GN112

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Contents

Hippocampus Consortium M430v2 (June06) PDNN

Download datasets and supplementary data files

GN112 data sharing

ftp://atlas.uthsc.edu/users/shared/Genenetwork/GN112/

Summary:

MOST HIGHLY RECOMMENDED DATA SET (Overall et al., 2009): The Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of 99 genetically diverse strains of mice including 67 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a diverse set of common inbred strains, and two reciprocal F1 hybrids. Please cite: Overall RW, Kempermann G, Peirce J, Lu L, Goldowitz D, Gage FH, Goodwin S, Smit AB, Airey DC, Rosen GD, Schalkwyk LC, Sutter TR, Nowakowski RS, Whatley S, Williams RW (2009) Genetics of the hippocampal transcriptome in mice: a systematic survey and online neurogenomic resource. Front. Neurogen. 1:3 Full Text HTML

The hippocampus is an important and intriguing part of the forebrain that is crucial in memory formation and retrieval, and that is often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3) is a joint effort of 14 investigators that is supported by numerous agencies described in the acknowledgments section.

Samples were processed using a total of 206 Affymetrix GeneChip Mouse Expression 430 2.0 short oligomer arrays (MOE430 2.0 or M430v2; see GEO platform ID GPL1261), of which 201 passed quality control and error checking. This particular data set was processed using the PDNN protocol. To simplify comparisons among transforms, PDNN values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.

About the strains used to generate this set of data:

The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 27 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 39 inbred (25 strains at F20+) and nearly inbred (14 strains between F14 and F20) BXD lines generated by Lu and Peirce. All of these strains, including those between F14 and F20, have been genotyped at 13,377 SNPs.

Mouse Diversity Panel (MDP). We have profiled a MDP consisting 16 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
  • 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

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.

COMPARISON with December 2005 Data Set:

Both BXD14 arrays in the Dec05 data set were found to actually be from BXD23 cases. This error of strain identification has been corrected in the present data set. Four arrays in the Dec05 data set have been deleted because we judged them to be of poor quality (strain_sex_sample_firstreaction_group):

BXD21_F_1_1_G1 BXD23_M_1_1_G7 BXD36_M_1_1_G2 BXD36_F_1_1_G3

In the Dec05 data set there are a total of 1986 transcripts with QTLs that have LRS scores above 50, whereas in the corrected June06 data sets there are a total of 2074 transcripts with QTLs above 50.

Data Table 1:

This table lists all arrays by file order (Index), tube/sample ID, age, sex, batch, and numbers of animals in each sample pool (pool size). The next columns (RMA outlier, scale factor, background average, present, absent, marginal, AFFY-b-ActinMur(3'/5'), AFFY-GapdhMur(3'/5')) are all Affymetrix QC data. Finally, source lists the source colony of the animals. (Final version, fully corrected, by Arthur Centeno, October 2008)

index tube ID strain age sex batch ID pool size RMA outlier scale factor back ground average present absent marginal AFFX-b-ActinMur (3'/5') AFFX-GapdhMur (3'/5') source
1R1289H2B6D2F164F630.022.40653.840.4920.4890.0191.610.96UTM RW
2R1291H3B6D2F166M 130.013.52448.540.4870.4940.0191.211.52UTM RW
3R1291H4B6D2F166M technical duplicate of above630.083.89146.690.5120.4690.0191.90.89UTM RW
4R2045H2D2B6F165F120.014.40347.990.4970.4850.0181.091.53UTM RW
5R1595H2D2B6F163F530.062.57958.490.5060.4750.0192.491.21UTM RW
6R1551H1D2B6F172F630.022.6253.760.5060.4760.0181.370.76UTM RW
7R1361H1C57BL/6J69F640.013.05851.870.4770.5030.021.670.76UTM RW
8R2041H2C57BL/6J65M140.043.34149.260.5270.4560.0181.141.45UTM RW
9R1449H2C57BL/6J71M530.093.59244.320.470.510.021.680.77UTM DG
10R1290H2DBA/2J63F720.042.57659.60.5130.4680.0181.30.78JAX
11R1468H1DBA/2J64F530.032.92953.80.5150.4650.0191.280.79UTM RW
12R1507H1BXD158M330.024.05660.170.4780.5030.0191.150.76Glenn
13R1542H1BXD159F730.031.79280.560.4920.4890.0181.570.79Glenn
14R1520H1BXD256F440.091.71571.620.5150.4670.0182.361.6Glenn
15R1516H1BXD261M140.012.23164.860.5080.4740.0191.31.53Glenn
16R1593H2BXD560F1401.91359.960.4870.4930.020.981.44Glenn
17R1692H1BXD560M320.073.76472.740.4650.5160.021.150.74Glenn
18R1539H2BXD659F1402.48854.970.5180.4630.0181.081.33Glenn
19R1538H1BXD659M430.012.58550.270.5050.4750.021.460.79Glenn
20R1518H1BXD856F1302.9254.840.5150.4650.021.321.24Glenn
21R1548H1BXD859M630.072.13259.370.5040.4770.0192.161.54Glenn
22R1350H2BXD986F130.052.77160.620.50.4820.0181.011.28UMemphis
23R1523H3BXD957MF (mixed)730.143.978.360.4350.5470.0181.360.77UTM RW
24R1531H1BXD1156F630.062.22956.360.5050.4750.022.231.02Glenn
25R1367H1BXD1156M130.012.1178.780.5030.4770.021.071.27Glenn
26R1530H1BXD1258F1303.22753.770.5050.4770.0180.951.4Glenn
27R2674H1BXD1259M730.031.92483.440.5190.4640.0181.210.78Glenn
28R1529H1BXD1358F630.052.5559.050.4970.4850.01821.54Glenn
29R1662H2BXD1360M130.034.60345.810.5090.4720.0191.30.82Glenn
30R1304H2BXD1472F730.033.94661.870.4840.4980.0181.220.77UTM RW
31R1278H2BXD1455M730.064.7567.520.4490.5320.0191.10.73UTM RW
32R1524H1BXD1560F640.022.96150.930.4970.4840.0191.740.91Glenn
33R1515H1BXD1561M130.013.31657.050.5030.4780.0191.321.21Glenn
34R1661H1BXD1661F130.012.77859.810.5160.4660.0191.391.2Glenn
35R1594H1BXD1661M430.032.63453.660.5040.4780.0181.961.51Glenn
36R2666H1BXD1960F730.022.49876.20.4950.4860.0191.410.77Glenn
37R1471H1BXD19157M130.023.16543.340.5190.4620.0181.011.29UTM JB
38R1573H1BXD2059F130.023.74952.70.5130.4690.0181.011.27Glenn
39R2507H1BXD2060M630.063.568570.4720.5080.021.290.76Glenn
40R2668H1BXD2160M740.072.60544.90.5350.4490.0171.540.76Glenn
41R1337H2BXD21102F2402.67358.050.4920.4890.0191.40.76UAB
42R1848H3BXD22196F640.022.94351.70.4940.4850.0212.20.78UAB
43R1525H1BXD2259M230.022.24855.760.5480.4330.0181.260.74Glenn
44R1280H2BXD2356F130.013.18754.630.4580.5230.0190.961.2UTM RW
45R1537H1BXD2358F530.13.71967.540.4680.5130.0191.510.96Glenn
46R1343H2BXD2471F230.012.08365.070.5060.4740.0191.460.75UMemphis
47R1517H1BXD2457M330.013.47153.660.5040.4760.0191.280.78Glenn
48R1366H1BXD2760F2402.2648.460.5180.4630.0191.290.77Glenn
49R1849H1BXD2770M530.068.80138.340.4680.5120.0192.421.08UAB
50R1353H1BXD2879F340.013.2276.220.480.50.021.330.78UMemphis
51R2332H1BXD2860M230.013.21763.680.4910.490.0191.370.79Glenn
52R1532H1BXD2957F230.012.12259.180.5240.4560.0191.170.76Glenn
53R1356H1BXD2976M530.014.03347.670.520.4630.0171.170.78UMemphis
54R1240H2BXD3161M230.022.33565.170.5070.4740.0191.310.78UTM RW
55R1526H2BXD3157F740.17.26789.540.4350.5470.0171.350.78UTM RW
56R2675H1BXD3257F730.032.26878.010.5020.4780.021.220.78Glenn
57R1508H2BXD3258M240.011.91767.780.5390.4420.0191.280.73Glenn
58R1345H3BXD3365F220.012.09863.140.5220.4590.0191.270.73UMemphis
59R1581H1BXD3359M330.013.22953.160.4960.4850.0191.190.78Glenn
60R1527H1BXD3459F230.012.358.920.510.4710.0191.240.76Glenn
61R1339H3BXD3474M530.122.88853.490.5060.4760.0182.391.35UMemphis
62R1855H1BXD3855F340.013.53654.540.490.4920.0181.390.75Glenn
63R1510H1BXD3859M230.012.18668.060.5210.460.0191.260.79Glenn
64R1528H2BXD3959F230.034.71738.30.5110.470.021.120.75Glenn
65R1514H1BXD3959M330.033.99256.060.4770.5040.0191.430.81Glenn
66R1522H1BXD4059F4402.63167.160.490.4910.0181.560.77Glenn
67R1359H1BXD4073M230.097.45839.860.4510.5270.0211.280.74UMemphis
68R1541H2BXD4258F730.076.78452.120.4830.4990.0171.130.66Glenn
69R1540H1BXD4258M740.032.42375.140.4920.4880.021.480.78Glenn
70R1334H2BXD4359F1302.67254.360.4920.4910.0171.22.06UTM RW
71R1303H1BXD4363M340.023.49751.90.4860.4950.0191.150.8UTM RW
72R1326H1BXD4465F3403.41253.960.4960.4850.0181.350.78UTM RW
73R1577H2BXD4456M130.022.15967.520.5120.4690.0191.181.71UTM RW
74R1403H2BXD4563F720.033.14644.50.5240.4570.0181.410.78Glenn
75R1472H1BXD4565M740.041.65173.310.5430.440.0181.630.74UTM RW
76R1316H1BXD4858F4302.44568.590.5150.4670.0191.160.73UTM RW
77R1575H3BXD4865M340.054.57755.780.4660.5140.0191.590.9UTM RW
78R2521H1BXD5063F640.013.10957.280.4950.4850.021.230.78UTM RW
79R1944H2BXD5081M130.012.54663.390.4950.4850.020.91.57UTM RW
80R2331H1BXD5166F330.033.53444.420.5010.4810.0171.20.9UTM RW
81R1582H1BXD5171M640.032.9247.870.4890.4910.021.360.75UTM RW
82R2680H1BXD5565M730.071.70779.750.5030.480.0171.911.05UTM RW
83R1331H1BXD6060F430.012.86750.330.4920.4870.0211.340.78UTM RW
84R1281H2BXD6059M1302.3958.440.5110.4690.020.941.2UTM RW
85R2667H1BXD6170F740.033.3659.040.4950.4880.0181.160.76UTM RW
86R1856H2BXD6194M1203.50249.60.5010.480.0190.961.3UTM RW
87R1246H1BXD6254F140.023.40551.470.5110.4710.0181.141.34UTM RW
88R1585H2BXD6264M640.013.15655.770.5180.4640.0181.430.82UTM RW
89R1945H1BXD63107F130.022.81152.650.5220.4590.0191.051.36UTM RW
90R2093H3BXD6370M630.023.89442.850.5030.4770.0191.291.01UTM RW
91R2062H2BXD6465F130.053.79578.480.5130.4680.0190.981.43UTM RW
92R2061H1BXD6487M340.013.53661.570.4770.5040.0191.310.78UTM RW
93R2054H2BXD6555F120.033.15980.960.480.5020.0181.091.24UTM RW
94R2056H2BXD6589M6202.83659.60.5040.4770.0191.30.75UTM RW
95R1941H2BXD6678F140.012.73450.930.4990.4810.021.181.29UTM RW
96R1949H2BXD6696M420.042.82851.270.4740.5080.0192.051.12UTM RW
97R2060H1BXD6754F630.012.56143.880.5020.4790.021.70.84UTM RW
98R2052H1BXD6761M140.013.16143.230.5210.460.0181.091.31UTM RW
99R2074H1BXD6860F530.026.52849.620.4790.5020.0191.480.83UTM RW
100R1928H1BXD6872M220.012.40448.280.5210.4590.021.30.74UTM RW
101R1439H3BXD6960F230.022.46359.140.5220.4590.0181.310.78UTM RW
102R1559H1BXD6964M330.032.98767.740.4860.4960.0171.380.8UTM RW
103R2134H1BXD7064F520.022.14858.640.5320.450.0191.40.85UTM RW
104R2063H1BXD7055M230.023.48155.320.5130.4690.0181.280.71UTM RW
105R1277H1BXD7360F420.012.57662.450.5020.4790.0191.350.79UTM RW
106R1443H2BXD7376M230.012.31264.340.4990.4810.021.480.77UTM RW
107R2055H2BXD7479M230.012.57656.840.5090.4730.0181.460.88UTM RW
108R2316H1BXD74193M520.013.45755.350.5080.4710.021.170.78UTM RW
109R1871H1BXD7561F230.041.72356.40.530.4510.0191.30.76UTM RW
110R1844H2BXD7590M340.011.93456.230.520.4610.0191.620.86UTM RW
111R1948H2BXD7681F230.011.50768.850.5530.4280.021.30.75UTM RW
112R2094H1BXD7661M540.013.29942.690.5190.4620.0191.390.88UTM RW
113R2262H1BXD7762F340.024.31747.160.4930.4880.0191.320.74UTM RW
114R1423H1BXD7762M230.023.07154.150.510.4710.0191.260.74UTM RW
115R1947H1BXD79108F220.012.59951.520.5240.4570.0191.350.74UTM RW
116R2092H1BXD7986M540.063.73542.250.5140.4680.0182.941.06UTM RW
117R1880H1BXD8068F530.064.85542.220.5010.4810.0182.171.36UTM RW
118R1881H2BXD8068M230.022.07348.930.5240.4580.0191.340.83UTM RW
119R2075H1BXD8360F230.012.45455.10.5020.480.0181.270.77UTM RW
120R2076H2BXD8360M630.032.62455.650.4950.4880.0182.210.94UTM RW
121R2077H2BXD8462F6202.171.870.5220.4590.0181.680.81UTM RW
122R2135H3BXD8475M220.012.46764.460.5050.4760.0191.20.74UTM RW
123R1473H1BXD8579F230.023.38455.340.4780.5020.021.240.77UTM RW
124R1474H1BXD8557M130.012.83155.240.5220.4610.0181.041.29UTM RW
125R1597H1BXD8586M440.092.02853.950.4870.4920.0211.280.83UTM RW
126R1415H1BXD8677F430.022.52553.160.4950.4850.021.660.91UTM RW
127R2669H2BXD8763F730.072.6157.590.5130.470.0181.60.91UTM RW
128R1710H1BXD8784M240.012.69756.40.5120.4690.0191.280.79UTM RW
129R1872H2BXD8990F220.023.01363.530.4920.4880.0211.220.72UTM RW
130R1850H3BXD8982M440.032.73644.890.4980.4830.0191.50.83UTM RW
131R2058H1BXD9061F230.013.38948.050.5020.4780.021.530.76UTM RW
132R1600H2BXD9074M740.033.26151.310.5170.4650.0181.160.75Glenn
133R1301H2BXD9258F230.023.54341.970.5220.460.0181.50.79UTM RW
134R1309H1BXD9259M430.051.65566.340.4980.4810.0211.520.82UTM RW
135R2057H1BXD9392F530.024.03344.410.5090.4710.021.220.78UTM RW
136R2059H1BXD9358M1303.05860.290.4930.4880.0191.181.37UTM RW
137R2313H1BXD9459F3303.09159.450.4870.4950.0181.340.73UTM RW
138R1915H1BXD9665F520.045.14546.190.5020.4810.0171.370.74UTM RW
139R1846H2BXD9663M1303.15955.850.4870.4930.020.921.26UTM RW
140R2648H1BXD9774F740.021.66482.080.5180.4640.0191.40.78UTM RW
141R1927H2BXD9767M130.042.62257.810.5390.4440.0171.451.32UTM RW
142R1942H1BXD9862F530.043.10448.420.5280.4540.0192.221.08UTM RW
143R1943H2BXD9862M330.024.0456.850.4840.4970.0191.180.76UTM RW
144R2197H1BXD9970F330.024.28851.750.490.4920.0181.350.81UTM RW
145R2315H1BXD9984M520.036.03643.050.4840.4970.0181.70.96UTM RW
146R2028H2129S1/SvImJ66F530.14.36264.490.4970.4840.0192.781.13JAX
147R2029H2129S1/SvImJ66M630.045.20841.210.490.490.021.620.95JAX
148R2670H1A/J65F730.043.95146.80.4980.4850.0171.320.75UTM RW
149R2030H1A/J57M520.063.30745.160.5270.4540.0181.630.99UTM RW
150R2032H3AKR/J66F530.043.05461.030.510.4710.0181.460.79JAX
151R2454H1AKR/J66M640.112.89258.550.4740.5070.0191.990.78JAX
152R1675H1BALB/cByJ83M730.033.40548.130.5090.4740.0181.130.78JAX
153R2036H3BALB/cJ51F530.122.61156.290.5180.4660.0173.31.23UTM RW
154R2053H1BALB/cJ55M530.12.50563.270.4990.4830.0183.11.34UTM RW
155R2037H2BALB/cJ51M640.012.54658.130.4970.4850.0181.260.77UTM RW
156R2038H3C3H/HeJ63F630.022.67166.740.4760.5040.021.410.77UTM RW
157R2039H1C3H/HeJ63M530.13.38444.150.5280.4540.0172.160.88UTM RW
158R2137H1C57BL/6ByJ55F530.024.74647.010.4880.4930.0181.230.79JAX
159R2673H1C57BL/6ByJ55M730.081.84267.690.5140.4690.0171.750.78JAX
160R2619H1CAST/EiJ64F530.144.07751.870.4550.5280.0182.741.2JAX
161R1683H1KK/HIJ72F630.023.91954.230.4910.4890.021.310.83JAX
162R1687H3KK/HIJ72F530.043.88840.860.4990.4830.0191.860.88JAX
163R2046H1LG/J63F520.032.82259.180.5140.4680.0181.680.8UTM RW
164R2047H2LG/J63M630.072.03860.340.5090.4710.022.160.95UTM RW
165R2048H1NOD/LtJ77F620.144.04550.210.4890.490.0212.890.95UTM RW
166R2049H3NOD/LtJ76M530.12.32852.780.5190.4620.0193.091.35UTM RW
167R2200H1NZO/HlLtJ62F520.032.64854.290.5430.4380.0191.270.8JAX
168R2350H1NZO/HlLtJ96M620.192.39150.520.5180.4630.023.712.21JAX
169R2677H1PWD/PhJ65M720.122.76465.490.4620.520.0181.891.16UTM RW
170R2051H3PWD/PhJ64M530.073.26651.50.4750.5060.0192.81.01UTM RW
171R2322H1PWK/PhJ63F520.092.9454.910.5110.470.0192.321.02JAX
172R2349H1PWK/PhJ83M620.153.30654.930.4590.5220.0194.651.45JAX
173R2198H2WSB/EiJ58F610.022.92257.970.5020.4790.0191.440.76JAX
174R2199H1WSB/EiJ58M530.043.17154.950.4750.5050.021.320.81JAX
175R2116H1CXB155F330.075.79251.590.4590.5210.021.170.8JAX
176R2096H1CXB155M420.013.43553.780.4950.4850.021.220.79JAX
177R2117H2CXB262F420.043.3945.970.5330.450.0172.050.89JAX
178R2098H1CXB268M330.022.57254.220.4960.4850.0191.380.86JAX
179R2118H1CXB347F330.033.64663.160.4780.5030.0191.220.77JAX
180R2100H1CXB347M430.025.7651.380.480.5030.0171.240.81JAX
181R2119H1CXB458F430.023.89749.210.4880.4940.0181.310.79JAX
182R2101H1CXB458M330.137.37253.770.4330.5480.0191.20.97JAX
183R2505H1CXB580F630.022.8349.60.4990.480.021.330.76UTM RW
184R2131H1CXB542M430.15.57751.150.4340.5470.0191.70.89JAX
185R0129H2CXB570M330.074.82945.420.4880.4930.0191.230.83UTM RW
186R2676H1CXB647F720.052.14662.510.5070.4750.0181.520.78JAX
187R2102H1CXB649M430.075.14851.630.4530.5290.0181.430.87JAX
188R2121H1CXB763F420.064.90448.710.4640.5170.0191.190.92JAX
189R2104H2CXB758M320.063.38948.790.5020.4790.0191.741.48JAX
190R2122H1CXB854F330.044.12859.770.4510.5290.021.120.76JAX
191R2105H1CXB841M430.163.14661.040.4510.530.0191.340.84JAX
192R2123H1CXB954F330.085.70855.940.4380.5430.0191.320.78JAX
193R2106H1CXB954M430.065.86846.550.4690.5120.0191.180.82JAX
194R2124H1CXB1053F420.114.86739.880.4510.5280.021.550.8JAX
195R2671H1CXB1053M730.092.34871.450.4880.4940.0182.21.14JAX
196R2125H1CXB1158F330.033.25654.950.4610.5190.021.460.77JAX
197R2128H1CXB1158M420.064.98654.130.4650.5150.021.110.83JAX
198R2126H1CXB1247F430.113.93554.110.4690.5110.0211.50.79JAX
199R2109H1CXB1247M330.074.51849.260.4880.4920.021.230.77JAX
200R2672H1CXB1349F730.031.72279.520.5160.4650.0191.640.75JAX
201R2110H1CXB1356M430.213.47848.080.4610.5170.0221.210.78JAX
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