</td><td>F</td><td>BXD86</td><td>Striatum</td><td>58</td><td>M</td><td>7.6.07</td></tr> +<tr bgcolor="#eeeeee"><td>93</td><td>1736925299</td><td>A</td><td>BXD87</td><td>Striatum</td><td>31</td><td>M</td><td>7.6.07</td></tr> +<tr bgcolor="#eeeeee"><td>94</td><td>1736925299</td><td>B</td><td>BXD89</td><td>Striatum</td><td>63</td><td>M</td><td>7.6.07</td></tr> +<tr bgcolor="#eeeeee"><td>95</td><td>1736925299</td><td>C</td><td>BXD90</td><td>Striatum</td><td>66</td><td>M</td><td>7.6.07</td></tr> +<tr bgcolor="#eeeeee"><td>96</td><td>1736925292</td><td>C</td><td>BXD96</td><td>Striatum</td><td>61</td><td>F</td><td>7.6.07</td></tr> +<tr bgcolor="#eeeeee"><td>97</td><td>1736925339</td><td>C</td><td>BXD96</td><td>Striatum</td><td>61</td><td>M</td><td>7.3.07</td></tr> +<tr bgcolor="#eeeeee"><td>98</td><td>1736925299</td><td>D</td><td>BXD97</td><td>Striatum</td><td>61</td><td>M</td><td>7.6.07</td></tr> +<tr bgcolor="#eeeeee"><td>99</td><td>1736925339</td><td>D</td><td>BXD100</td><td>Striatum</td><td>61</td><td>F</td><td>7.3.07</td></tr> +<tr bgcolor="#eeeeee"><td>100</td><td>1736925140</td><td>F</td><td>129S1/SvImJ</td><td>Striatum</td><td>60</td><td>F</td><td>6.12.07</td></tr> +<tr bgcolor="#eeeeee"><td>101</td><td>1736925204</td><td>F</td><td>129S1/SvImJ</td><td>Striatum</td><td>59</td><td>M</td><td>6.7.07</td></tr> +<tr bgcolor="#eeeeee"><td>102</td><td>1736925129</td><td>A</td><td>A/J</td><td>Striatum</td><td>59</td><td>F</td><td>6.7.07</td></tr> +<tr bgcolor="#eeeeee"><td>103</td><td>1736925241</td><td>A</td><td>A/J</td><td>Striatum</td><td>59</td><td>M</td><td>6.12.07</td></tr> +<tr bgcolor="#eeeeee"><td>104</td><td>1736925129</td><td>B</td><td>AKR/J</td><td>Striatum</td><td>59</td><td>F</td><td>6.7.07</td></tr> +<tr bgcolor="#eeeeee"><td>105</td><td>1736925241</td><td>B</td><td>AKR/J</td><td>Striatum</td><td>59</td><td>M</td><td>6.12.07</td></tr> +<tr bgcolor="#eeeeee"><td>106</td><td>1736925241</td><td>C</td><td>BALB/CByJ</td><td>Striatum</td><td>59</td><td>F</td><td>6.12.07</td></tr> +<tr bgcolor="#eeeeee"><td>107</td><td>1736925129</td><td>C</td><td>BALB/CByJ</td><td>Striatum</td><td>59</td><td>M</td><td>6.7.07</td></tr> +<tr bgcolor="#eeeeee"><td>108</td><td>1716756045</td><td>A</td><td>BTBRT+tf/J</td><td>Striatum</td><td>59</td><td>F</td><td>6.28.07</td></tr> +<tr bgcolor="#eeeeee"><td>109</td><td>1736925139</td><td>E</td><td>BTBRT+tf/J</td><td>Striatum</td><td>60</td><td>M</td><td>6.12.07</td></tr> +<tr bgcolor="#eeeeee"><td>110</td><td>1716756045</td><td>F</td><td>BXSB/MpJ</td><td>Striatum</td><td>61</td><td>F</td><td>6.28.07</td></tr> +<tr bgcolor="#eeeeee"><td>111</td><td>1736925351</td><td>E</td><td>BXSB/MpJ</td><td>Striatum</td><td>61</td><td>M</td><td>6.15.07</td></tr> +<tr bgcolor="#eeeeee"><td>112</td><td>1736925129</td><td>D</td><td>C3H/HeJ</td><td>Striatum</td><td>60</td><td>F</td><td>6.7.07</td></tr> +<tr bgcolor="#eeeeee"><td>113</td><td>1736925241</td><td>D</td><td>C3H/HeJ</td><td>Striatum</td><td>60</td><td>M</td><td>6.12.07</td></tr> +<tr bgcolor="#eeeeee"><td>114</td><td>1736925129</td><td>E</td><td>CAST/Ei</td><td>Striatum</td><td>57</td><td>F</td><td>6.7.07</td></tr> +<tr bgcolor="#eeeeee"><td>115</td><td>1736925241</td><td>E</td><td>CAST/Ei</td><td>Striatum</td><td>61</td><td>M</td><td>6.12.07</td></tr> +<tr bgcolor="#eeeeee"><td>116</td><td>1736925129</td><td>F</td><td>FVB/NJ</td><td>Striatum</td><td>60</td><td>F</td><td>6.7.07</td></tr> +<tr bgcolor="#eeeeee"><td>117</td><td>1736925241</td><td>F</td><td>FVB/NJ</td><td>Striatum</td><td>60</td><td>M</td><td>6.12.07</td></tr> +<tr bgcolor="#eeeeee"><td>118</td><td>1716756057</td><td>A</td><td>KK/HiJ</td><td>Striatum</td><td>62</td><td>F</td><td>6.7.07</td></tr> +<tr bgcolor="#eeeeee"><td>119</td><td>1736925303</td><td>A</td><td>KK/HiJ</td><td>Striatum</td><td>62</td><td>F</td><td>6.15.07</td></tr> +<tr bgcolor="#eeeeee"><td>120</td><td>1716756057</td><td>B</td><td>MOLF/EiJ</td><td>Striatum</td><td>60</td><td>F</td><td>6.7.07</td></tr> +<tr bgcolor="#eeeeee"><td>121</td><td>1736925303</td><td>B</td><td>MOLF/EiJ</td><td>Striatum</td><td>60</td><td>M</td><td>6.15.07</td></tr> +<tr bgcolor="#eeeeee"><td>122</td><td>1716756057</td><td>D</td><td>NOD/LtJ</td><td>Striatum</td><td>58</td><td>F</td><td>6.7.07</td></tr> +<tr bgcolor="#eeeeee"><td>123</td><td>1736925303</td><td>C</td><td>NOD/LtJ</td><td>Striatum</td><td>58</td><td>M</td><td>6.15.07</td></tr> +<tr bgcolor="#eeeeee"><td>124</td><td>1736925303</td><td>D</td><td>NZB/BlnJ</td><td>Striatum</td><td>61</td><td>F</td><td>6.15.07</td></tr> +<tr bgcolor="#eeeeee"><td>125</td><td>1716756057</td><td>E</td><td>NZB/BlnJ</td><td>Striatum</td><td>58</td><td>M</td><td>6.7.07</td></tr> +<tr bgcolor="#eeeeee"><td>126</td><td>1736925303</td><td>E</td><td>NZO/HiltJ</td><td>Striatum</td><td>61</td><td>F</td><td>6.15.07</td></tr> +<tr bgcolor="#eeeeee"><td>127</td><td>1716756057</td><td>F</td><td>NZO/HiltJ</td><td>Striatum</td><td>61</td><td>M</td><td>6.7.07</td></tr> +<tr bgcolor="#eeeeee"><td>128</td><td>1736925139</td><td>F</td><td>NZW/LacJ</td><td>Striatum</td><td>65</td><td>F</td><td>6.12.07</td></tr> +<tr bgcolor="#eeeeee"><td>129</td><td>1825397021</td><td>D</td><td>NZW/LacJ</td><td>Striatum</td><td>70</td><td>M</td><td>7.10.07</td></tr> +<tr bgcolor="#eeeeee"><td>130</td><td>1736925303</td><td>F</td><td>PWD/PhJ</td><td>Striatum</td><td>70</td><td>F</td><td>6.15.07</td></tr> +<tr bgcolor="#eeeeee"><td>131</td><td>1716756057</td><td>C</td><td>PWD/PhJ</td><td>Striatum</td><td>70</td><td>M</td><td>6.7.07</td></tr> +<tr bgcolor="#eeeeee"><td>132</td><td>1736925139</td><td>A</td><td>PWK/PhJ</td><td>Striatum</td><td>59</td><td>F</td><td>6.12.07</td></tr> +<tr bgcolor="#eeeeee"><td>133</td><td>1736925351</td><td>A</td><td>PWK/PhJ</td><td>Striatum</td><td>60</td><td>M</td><td>6.15.07</td></tr> +<tr bgcolor="#eeeeee"><td>134</td><td>1736925351</td><td>B</td><td>WSB/EiJ`</td><td>Striatum</td><td>71</td><td>F</td><td>6.15.07</td></tr> +<tr bgcolor="#eeeeee"><td>135</td><td>1736925139</td><td>B</td><td>WSB/EiJ</td><td>Striatum</td><td>71</td><td>M</td><td>6.12.07</td></tr> +</table></td> +</p> +<P>Illumina Mouse-6.1 array (second generation of the Illumina Mouse 6 platform) + +<P>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. + +<P><B>Figure 1: Sex balance illustrated by the expression of <I>Xist</I> (Illumina probe 104280446)</B>. 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 <I>Xist</I> signal intensity in females of the wild strains (PWK, PWD, MOLF, CAST and WSB) is lower than in standard mouse strains. +<P> + +<img src="/images/upload/Striatum_Illumina_SexTest.gif" border= 0 valign="left"> +</p> + +<P><B>Useful links</B> +<OL> + +<LI> <A HREF="http://rosenlab.net/Movie/P14.mov" target="_blank" class="fs14">A movie of the dissection of the brain, including the striatum, by Dr. Glenn Rosen.</a> + +</OL> + + +<P>Notes for Dr. Lu on the RNA cleanup (Jan 22, 2008) + +<P>We purify RNA by using Na4OAc before running arrays. Here is the detailed method: + +<P>Final RNA purification protocol + +<OL> +<LI>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. +<LI>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. +<LI>Centrifuge at speed of 1,3000 rpm for 20 min at 4°C,Carefully remove and discard the supernatant. +<LI>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. +<LI>To remove the last traces of ethanol, quickly respin the tube, and aspirate any residual fluid. +<LI>Air dry the pellet. +<LI>Resuspend pellet in nuclease-free water. +</UL> + +</TD> + +<!-- Body End Here --> +</TR></TABLE> +</TD> +</TR> +<TR> +<TD align=center bgColor=#ddddff class="solidBorder"> + + + + +<!--Start of footer--> +<TABLE width="90%"> +<script language='JavaScript' src='/javascript/footer.js'></script> +</TABLE> +<!--End of footer--> + + + + +</TD> +</TR> +</TABLE> +<!-- /Footer --> +<!-- menu script itself. you should not modify this file --> +<script language="JavaScript" src="/javascript/menu_new.js"></script> +<!-- items structure. menu hierarchy and links are stored there --> +<script language="JavaScript" src="/javascript/menu_items.js"></script> +<!-- files with geometry and styles structures --> +<script language="JavaScript" src="/javascript/menu_tpl.js"></script> +<script language="JavaScript"> +<!--// +// Note where menu initialization block is located in HTML document. +// Don't try to position menu locating menu initialization block in +// some table cell or other HTML element. 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