Virginia Commonwealth University LXS Prefrontal Cortex Ethanol vs Saline M430A 2.0 (Aug06) Sscore data set by Michael F. Miles and colleagues

Accession number: GN132

    Summary:

VCU LXS PFC Et vs Sal M430A 2.0 (Aug06) Sscore DATA SET: This LXS data set provides estimates of ethanol-responsive differences in mRNA expression in the prefrontal cortex of 43 LXS recombinant inbred strains generated by crossing ILS/Ibg and ISS/Ibg (Inbred Long Sleep and Inbred Short Sleep strains from the Institute of Behavioral Genetics). All samples are from a total of 376 adult male animals raised in a standard laboratory environment. An average of 8 males per strain were used for basal or post-saline injection activity measurements on days 1-2, respectively. 4 animals of each strain were then injected IP with saline or ethanol (1.8 g/kg) on day 3 and locomotor activity measured for 15 minutes prior to returning to home cages. 4 hours after testing, animals were rapidly sacrificed by cervical dislocation and brains removed, cooled and microdissected as described previously (Kerns et al., J. Neurosci. 25:2255, 2005).

RNA was isolated from pools of 3-4 animals per strain/treatment group. All RNA isolation and subsequent probe generation and hybridization to microarrays was done using a supervised randomization procedure to minimize batch effects. Affymetrix M430A 2.0 microarrays were used for hybridization using standard procedures. A total of 22626 estimates of expression (some of which are controls) were transformed using the S-score method to compare ethanol vs. saline expression from pairs of arrays for each strain (Kerns et al., Methods 31:274, 2003, ). The S-score is a method developed for Affymetrix oligonucleotide arrays that is particularly suited to comparing expression on 2 or a small number of chips The S-score output for each probeset is not an indication of expression magnitude but rather, the change in expression between compared arrays. The S-score is essentially a z-score centered around zero with positive S-scores reflecting increased gene expression with ethanol and negative scores reflecting ethanol-induced decreases in expression. Larger magnitude S-scores show more significant changes in expression and are generally correlated with the "fold-change".

As a measure of data quality we often count the number of probes that are associated with higher LOD scores. In this data set, 91 probes have LRS values >23 (LOD >5). The maximum LRS achieved in this data set is 36.63 for probe set 1460695_at ( 2300006M17Rik).

Legend: Bar chart of the expression of 2300006M17Rik probe set 1460695_at in the LXS PFC Et vs Sal Sscore data set. This probe is associated with a LOD score of 7.96 (LRS 36.63).

    About the strains used to generate this set of data:

The LXS genetic reference panel of recombinant inbred strains consists of just over 77 strains. All of these strains have been inbred for more than 23 generations (F23). All strains have been genotyped at 13,377 SNPs. Thanks to the efforts of Dr. Timothy Wiltshire at the Genome Institute of the Novartis Research Foundation, the two parental strains have been genotyped at 156,551 SNPs. These genotypes are incorporated in the GeneNetwork SNP Browser.

Strains are currently available from Drs. Beth Bennett and Tom Johnson at the Institute of Behavioral Genetics (IBG) in Boulder Colorado.

    About the animals and tissue used to generate this set of data:

All animals were raised at the IBG by Bennett and colleagues in an SPF facility. No cases were MHV positive. All animals were treated and brains dissected by Chris Downing and colleagues at IBG. Dissections were according to protocols routinely used by the Miles' laboratory (Kerns et al., J. Neurosci. 2005). Prefrontal cortex tissue was isolated by microdissection using a wedge-shaped slice taken from a 4 mm thick brain slice extending rostrally from the optic chiasm. The wedge was centered on the inter-hemispheric fissure and extending 2 mm laterally on each side and ventrally to just above the corpus callosum. This tissue and all other brain regions were dissected in less than 5 minutes per mouse and were immediated frozen in liquid nitrogen followed by storage at -80 oC prior to RNA isolation.

A pool of dissected tissue from 3-4 adults of the same strain, sex, age and treatment group (saline or ethanol) was used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at VCU by Paul Vorster between 1/06 and 2/06. Strains were randomized in terms of order of RNA isolation but paired saline and ethanol samples from the same strain were always processed at the same time to decrease technical causes for differences in gene expression between saline and ethanol treated animals.

All animals used in this study were between 53 and 90 days of age (average of 72 days; see Table 1 below).

Sample Processing: Samples were processed by Paul Vorster at VCU between 2/06 and 4/06. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio with all values between 1.9 and 2.1. Total RNA integrity was assessed using the BioRad Experion RNA analyzer and used to verify equal molar ratios of 18S and 28S ribosomal RNA. Standard Affymetrix reagents and protocols were used for generation of cDNA and biotinylated cRNA from total RNA samples. Integrity of cRNA was checked by Experion analysis prior to microarray hybridizations. All probes exceeded a maximum size of 3000 nt for the upper border of the cRNA size distribution.

Replication and Sample Balance: At present, all strains are represented by a total of 2 microrarrays, one each for saline- and ethanol-treated animals.

Experimental Design and Batch Structure: CHANGE THIS This data set consists arrays processed in 13 groups over a five month period (July 2006 to Dec 2006). Most groups consisted of 12 samples. All arrays in this data set were processed using a single protocol by a single operator, Feng Yiao. Processing was supervised directly by Dr. Lu Lu. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between July 28 and Dec 21, 2006. Details on sample assignment to slides and batches is provide in the table below.

    Data Table 1:

CHANGE THIS This table lists all arrays by order of strain (index) and includes data on tube ID, strain, age, sex, F generation number, number of animals in each sample pool (pool size), slide ID, slide position (A through F), scan date, and scan batch.

index tube ID strain age sex gener- ation pool size slide ID slide position batch by slide scan batch 1 R2851H2 ILS 77 F >100 4 1523516003 B 1 1 2 R0595H2 ILS 71 F >100 2 1523516030 B 4 2 3 R2874H2 ILS 78 M >100 4 1523516011 B 2 1 4 R0585H2 ILS 65 M >100 2 1523516028 A 3 2 6 R2857H2 ISS 75 F >100 4 1523516011 A 2 1 7 R0589H2 ISS 73 F >100 2 1523516028 B 3 2 8 R2955H2 ISS 53 M >100 3 1523516003 A 1 1 9 R0578H2 ISS 67 M >100 2 1523516030 A 4 2 11 R2013H2 LXS10 84 F 27 2 1562224049 E 18 9 12 R1993H2 LXS10 78 M 27 2 1562224036 E 17 9 13 R1997H2 LXS100 70 F 25 2 1562224049 A 18 9 14 R1983H2 LXS100 77 M 25 2 1562224047 F 16 8 15 R2083H2 LXS101 85 F 28 2 1562224050 B 19 9 16 R2084H2 LXS101 85 M 28 2 1562224050 C 19 9 17 R2186H2 LXS102 73 F 29 2 1523516001 C 9 5 18 R2187H2 LXS102 73 M 29 2 1562224053 C 20 10 19 R2809H2 LXS103 72 F 26 2 1562224034 C 23 11 20 R2854H1 LXS103 69 M 26 2 1523516006 D 6 3 21 R2735H2 LXS107 78 F 26 2 1523516028 D 3 2 22 R2738H2 LXS107 78 M 26 2 1562224054 C 21 10 23 R2840H2 LXS110 67 F 25 2 1562224037 D 24 11 24 R2157H2 LXS110 75 M 27 2 1523516033 E 8 4 25 R2172H2 LXS112 72 F 27 2 1523516001 B 9 5 26 R2841H2 LXS112 84 M 27 2 1562224042 D 27 12 27 R2188H2 LXS114 72 F 28 2 1562224053 D 20 10 28 R2204H2 LXS114 72 M 28 2 1523516001 D 9 5 29 R2168H2 LXS115 80 F 27 2 1523516001 A 9 5 30 R2085H2 LXS115 71 M 27 2 1562224050 D 19 9 31 R2811H2 LXS117 72 F 28 2 1562224034 D 23 11 32 R2212H2 LXS117 74 M 27 2 1523516001 E 9 5 33 R1992H2 LXS122 86 F 26 2 1562224036 D 17 9 34 R2219H2 LXS122 72 M 26 2 1562224054 A 21 10 35 R2876H2 LXS123 87 F 28 2 1562224038 C 25 11 36 R2832H1 LXS123 77 M 27 2 1523516011 E 2 1 37 R2872H1 LXS124 83 F 28 2 1523516006 E 6 3 38 R2871H2 LXS124 85 M 28 2 1562224042 F 27 12 39 R1909H2 LXS13 79 F 25 2 1523516024 D 13 7 40 R1901H2 LXS13 81 M 26 2 1562224041 D 26 12 41 R2023H2 LXS14 86 F 25 2 1562224050 A 19 9 42 R1612H2 LXS14 85 M 26 2 1523516015 A 10 5 43 R1936H2 LXS16 81 F 25 2 1523516024 E 13 7 44 R1912H2 LXS16 81 M 25 2 1523516033 B 8 4 45 R1961H2 LXS19 66 F 26 2 1523516029 F 14 7 46 R1904H2 LXS19 66 M 26 2 1523516024 B 13 7 47 R1883H2 LXS2 71 F 27 2 1523516009 F 12 6 48 R2753H2 LXS2 74 M 28 2 1523516030 E 4 2 49 R1729H2 LXS22 72 F 27 2 1523516032 E 7 4 50 R2743H2 LXS22 79 M 27 2 1562224054 D 21 10 51 R1966H2 LXS23 73 F 26 2 1562224032 D 15 8 52 R1971H2 LXS23 73 M 26 2 1562224047 A 16 8 53 R2795H2 LXS24 74 F 26 2 1523516003 C 1 1 54 R1755H2 LXS24 56 M 25 2 1523516007 A 11 6 55 R1986H2 LXS25 75 F 27 2 1562224036 A 17 9 56 R2006H2 LXS25 75 M 27 2 1562224049 C 18 9 57 R2014H2 LXS26 82 F 25 2 1562224049 F 18 9 58 R2009H2 LXS26 82 M 26 2 1562224049 D 18 9 59 R2824H1 LXS28 67 F 28 2 1562224042 A 27 12 60 R1753H1 LXS28 72 M 27 2 1562224041 F 26 12 61 R2765H2 LXS3 63 F 27 2 1523516005 B 5 3 62 R1898H2 LXS3 81 M 26 2 1562224041 C 26 12 63 R2764H2 LXS31 73 F 29 2 1562224060 C 22 10 64 R1908H2 LXS31 80 M 28 2 1523516024 C 13 7 65 R2758H2 LXS32 70 F 26 2 1523516030 F 4 2 66 R1743H1 LXS32 67 M 25 2 1562224041 E 26 12 67 R2794H2 LXS34 75 F 27 2 1562224034 B 23 11 68 R2870H2 LXS34 78 F 27 2 1562224029 C 28 13 69 R2746H2 LXS35 80 F 22 2 1523516030 C 4 2 70 R2747H2 LXS35 81 M 22 2 1562224060 A 22 10 71 R1968H2 LXS36 76 F 25 2 1562224032 E 15 8 72 R1640H2 LXS36 76 M 25 2 1523516032 C 7 4 73 R2835H1 LXS38 67 F 27 2 1523516011 F 2 1 74 R2842H2 LXS38 67 M 27 2 1562224042 E 27 12 75 R2210H2 LXS39 81 F 28 2 1562224053 E 20 10 76 R2736H2 LXS39 75 M 27 2 1523516028 E 3 2 77 R1978H2 LXS41 78 F 26 2 1562224047 C 16 8 78 R1783H2 LXS41 56 M 26 2 1523516007 D 11 6 79 R2822H2 LXS42 66 F 27 2 1562224034 F 23 11 80 R2769H2 LXS42 70 M 27 2 1562224042 B 27 12 81 R1974H2 LXS43 84 F 26 2 1562224047 B 16 8 82 R1733H2 LXS43 72 M 26 2 1523516015 C 10 5 83 R1756H2 LXS46 56 F 25 2 1523516007 B 11 6 84 R1727H2 LXS46 70 M 25 2 1523516032 D 7 4 85 R1970H2 LXS48 72 F 27 2 1562224032 F 15 8 86 R1981H2 LXS48 72 M 27 2 1562224042 C 27 12 87 R1957H2 LXS49 72 F 25 2 1523516029 C 14 7 88 R2259H2 LXS49 72 M 25 2 1523516028 C 3 2 89 R2836H1 LXS5 68 F 28 2 1523516006 A 6 3 90 R2213H2 LXS5 80 M 27 2 1562224053 F 20 10 91 R2791H2 LXS50 68 F 27 2 1562224034 A 23 11 92 R1789H2 LXS50 57 M 26 2 1523516033 A 8 4 93 R1740H2 LXS51 68 F 27 2 1523516032 F 7 4 94 R1734H2 LXS51 68 M 26 2 1523516015 D 10 5 95 R2786H2 LXS52 61 F 27 2 1562224060 D 22 10 96 R2768H2 LXS52 61 M 27 2 1523516005 C 5 3 97 R2154H2 LXS54 70 F 27 2 1523516033 D 8 4 98 R2155H2 LXS54 70 M 27 2 1562224053 A 20 10 99 R1821H2 LXS55 77 F 25 2 1523516009 C 12 6 100 R1951H2 LXS55 74 M 26 2 1523516024 F 13 7 101 R2789H2 LXS56 71 F 25 2 1523516005 F 5 3 102 R2788H2 LXS56 71 M 25 2 1562224060 F 22 10 103 R2787H2 LXS59 66 F 29 2 1562224060 E 22 10 104 R2785H2 LXS59 62 M 29 2 1523516005 E 5 3 105 R1791H2 LXS60 58 F 27 2 1562224038 D 25 11 106 R1792H2 LXS60 64 M 27 2 1523516007 E 11 6 107 R1796H2 LXS62 58 F 27 2 1523516007 F 11 6 108 R1797H2 LXS62 58 M 27 2 1562224038 E 25 11 109 R2220H2 LXS64 71 F 28 2 1523516001 F 9 5 110 R2221H2 LXS64 71 M 28 2 1562224054 B 21 10 111 R1989H2 LXS66 73 F 26 2 1562224036 B 17 9 112 R1843H2 LXS66 78 M 27 2 1523516009 E 12 6 113 R2820H2 LXS68 67 F 29 2 1523516003 E 1 1 114 R2819H2 LXS68 67 M 29 2 1562224034 E 23 11 115 R1963H2 LXS7 78 F 28 2 1562224032 B 15 8 116 R1964H2 LXS7 78 M 28 2 1562224032 C 15 8 117 R2166H2 LXS70 72 F 27 2 1523516033 F 8 4 118 R2745H2 LXS70 71 M 28 2 1562224054 F 21 10 119 R2848H2 LXS72 72 F 27 2 1562224038 A 25 11 120 R1902H2 LXS72 66 M 27 2 1523516024 A 13 7 121 R2750H2 LXS73 81 F 25 2 1523516030 D 4 2 122 R1835H2 LXS73 90 M 24 2 1523516009 D 12 6 123 R1979H2 LXS75 59 F 27 2 1562224047 D 16 8 124 R2826H2 LXS75 72 M 27 2 1523516003 F 1 1 125 R2142H2 LXS76 77 F 26 2 1562224050 E 19 9 126 R1884H2 LXS76 85 M 26 2 1562224041 A 26 12 127 R1959H2 LXS78 69 F 26 2 1523516029 E 14 7 128 R1958H2 LXS78 69 M 26 2 1523516029 D 14 7 129 R2845H1 LXS8 70 F 28 2 1523516006 C 6 3 130 R2156H2 LXS8 76 M 27 2 1562224053 B 20 10 131 R1955H2 LXS80 71 F 25 2 1523516029 A 14 7 132 R1956H2 LXS80 71 M 25 2 1523516029 B 14 7 133 R2830H1 LXS84 66 F 26 2 1523516011 D 2 1 134 R2829H2 LXS84 66 M 26 2 1562224037 A 24 11 135 R2839H2 LXS86 68 F 27 2 1562224037 C 24 11 136 R2838H1 LXS86 68 M 27 2 1523516006 B 6 3 137 R2882H1 LXS87 66 F 27 2 1523516006 F 6 3 138 R2744H2 LXS87 71 M 26 2 1562224054 E 21 10 139 R2831H2 LXS88 69 F 27 2 1562224037 B 24 11 140 R2762H2 LXS88 71 M 27 2 1523516005 A 5 3 141 R2828H1 LXS89 75 F 26 2 1523516011 C 2 1 142 R1962H2 LXS89 73 M 25 2 1562224032 A 15 8 143 R1746H2 LXS9 66 F 26 2 1523516015 F 10 5 144 R2801H2 LXS9 68 M 27 2 1523516003 D 1 1 145 R1812H2 LXS90 61 F 25 2 1562224038 F 25 11 146 R1813H2 LXS90 61 M 25 2 1523516009 A 12 6 147 R1736H2 LXS92 66 F 23 2 1523516015 E 10 5 148 R1609H2 LXS92 87 M 23 2 1523516032 A 7 4 149 R1624H2 LXS93 74 F 26 2 1523516032 B 7 4 150 R1815H2 LXS93 61 M 26 2 1523516009 B 12 6 151 R1991H2 LXS94 70 F 25 2 1562224036 C 17 9 152 R2002H2 LXS94 70 M 25 2 1562224049 B 18 9 153 R1996H2 LXS96 75 F 23 2 1562224036 F 17 9 154 R1772H2 LXS96 63 M 23 2 1523516007 C 11 6 155 R2759H2 LXS97 73 F 26 2 1562224060 B 22 10 156 R2739H2 LXS97 79 M 26 2 1523516028 F 3 2 157 R2149H2 LXS98 78 F 26 2 1523516033 C 8 4 158 R1888H2 LXS98 76 M 26 2 1562224041 B 26 12 159 R1644H2 LXS99 79 F 26 2 1523516015 B 10 5 160 R2145H2 LXS99 77 M 27 2 1562224050 F 19 9

    Downloading all data:

All data links (right-most column above) will be made active as soon as the global analysis of these data has been accepted for publication. Please see text on Data Sharing Policies, and Conditions and Limitations, and Contacts. Following publication, download a summary text file or Excel file of data. Please contact Dr. Lu Lu if you have any questions on the use of these open data.

    About the array platform:

PLEASE ADD TEXT REGARDING AFFYMETRIX M430A version 2