Hippocampus Consortium M430v2 (June06) PDNN modify this page

Accession number: GN112


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. Neurosci. 3:55 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, 2010). 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.

  1. 129S1/SvImJ
        Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
  2. A/J
        Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
  3. AKR/J
        Sequenced by NIEHS; Phenome Project B list
  4. BALB/cByJ
        Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
  5. BALB/cJ
        Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
  6. C3H/HeJ
        Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
  7. C57BL/6J
        Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
  8. C57BL/6ByJ
        Paternal substrain of B6 used to generate the CXB panel
  9. CAST/Ei
        Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
  10. DBA/2J
        Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
  11. KK/HlJ
        Sequenced by Perlegen/NIEHS
  12. LG/J
        Paternal parent of the LGXSM panel
  13. NOD/LtJ
        Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
  14. NZO/HlLtJ
        Collaborative Cross strain
  15. PWD/PhJ
        Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
  16. PWK/PhJ
        Collaborative Cross strain; Phenome Project D list
  17. WSB/EiJ
        Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
  18. B6D2F1 and D2B6F1
    F1 hybrids generated by crossing C57BL/6J with DBA/2J

We have not combined data from reciprocal F1s because they have different Y chromosome and mitochondrial haplotypes. Parent-of-origin effects (imprinting, maternal environment) may also lead to interesting differences in hippocampal transcript levels.

These strains are available from The Jackson Laboratory. BXD43 through BXD100 strains are available from Lu Lu and colleagues at UTHSC.

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

BXD animals were obtained from UTHSC, UAB, or directly from The Jackson Laboratory (see Table 1 below). Animals were housed at UTHSC, Beth Israel Deaconess, or the Jackson Laboratory before sacrifice. Virtually all CXB animals were obtained directly at the Jackson Laboratory by Lu Lu. We thank Muriel Davisson for making it possible to collect these cases on site. Standard inbred strain stock was from The Jackson Laboratory, but most animals were housed or reared at UTHSC. Mice were killed by cervical dislocation and brains were removed and placed in RNAlater prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both hippocampi were dissected whole by Hong Tao Zhang in the Lu lab. Hippocampal samples are very close to complete (see Lu et al., 2001) but probably include variable amounts of subiculum and fimbria.

A great majority of animals used in this study were between 45 and 90 days of age (average of 66 days, maximum range from 41 to 196 days; see Table 1 below). All animals were sacrifice between 9 AM and 5 PM during the light phase.

A pool of dissected tissue typically from six hippocampi and three naive adults of the same strain, sex, and age was collected in one session and used to generate cRNA samples. Two-hundred and one RNA samples were extracted at UTHSC by Zhiping Jia, four samples by Shuhua Qi (R2331H1, R2332H1, P2350H1, R2349H1), and one by Siming Shou (R0129H2).

RNA Extraction: In brief, we used the RNA STAT-60 protocol (TEL-TEST "B" Bulletin No. 1), steps 5.1A (homogenization of tissue), 5.2 (RNA extraction), 5.3 (RNA precipitation), and 5.4 (RNA wash). In Step 5.4 we stopped after adding 75% ethanol (1 ml per 1 ml RNA STAT-60) and stored the mix at -80°C until further use. Before RNA labeling we thawed samples and proceeded with the remainder of Step 5.4; pelleting, drying, and redissolving the pellet in RNase-free water.

We finally purify RNA by using Na4OAc before running arrays. Here is the detailed method:

Final RNA purification protocol

  1. Add 1/10th volume of 3M Na4OAc , pH 5.2. If the sample was eluted with 100 µl nuclease-free water as suggested, this will be 10 µl of 3M Na4OAc.
  2. Add 2.5 volumes of 100% ethanol (250 µl if the RNA was eluted in100 µl). Mix well and incubate at –20°C for 2 hrs.
  3. Centrifuge at speed of 13,000 rpm for 20 min at 4°C. Carefully remove and discard the supernatant.
  4. Wash the pellet with 800 µl 75% cold ethanol, centrifuge at speed of 8,600 rpm for 5 min, and remove the 75% ethanol. Wash again.
  5. To remove the last traces of ethanol, quickly respin the tube, and aspirate any residual fluid.
  6. Air dry the pellet.
  7. Resuspend pellet in nuclease-free water.

Sample Processing: Samples were processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center for Genomic Research, The University of Memphis, led by Thomas R. Sutter. All processing steps were performed by Shirlean Goodwin. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8. The majority of samples were 1.9 to 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. We required an RNA integrity number (RIN) of greater than 8. This RIN value is based on the intensity ratio and amplitude of 18S and 28S rRNA signals. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using Superscript II reverse transcriptase (Invitrogen Inc.). The Enzo Life Sciences, Inc., BioArray High Yield RNA Transcript Labeling Kit (T7, Part No. 42655) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 2.0 or 2.1 are acceptable) and the Bioanalyzer output (a dark cRNA smear on the 2100 output centered roughly between 600 and 2000 nucleotides is required). Those samples that passed both QC steps (10% usually failed and new RNA samples had to be acquired and processed) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No. 900371). Fragmented cRNA samples were either stored at -80°C until use or were immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.

Replication and Sample Balance: Our goal was to obtain a male sample pool and female sample pool from each isogenic group. While almost all strains were orginally represented by matched male and female samples, not all data sets passed the final quality control steps. All but 5 of 99 strains (BXD55, BXD86, BXD94, BALB/cByJ, and CAST/EiJ) are represented by pairs or (rarely) trios of arrays. The first and last samples are technical replicates of a B6D2F1 hippocampal pool (aliquots R1291H3 and R1291H4).

Sex Balance: Based on the expression of Xist, probe set 1427262_at, DBA/2J and KK/HlJ are represented only by female samples, BXD55, and BALB/cByJ are only represented by a single male sample, BXD74 is represented by two male samples, and BXD86, BXD94, and CAST/EiJ are possibly mixed sex samples. One of the BXD9 samples, array R1523, may be a mixed sex sample pool because the expression of Xist is intermediate.

Experimental Design and Batch Structure: This data set consists arrays processed in six groups over a three month period (May 2005 to August 2005). Each group consists of 32 to 34 arrays. Sex, strain, and strain type (BXD, CXB, and MDP) were interleaved among groups to ensure reasonable balance and to minimize group-by-strain statistical confounds in group normalization. The two independent samples from a single strain were always run in different groups. All arrays were processed using a single protocol by a single operator, Shirlean Goodwin.

All samples in a group were labeled on one day, except for a few cases that failed QC on their first pass. The hybridization station accommodates up to 20 samples, and for this reason each group was split into a large first set of 20 samples and a second set of 12 to 14 samples. Samples were washed in groups of four and then held in at 4°C until all 20 (or 12-14) arrays were ready to scan. The last four samples out of the wash stations were scanned directly. Samples were scanned in sets of four.

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):

  1. BXD21_F_1_1_G1
  2. BXD23_M_1_1_G7
  3. BXD36_M_1_1_G2
  4. 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
11R1468H1DBA/2J64F530.032.92953.80.5150.4650.0191.280.79UTM RW
23R1523H3BXD957MF (mixed)730.143.978.360.4350.5470.0181.360.77UTM RW
30R1304H2BXD1472F730.033.94661.870.4840.4980.0181.220.77UTM RW
31R1278H2BXD1455M730.064.7567.520.4490.5320.0191.10.73UTM RW
37R1471H1BXD19157M130.023.16543.340.5190.4620.0181.011.29UTM JB
44R1280H2BXD2356F130.013.18754.630.4580.5230.0190.961.2UTM RW
54R1240H2BXD3161M230.022.33565.170.5070.4740.0191.310.78UTM RW
55R1526H2BXD3157F740.17.26789.540.4350.5470.0171.350.78UTM RW
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
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
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
148R2670H1A/J65F730.043.95146.80.4980.4850.0171.320.75UTM RW
149R2030H1A/J57M520.063.30745.160.5270.4540.0181.630.99UTM RW
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
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
169R2677H1PWD/PhJ65M720.122.76465.490.4620.520.0181.891.16UTM RW
170R2051H3PWD/PhJ64M530.073.26651.50.4750.5060.0192.81.01UTM RW
183R2505H1CXB580F630.022.8349.60.4990.480.021.330.76UTM RW
185R0129H2CXB570M330.074.82945.420.4880.4930.0191.230.83UTM RW

    Downloading all data:

All data links (right-most column above) will be made active as sooon as the global analysis of these data by the Consortium 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 the PDNN probe set data. Contact RW Williams regarding data access problems.

    About the array platform:

Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.

    About data processing:

Harshlight was used to examine the image quality of the array (CEL files). Bad areas (bubbles, scratches, blemishes) of arrays were masked.

First pass data quality control: Affymetrix GCOS provides useful array quality control data including:

  1. The scale factor used to normalize mean probe intensity. This averaged 3.3 for the 179 arrays that passed and 6.2 for arrays that were excluded. The scale factor is not a particular critical parameter.
  2. The average background level. Values averaged 54.8 units for the data sets that passed and 55.8 for data sets that were excluded. This factor is not important for quality control.
  3. The percentage of probe sets that are associated with good signal ("present" calls). This averaged 50% for the 179 data sets that passed and 42% for those that failed. Values for passing data sets extended from 43% to 55%. This is a particularly important criterion.
  4. The 3':5' signal ratios of actin and Gapdh. Values for passing data sets averaged 1.5 for actin and 1.0 for Gapdh. Values for excluded data sets averaged 12.9 for actin and 9.6 for Gapdh. This is a highly discriminative QC criterion, although one must keep in mind that only two transcripts are being tested. Sequence variation among strains (particularly wild derivative strains such as CAST/Ei) may affect these ratios.

The second step in our post-processing QC involves a count of the number of probe sets in each array that are more than 2 standard deviations (z score units) from the mean across the entire 206 array data sets. This was the most important criterion used to eliminate "bad" data sets. All 206 arrays were processed togther using standard RMA and PDNN methods. The count and percentage of probe sets in each array that were beyond the 2 z theshold was computed. Using the RMA transform the average percentage of probe sets beyond the 2 z threshold for the 179 arrays that finally passed of QC procedure was 1.76% (median of 1.18%). In contrast the 2 z percentage was more than 10-fold higher (mean of 22.4% and median 20.2%) for those arrays that were excluded. This method is not very sensitive to the transformation method that is used. Using the PDNN transform, the average percent of probe sets exceeding was 1.31% for good arrays and was 22.6% for those that were excluded. In our opinion, this 2 z criterion is the most useful criterion for the final decision of whether or not to include arrays, although again, allowances need to be made for wild strains that one expects to be different from the majority of conventional inbred strains. For example, if a data set has excellent characteristics on all of the Affymetrix GCOS metrics listed above, but generates a high 2 z percentage, then one would include the sample if one can verify that there are no problems in sample and data set identification.

The entire procedure can be reapplied once the initial outlier data sets have been eliminated to detect any remaining outlier data sets.

DataDesk was used to examine the statistical quality of the probe level (CEL) data after step 5 below. DataDesk allows the rapid detection of subsets of probes that are particularly sensitive to still unknown factors in array processing. Arrays can then be categorized at the probe level into "reaction classes." A reaction class is a group of arrays for which the expression of essentially all probes are colinear over the full range of log2 values. A single but large group of arrays (n = 32) processed in essentially the identical manner by a single operator can produce arrays belonging to as many as four different reaction classes. Reaction classes are NOT related to strain, age, sex, treatment, or any known biological parameter (technical replicates can belong to different reaction classes). We do not yet understand the technical origins of reaction classes. The number of probes that contribute to the definition of reaction classes is quite small (<10% of all probes). We have categorized all arrays in this data set into one of 5 reaction classes. These have then been treated as if they were separate batches. Probes in these data type "batches" have been aligned to a common mean as described below.

Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.

  1. We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
  2. We performed a quantile normalization of the log base 2 values for all arrays using the same initial steps used by the RMA transform.
  3. We computed the Z scores for each cell value.
  4. We multiplied all Z scores by 2.
  5. We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level (probe brightness level) corresponds approximately to a 1 unit difference.
  6. Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.

Probe set data from the CHP file: The expression values were generated using PDNN. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1 unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.

Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients. XY plots of probe expression and signal variance were also examined. Probe level array data sets were organized into reaction groups. Arrays with probe data that were not homogeneous when compared to other arrays were flagged.

Probe set level QC: The final normalized individual array data were evaluated for outliers. This involved counting the number of times that the probe set value for a particular array was beyond two standard deviations of the mean. This outlier analysis was carried out using the PDNN, RMA and MAS5 transforms and outliers across different levels of expression. Arrays that were associated with an average of more than 8% outlier probe sets across all transforms and at all expression levels were eliminated. In contrast, most other arrays generated fewer than 5% outliers.

Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.

Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.

    Data source acknowledgment:

Data were generated with funds provided by a variety of public and private source to members of the Consortium. All of us thank Muriel Davisson, Cathy Lutz, and colleagues at the Jackson Laboratory for making it possible for us to add all of the CXB strains, and one or more samples from KK/HIJ, WSB/Ei, NZO/HILtJ, LG/J, CAST/Ei, PWD/PhJ, and PWK/PhJ to this study. We thank Yan Cui at UTHSC for allowing us to use his Linux cluster to align all M430 2.0 probes and probe sets to the mouse genome. We thank Hui-Chen Hsu and John Mountz for providing us BXD tissue samples, as well as many strains of BXD stock. We thanks Douglas Matthews (UMem in Table 1) and John Boughter (JBo in Table 1) for sharing BXD stock with us. Members of the Hippocampus Consortium thank the following sources for financial support of this effort:

  • David C. Airey, Ph.D.
    Grant Support: Vanderbilt Institute for Integratie Genomics
    Department of Pharmacology
    david.airey at vanderbilt.edu
  • Lu Lu, M.D.
    Grant Support: NIH U01AA13499, U24AA13513
  • Fred H. Gage, Ph.D.
    Grant Support: Lookout Foundation
  • Dan Goldowitz, Ph.D.
    Grant Support: NIAAA INIA AA013503
    University of Tennessee Health Science Center
    Dept. Anatomy and Neurobiology
    email: dgold@nb.utmem.edu
  • Shirlean Goodwin, Ph.D.
    Grant Support: NIAAA INIA U01AA013515
  • Gerd Kempermann, M.D.
    Grant Support: The Volkswagen Foundation Grant on Permissive and Persistent Factors in Neurogenesis in the Adult Central Nervous System
    Humboldt-Universitat Berlin
    Universitatsklinikum Charite
    email: gerd.kempermann at mdc-berlin.de
  • Kenneth F. Manly, Ph.D.
    Grant Support: NIH P20MH062009 and U01CA105417
  • Richard S. Nowakowski, Ph.D.
    Grant Support: R01 NS049445-01
  • Glenn D. Rosen, Ph.D.
    Grant Support: NIH P20
  • Leonard C. Schalkwyk, Ph.D.
    Grant Support: MRC Career Establishment Grant G0000170
    Social, Genetic and Developmental Psychiatry
    Institute of Psychiatry,Kings College London
    PO82, De Crespigny Park London SE5 8AF
  • Guus Smit, Ph.D.
    Dutch NeuroBsik Mouse Phenomics Consortium
    Center for Neurogenomics & Cognitive Research
    Vrije Universiteit Amsterdam, The Netherlands
    e-mail: guus.smit at falw.vu.nl
    Grant Support: BSIK 03053
  • Thomas Sutter, Ph.D.
    Grant Support: INIA U01 AA13515 and the W. Harry Feinstone Center for Genome Research
  • Stephen Whatley, Ph.D.
    Grant Support: XXXX
  • Robert W. Williams, Ph.D.
    Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513

    About this text file:

This text file originally generated by RWW on July 9, 2006. Updated by RWW July 9, 2006. Finalized table, Oct 13, 2008 by Rob Williams and Arthur Centeno.