From b2feda451ccfbeaed02dce9088d6dd228cf15861 Mon Sep 17 00:00:00 2001 From: Bonface Date: Tue, 13 Feb 2024 23:52:26 -0600 Subject: Update dataset RTF Files. --- general/datasets/Hc_m2_1205_r/acknowledgment.rtf | 54 + general/datasets/Hc_m2_1205_r/cases.rtf | 60 + .../datasets/Hc_m2_1205_r/experiment-design.rtf | 3252 ++++++++++++++++++++ general/datasets/Hc_m2_1205_r/notes.rtf | 15 + general/datasets/Hc_m2_1205_r/platform.rtf | 1 + general/datasets/Hc_m2_1205_r/processing.rtf | 40 + general/datasets/Hc_m2_1205_r/summary.rtf | 1 + general/datasets/Hc_m2_1205_r/tissue.rtf | 7 + 8 files changed, 3430 insertions(+) create mode 100644 general/datasets/Hc_m2_1205_r/acknowledgment.rtf create mode 100644 general/datasets/Hc_m2_1205_r/cases.rtf create mode 100644 general/datasets/Hc_m2_1205_r/experiment-design.rtf create mode 100644 general/datasets/Hc_m2_1205_r/notes.rtf create mode 100644 general/datasets/Hc_m2_1205_r/platform.rtf create mode 100644 general/datasets/Hc_m2_1205_r/processing.rtf create mode 100644 general/datasets/Hc_m2_1205_r/summary.rtf create mode 100644 general/datasets/Hc_m2_1205_r/tissue.rtf (limited to 'general/datasets/Hc_m2_1205_r') diff --git a/general/datasets/Hc_m2_1205_r/acknowledgment.rtf b/general/datasets/Hc_m2_1205_r/acknowledgment.rtf new file mode 100644 index 0000000..08c9160 --- /dev/null +++ b/general/datasets/Hc_m2_1205_r/acknowledgment.rtf @@ -0,0 +1,54 @@ +
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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:

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diff --git a/general/datasets/Hc_m2_1205_r/cases.rtf b/general/datasets/Hc_m2_1205_r/cases.rtf new file mode 100644 index 0000000..3e78bb4 --- /dev/null +++ b/general/datasets/Hc_m2_1205_r/cases.rtf @@ -0,0 +1,60 @@ +

This analysis has used 68 of BXD strains, the complete set of 13 CXB recombinant inbred strain sets, and a mouse diversity panel consisting of 16 inbred strains and a pair of reciprocal F1 hybrids (B6D2F1 and D2B6F1).

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The BXD genetic reference population of recombinant inbred strains consists of approximately 80 strains. Approximately 800 classical phenotypes from sets of 10 to 70 of these strains been integrated in the GeneNetwork. The BXD strains in this data set include 29 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD40). 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.

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The CXB is the first and oldest set of recombinant inbred strains. Over 500 classical phenotypes from these strains been integrated in the GeneNetwork. It is noteworthy that the CXB strains segregate for the hippocampal lamination defect (Hld),characterized by Nowakowski and colleagues (1984). All of the CXBs have been recently genotyped at 13,377 SNPs.

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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:

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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.

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  1. 129S1/SvImJ
    +     Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
    2. +
  2. A/J
    +     Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
    3. +
  3. AKR/J
    +     Sequenced by NIEHS; Phenome Project B list
    4. +
  4. BALB/cByJ
    +     STILL IN PROGRESS (samples did not pass quality control); Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
    5. +
  5. BALB/cJ
    +     Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
    6. +
  6. C3H/HeJ
    +     Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
    7. +
  7. C57BL/6J
    +     Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
    8. +
  8. C57BL/6ByJ
    +     Paternal substrain of B6 used to generate the CXB panel
    9. +
  9. CAST/Ei
    +     Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
    10. +
  10. DBA/2J
    +     Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
    11. +
  11. KK/HIJ
    +     Sequenced by Perlegen/NIEHS
    12. +
  12. LG/J
    +     Paternal parent of the LGXSM panel
    13. +
  13. NOD/LtJ
    +     Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
    14. +
  14. NZO/HILtJ
    +     Collaborative Cross strain
    15. +
  15. PWD/PhJ
    +     Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
    16. +
  16. PWK/PhJ
    +     Collaborative Cross strain; Phenome Project D list
    17. +
  17. WSB/EiJ
    +     Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
    18. +
  18. B6D2F1 and D2B6F1
    + F1 hybrids generated by crossing C57BL/6J with DBA/2J
    19. +
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We have not combined data from reciprocal F1s because they have different Y chromosome and mitochondial haplotypes. Parent-of-origin effects (imprinting, maternal environment) may also lead to interesting differences in hippocampal transcript levels.

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

diff --git a/general/datasets/Hc_m2_1205_r/experiment-design.rtf b/general/datasets/Hc_m2_1205_r/experiment-design.rtf new file mode 100644 index 0000000..68713a4 --- /dev/null +++ b/general/datasets/Hc_m2_1205_r/experiment-design.rtf @@ -0,0 +1,3252 @@ +
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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 deg. C until use or were immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.

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Replication and Sample Balance: We obtained a male sample pool and female sample pool from each isogenic group. While all strains were orginally represented by matched male and female samples, not all data sets passed the final quality control steps. Seventy-seven of 99 strains are represented by pairs or (rarely) trios of arrays. The first and last samples are technical replicates of a B6D2F1 hippocampal pool (aliquotes R1291H3 and R1291H4).

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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.

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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 deg 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.

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    Data Table 1:

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This table lists all arrays by order of processing (Run), Sample ID, Strain, Sex, Age, number of animals in each sample pool (Pool), F generation number when less than 30 (GenN, and the Source of animals. SampleID is the ID number of the pooled RNA sample with a H1 through H3 suffix to indicate the actual hippocampal RNA aliquot used to prepare cRNA. Grp is the sequential group processing number (1 - 6).
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indextube IDstrainagesexbatch IDpool sizelRMA outlierscale factorback ground averagepresentabsentmarginalAFFX-b-ActinMur (3'/5')AFFX-GapdhMur (3'/5')source
1R2028H2129S1/SvImJ66F530.14.36264.490.4970.4840.0192.781.13JAX
2R2029H2129S1/SvImJ66M630.045.20841.210.490.490.021.620.95JAX
3R2030H1A/J57M520.063.30745.160.5270.4540.0181.630.99UTM RW
4R2032H3AKR/J66F530.043.05461.030.510.4710.0181.460.79JAX
5R2454H1AKR/J66M640.112.89258.550.4740.5070.0191.990.78JAX
6R1289H2B6D2F164F630.022.40653.840.4920.4890.0191.610.96UTM RW
7R1291H3B6D2F166M130.013.52448.540.4870.4940.0191.211.52UTM RW
8R1291H4B6D2F166M630.083.89146.690.5120.4690.0191.90.89UTM RW
9R2036H3BALB/cJ51F530.122.61156.290.5180.4660.0173.31.23UTM RW
10R2053H1BALB/cJ55M530.12.50563.270.4990.4830.0183.11.34UTM RW
11R2037H2BALB/cJ51M640.012.54658.130.4970.4850.0181.260.77UTM RW
12R1507H1BXD158M330.024.05660.170.4780.5030.0191.150.76Glenn
13R1520H1BXD256F440.091.71571.620.5150.4670.0182.361.6Glenn
14R1516H1BXD261M140.012.23164.860.5080.4740.0191.31.53Glenn
15R1593H2BXD560F1401.91359.960.4870.4930.020.981.44Glenn
16R1692H1BXD560M320.073.76472.740.4650.5160.021.150.74Glenn
17R1539H2BXD659F1402.48854.970.5180.4630.0181.081.33Glenn
18R1538H1BXD659M430.012.58550.270.5050.4750.021.460.79Glenn
19R1518H1BXD856F1302.9254.840.5150.4650.021.321.24Glenn
20R1548H1BXD859M630.072.13259.370.5040.4770.0192.161.54Glenn
21R1350H2BXD986F130.052.77160.620.50.4820.0181.011.28UMemphis
22R1531H1BXD1156F630.062.22956.360.5050.4750.022.231.02Glenn
23R1367H1BXD1156M130.012.1178.780.5030.4770.021.071.27Glenn
24R1530H1BXD1258F1303.22753.770.5050.4770.0180.951.4Glenn
25R1529H1BXD1358F630.052.5559.050.4970.4850.01821.54Glenn
26R1662H2BXD1360M130.034.60345.810.5090.4720.0191.30.82Glenn
27R1524H1BXD1560F640.022.96150.930.4970.4840.0191.740.91Glenn
28R1515H1BXD1561M130.013.31657.050.5030.4780.0191.321.21Glenn
29R1661H1BXD1661F130.012.77859.810.5160.4660.0191.391.2Glenn
30R1594H1BXD1661M430.032.63453.660.5040.4780.0181.961.51Glenn
31R1471H1BXD19157M130.023.16543.340.5190.4620.0181.011.29UTM JB
32R1573H1BXD2059F130.023.74952.70.5130.4690.0181.011.27Glenn
33R2507H1BXD2060M630.063.568570.4720.5080.021.290.76Glenn
34R1347H2BXD2164F140.012.88161.490.4940.4860.0190.921.22UMemphis
35R1337H2BXD21102F2402.67358.050.4920.4890.0191.40.76UAB
36R1848H3BXD22196F640.022.94351.70.4940.4850.0212.20.78UAB
37R1525H1BXD2259M230.022.24855.760.5480.4330.0181.260.74Glenn
38R1280H2BXD2356F130.013.18754.630.4580.5230.0190.961.2UTM RW
39R1537H1BXD2358F530.13.71967.540.4680.5130.0191.510.96Glenn
40R1343H2BXD2471F230.012.08365.070.5060.4740.0191.460.75UMemphis
41R1517H1BXD2457M330.013.47153.660.5040.4760.0191.280.78Glenn
42R1366H1BXD2760F2402.2648.460.5180.4630.0191.290.77Glenn
43R1849H1BXD2770M530.068.80138.340.4680.5120.0192.421.08UAB
44R1353H1BXD2879F340.013.2276.220.480.50.021.330.78UMemphis
45R2332H1BXD2860M230.013.21763.680.4910.490.0191.370.79Glenn
46R1532H1BXD2957F230.012.12259.180.5240.4560.0191.170.76Glenn
47R1356H1BXD2976M530.014.03347.670.520.4630.0171.170.78UMemphis
48R1240H2BXD3161M230.022.33565.170.5070.4740.0191.310.78UTM RW
49R1508H2BXD3258M240.011.91767.780.5390.4420.0191.280.73Glenn
50R1345H3BXD3365F220.012.09863.140.5220.4590.0191.270.73UMemphis
51R1581H1BXD3359M330.013.22953.160.4960.4850.0191.190.78Glenn
52R1527H1BXD3459F230.012.358.920.510.4710.0191.240.76Glenn
53R1339H3BXD3474M530.122.88853.490.5060.4760.0182.391.35UMemphis
54R1469H1BXD3683F330.023.47349.90.4940.4860.021.110.76UMemphis
55R1363H1BXD3677M240.012.18448.190.5380.4430.021.280.77UMemphis
56R1855H1BXD3855F340.013.53654.540.490.4920.0181.390.75Glenn
57R1510H1BXD3859M230.012.18668.060.5210.460.0191.260.79Glenn
58R1528H2BXD3959F230.034.71738.30.5110.470.021.120.75Glenn
59R1514H1BXD3959M330.033.99256.060.4770.5040.0191.430.81Glenn
60R1522H1BXD4059F4402.63167.160.490.4910.0181.560.77Glenn
61R1359H1BXD4073M230.097.45839.860.4510.5270.0211.280.74UMemphis
62R1334H2BXD4359F1302.67254.360.4920.4910.0171.22.06UTM RW
63R1303H1BXD4363M340.023.49751.90.4860.4950.0191.150.8UTM RW
64R1326H1BXD4465F3403.41253.960.4960.4850.0181.350.78UTM RW
65R1577H2BXD4456M130.022.15967.520.5120.4690.0191.181.71UTM RW
66R1316H1BXD4858F4302.44568.590.5150.4670.0191.160.73UTM RW
67R1575H3BXD4865M340.054.57755.780.4660.5140.0191.590.9UTM RW
68R2521H1BXD5063F640.013.10957.280.4950.4850.021.230.78UTM RW
69R1944H2BXD5081M130.012.54663.390.4950.4850.020.91.57UTM RW
70R2331H1BXD5166F330.033.53444.420.5010.4810.0171.20.9UTM RW
71R1582H1BXD5171M640.032.9247.870.4890.4910.021.360.75UTM RW
72R1331H1BXD6060F430.012.86750.330.4920.4870.0211.340.78UTM RW
73R1281H2BXD6059M1302.3958.440.5110.4690.020.941.2UTM RW
74R1856H2BXD6194M1203.50249.60.5010.480.0190.961.3UTM RW
75R1246H1BXD6254F140.023.40551.470.5110.4710.0181.141.34UTM RW
76R1585H2BXD6264M640.013.15655.770.5180.4640.0181.430.82UTM RW
77R1945H1BXD63107F130.022.81152.650.5220.4590.0191.051.36UTM RW
78R2093H3BXD6370M630.023.89442.850.5030.4770.0191.291.01UTM RW
79R2062H2BXD6465F130.053.79578.480.5130.4680.0190.981.43UTM RW
80R2061H1BXD6487M340.013.53661.570.4770.5040.0191.310.78UTM RW
81R2054H2BXD6555F120.033.15980.960.480.5020.0181.091.24UTM RW
82R2056H2BXD6589M6202.83659.60.5040.4770.0191.30.75UTM RW
83R1941H2BXD6678F140.012.73450.930.4990.4810.021.181.29UTM RW
84R1949H2BXD6696M420.042.82851.270.4740.5080.0192.051.12UTM RW
85R2060H1BXD6754F630.012.56143.880.5020.4790.021.70.84UTM RW
86R2052H1BXD6761M140.013.16143.230.5210.460.0181.091.31UTM RW
87R2074H1BXD6860F530.026.52849.620.4790.5020.0191.480.83UTM RW
88R1928H1BXD6872M220.012.40448.280.5210.4590.021.30.74UTM RW
89R1439H3BXD6960F230.022.46359.140.5220.4590.0181.310.78UTM RW
90R1559H1BXD6964M330.032.98767.740.4860.4960.0171.380.8UTM RW
91R2134H1BXD7064F520.022.14858.640.5320.450.0191.40.85UTM RW
92R2063H1BXD7055M230.023.48155.320.5130.4690.0181.280.71UTM RW
93R1277H1BXD7360F420.012.57662.450.5020.4790.0191.350.79UTM RW
94R1443H2BXD7376M230.012.31264.340.4990.4810.021.480.77UTM RW
95R2055H2BXD7479M230.012.57656.840.5090.4730.0181.460.88UTM RW
96R2316H1BXD74193M520.013.45755.350.5080.4710.021.170.78UTM RW
97R1871H1BXD7561F230.041.72356.40.530.4510.0191.30.76UTM RW
98R1844H2BXD7590M340.011.93456.230.520.4610.0191.620.86UTM RW
99R1948H2BXD7681F230.011.50768.850.5530.4280.021.30.75UTM RW
100R2094H1BXD7661M540.013.29942.690.5190.4620.0191.390.88UTM RW
101R2262H1BXD7762F340.024.31747.160.4930.4880.0191.320.74UTM RW
102R1423H1BXD7762M230.023.07154.150.510.4710.0191.260.74UTM RW
103R1947H1BXD79108F220.012.59951.520.5240.4570.0191.350.74UTM RW
104R2092H1BXD7986M540.063.73542.250.5140.4680.0182.941.06UTM RW
105R1880H1BXD8068F530.064.85542.220.5010.4810.0182.171.36UTM RW
106R1881H2BXD8068M230.022.07348.930.5240.4580.0191.340.83UTM RW
107R2075H1BXD8360F230.012.45455.10.5020.480.0181.270.77UTM RW
108R2076H2BXD8360M630.032.62455.650.4950.4880.0182.210.94UTM RW
109R2077H2BXD8462F6202.171.870.5220.4590.0181.680.81UTM RW
110R2135H3BXD8475M220.012.46764.460.5050.4760.0191.20.74UTM RW
111R1473H1BXD8579F230.023.38455.340.4780.5020.021.240.77UTM RW
112R1474H1BXD8557M130.012.83155.240.5220.4610.0181.041.29UTM RW
113R1597H1BXD8586M440.092.02853.950.4870.4920.0211.280.83UTM RW
114R1415H1BXD8677F430.022.52553.160.4950.4850.021.660.91UTM RW
115R1710H1BXD8784M240.012.69756.40.5120.4690.0191.280.79UTM RW
116R1872H2BXD8990F220.023.01363.530.4920.4880.0211.220.72UTM RW
117R1850H3BXD8982M440.032.73644.890.4980.4830.0191.50.83UTM RW
118R2058H1BXD9061F230.013.38948.050.5020.4780.021.530.76UTM RW
119R1301H2BXD9258F230.023.54341.970.5220.460.0181.50.79UTM RW
120R1309H1BXD9259M430.051.65566.340.4980.4810.0211.520.82UTM RW
121R2057H1BXD9392F530.024.03344.410.5090.4710.021.220.78UTM RW
122R2059H1BXD9358M1303.05860.290.4930.4880.0191.181.37UTM RW
123R2313H1BXD9459F3303.09159.450.4870.4950.0181.340.73UTM RW
124R1915H1BXD9665F520.045.14546.190.5020.4810.0171.370.74UTM RW
125R1846H2BXD9663M1303.15955.850.4870.4930.020.921.26UTM RW
126R1927H2BXD9767M130.042.62257.810.5390.4440.0171.451.32UTM RW
127R1942H1BXD9862F530.043.10448.420.5280.4540.0192.221.08UTM RW
128R1943H2BXD9862M330.024.0456.850.4840.4970.0191.180.76UTM RW
129R2197H1BXD9970F330.024.28851.750.490.4920.0181.350.81UTM RW
130R2315H1BXD9984M520.036.03643.050.4840.4970.0181.70.96UTM RW
131R2038H3C3H/HeJ63F630.022.67166.740.4760.5040.021.410.77UTM RW
132R2039H1C3H/HeJ63M530.13.38444.150.5280.4540.0172.160.88UTM RW
133R2137H1C57BL/6ByJ55F530.024.74647.010.4880.4930.0181.230.79JAX
134R1361H1C57BL/6J69F640.013.05851.870.4770.5030.021.670.76UTM RW
135R2041H2C57BL/6J65M140.043.34149.260.5270.4560.0181.141.45UTM RW
136R1449H2C57BL/6J71M530.093.59244.320.470.510.021.680.77UTM DG
137R2619H1CAST/Ei64F530.144.07751.870.4550.5280.0182.741.2JAX
138R2116H1CXB155F330.075.79251.590.4590.5210.021.170.8JAX
139R2096H1CXB155M420.013.43553.780.4950.4850.021.220.79JAX
140R2124H1CXB1053F420.114.86739.880.4510.5280.021.550.8JAX
141R2125H1CXB1158F330.033.25654.950.4610.5190.021.460.77JAX
142R2128H1CXB1158M420.064.98654.130.4650.5150.021.110.83JAX
143R2126H1CXB1247F430.113.93554.110.4690.5110.0211.50.79JAX
144R2109H1CXB1247M330.074.51849.260.4880.4920.021.230.77JAX
145R2110H1CXB1356M430.213.47848.080.4610.5170.0221.210.78JAX
146R2117H2CXB262F420.043.3945.970.5330.450.0172.050.89JAX
147R2098H1CXB268M330.022.57254.220.4960.4850.0191.380.86JAX
148R2118H1CXB347F330.033.64663.160.4780.5030.0191.220.77JAX
149R2100H1CXB347M430.025.7651.380.480.5030.0171.240.81JAX
150R2119H1CXB458F430.023.89749.210.4880.4940.0181.310.79JAX
151R2101H1CXB458M330.137.37253.770.4330.5480.0191.20.97JAX
152R2505H1CXB580F630.022.8349.60.4990.480.021.330.76UTM RW
153R2131H1CXB542M430.15.57751.150.4340.5470.0191.70.89JAX
154R0129H2CXB570M330.074.82945.420.4880.4930.0191.230.83UTM RW
155R2102H1CXB649M430.075.14851.630.4530.5290.0181.430.87JAX
156R2121H1CXB763F420.064.90448.710.4640.5170.0191.190.92JAX
157R2104H2CXB758M320.063.38948.790.5020.4790.0191.741.48JAX
158R2122H1CXB854F330.044.12859.770.4510.5290.021.120.76JAX
159R2105H1CXB841M430.163.14661.040.4510.530.0191.340.84JAX
160R2123H1CXB954F330.085.70855.940.4380.5430.0191.320.78JAX
161R2106H1CXB954M430.065.86846.550.4690.5120.0191.180.82JAX
162R2045H2D2B6F165F120.014.40347.990.4970.4850.0181.091.53UTM RW
163R1595H2D2B6F163F530.062.57958.490.5060.4750.0192.491.21UTM RW
164R1551H1D2B6F172F630.022.6253.760.5060.4760.0181.370.76UTM RW
165R1468H1DBA/2J64F530.032.92953.80.5150.4650.0191.280.79UTM RW
166R1683H1KK/HIJ72F630.023.91954.230.4910.4890.021.310.83JAX
167R1687H3KK/HIJ72M530.043.88840.860.4990.4830.0191.860.88JAX
168R2046H1LG/J63F520.032.82259.180.5140.4680.0181.680.8UTM RW
169R2047H2LG/J63M630.072.03860.340.5090.4710.022.160.95UTM RW
170R2048H1NOD/LtJ77F620.144.04550.210.4890.490.0212.890.95UTM RW
171R2049H3NOD/LtJ76M530.12.32852.780.5190.4620.0193.091.35UTM RW
172R2200H1NZO/HlLtJ62F520.032.64854.290.5430.4380.0191.270.8JAX
173R2350H1NZO/HlLtJ96M620.192.39150.520.5180.4630.023.712.21JAX
174R2051H3PWD/PhJ64M530.073.26651.50.4750.5060.0192.81.01UTM RW
175R2322H1PWK/PhJ63F520.092.9454.910.5110.470.0192.321.02JAX
176R2349H1PWK/PhJ83M620.153.30654.930.4590.5220.0194.651.45JAX
177R2198H2WSB/EiJ58F610.022.92257.970.5020.4790.0191.440.76JAX
178R2199H1WSB/EiJ58M530.043.17154.950.4750.5050.021.320.81JAX
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+
+
diff --git a/general/datasets/Hc_m2_1205_r/notes.rtf b/general/datasets/Hc_m2_1205_r/notes.rtf new file mode 100644 index 0000000..4490ee3 --- /dev/null +++ b/general/datasets/Hc_m2_1205_r/notes.rtf @@ -0,0 +1,15 @@ +

This study includes the following datasets:

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+

Hippocampus Consortium M430v2 (Oct05) MAS5

+ +

Hippocampus Consortium M430v2 (Oct05) RMA

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Hippocampus Consortium M430v2 (Oct05) PDNN

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Hippocampus Consortium M430v2 (Dec05) RMA

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Hippocampus Consortium M430v2 (Dec05) PDNN

+
+ +

This text file originally generated prospectively by RWW on July 30 2005. Updated by RWW July 31, 2005.

diff --git a/general/datasets/Hc_m2_1205_r/platform.rtf b/general/datasets/Hc_m2_1205_r/platform.rtf new file mode 100644 index 0000000..af0948c --- /dev/null +++ b/general/datasets/Hc_m2_1205_r/platform.rtf @@ -0,0 +1 @@ +

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.

diff --git a/general/datasets/Hc_m2_1205_r/processing.rtf b/general/datasets/Hc_m2_1205_r/processing.rtf new file mode 100644 index 0000000..df5513b --- /dev/null +++ b/general/datasets/Hc_m2_1205_r/processing.rtf @@ -0,0 +1,40 @@ +
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:

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    +
  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. +
  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. +
  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. +
  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.
    5. +
+ +

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 senstive 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 examploe, 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 whould include the ssample 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 of the probe level (CEL) data after step 5 below. DataDesk allows a rapid detection of subsets of probes that are particular 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. <0L>

+ + +
+ +
+

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.

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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.

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

diff --git a/general/datasets/Hc_m2_1205_r/summary.rtf b/general/datasets/Hc_m2_1205_r/summary.rtf new file mode 100644 index 0000000..9b7c1d6 --- /dev/null +++ b/general/datasets/Hc_m2_1205_r/summary.rtf @@ -0,0 +1 @@ +
PRELIMINARY: The October 2005 Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of approximately 99 genetically diverse strains of mice including 68 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a set of 16 diverse inbred strains, and 2 reciprocal F1 hybrids. The hippocampus is an important and intriguing part of the forebrain that is crucial for memory formation, 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, and parts of the subiculum) 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 Mouse Expression 430 2.0 short oligomer microarrays (MOE430 2.0 or M430v2), of which 179 passed stringent quality control and error checking. This particular data set was processed using the MAS5 protocol. To simplify comparisons among transforms, MAS5 values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/Hc_m2_1205_r/tissue.rtf b/general/datasets/Hc_m2_1205_r/tissue.rtf new file mode 100644 index 0000000..2bb700d --- /dev/null +++ b/general/datasets/Hc_m2_1205_r/tissue.rtf @@ -0,0 +1,7 @@ +
+

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 thanks Muriel Davission 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.

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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).

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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).

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