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/Rthc_0211_r/cases.rtf | 824 +++++++++++++++++++++++++++++++++ 1 file changed, 824 insertions(+) create mode 100644 general/datasets/Rthc_0211_r/cases.rtf (limited to 'general/datasets/Rthc_0211_r/cases.rtf') diff --git a/general/datasets/Rthc_0211_r/cases.rtf b/general/datasets/Rthc_0211_r/cases.rtf new file mode 100644 index 0000000..5f97723 --- /dev/null +++ b/general/datasets/Rthc_0211_r/cases.rtf @@ -0,0 +1,824 @@ +
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Parental and 31 BXD lines were studied. Mice were received from Jackson Laboratory, or from The Oak Ridge National and were bred in the facility of the Neuro-BSIK consortium (VU University Amsterdam). The data set includes expression values for 18 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD40, as well as the two parental strains, C57BL/6J and DBA/2J. All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding.

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BXD spleen sample pools (from 2-3 mice) were obtained from a pathogen-free mice of the Dutch Mouse Phenomics Consortium (MPC) in Amsterdam. Mice were imported into the central animal facility at the HZI and kept in a pathogen-free vivarium. Mice were euthanized using CO2 and spleenocytes wre prepared. Most mice were between 17 and 22 weeks of age when samples were collected. FACS sorting was used to select the CD4-positive T cells. These cells were further separated into CD4+CD25+ and CD4+CD25- pools.

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Error-checking strain identity. A set of more than 20 probe sets with Mendelian segregation patterns in this HZI data set were used to confirm strain identify in early June, 2007. Two errors were detected and rectified. As of June 22, 2007, data are registered correctly. Prior to June 22, 2007, data listed as strains BXD33 and BXD39 were essentially hybrid (mixed) data sets.

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On Aug 23, 2007, we loaded the final QTL Reaper data into GeneNetwork for the corrected data set. The maximum LRS generated by any probe set is 84.6 for 1436240_at (Tra2a). A total of 41 probe sets are associated with QTLs that have LRS values above 46 (LOD > 10).

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    Table 1

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IndexProbeSet IDSample DescriptionSexStraincd25MicroarrayShort DescriptionAgePool No.Pool members (animal number)Date of preparation
1HZI1176BXD-06f (f1) CD25FBXD6CD25-YesBXD-06f17f11,3,41-31-2006
2HZI1177BXD-06m (m2) CD25MBXD6CD25-YesBXD-06m18m25,6,71-31-2006
3HZI1178BXD-14m (m3) CD25MBXD14CD25-YesBXD-14m17m31,3,41-31-2006
4HZI1179BXD-34f (f4) CD25FBXD34CD25-YesBXD-34f17f41,2,32-1-2006
5HZI1180BXD-34m (m5) CD25MBXD34CD25-YesBXD-34m17m55,7,82-1-2006
6HZI1181BXD-40f (f6) CD25FBXD40CD25-YesBXD-40f17f61,2,32-1-2006
7HZI1182BXD-40m (m7) CD25MBXD40CD25-YesBXD-40m17m75,6,72-2-2006
8HZI1183BXD-02f (f8) CD25FBXD2CD25-YesBXD-02f17f81,2,32-14-2006
9HZI1184BXD-02m (m20) CD25MBXD2CD25-YesBXD-02m21m204,5,64-6-2006
10HZI1185BXD-11f (f30) CD25FBXD11CD25-YesBXD-11f17f303,4,55-11-2006
11HZI1186BXD-11m (m9) CD25MBXD11CD25-YesBXD-11m18m91,22-14-2006
12HZI1187BXD-12f (f10) CD25FBXD12CD25-YesBXD-12f17f101,2,32-14-2006
13HZI1188BXD-39f (f23) CD25FBXD39CD25-YesBXD-39f19f234,5,64-11-2006
14HZI1191BXD-18m (m13) CD25MBXD18CD25-YesBXD-18m18m137,82-15-2006
15HZI1192BXD-23m (m15) CD25MBXD23CD25-YesBXD-23m18m151,2,32-15-2006
16HZI1194BXD-09f (f17) CD25FBXD9CD25-YesBXD-09f21f171,2,34-5-2006
17HZI1195BXD-09m (m16) CD25MBXD9CD25-YesBXD-09m221m165,64-5-2006
18HZI1196BXD-09m (m35) CD25MBXD9CD25-YesBXD-09m15m357,8,97-7-2006
19HZI1197BXD-32f (f18) CD25FBXD32CD25-YesBXD-32f21f181,2,34-6-2006
20HZI1198BXD-32m (m19) CD25MBXD32CD25-YesBXD-32m22m191,2,34-6-2006
21HZI1199BXD-33f (f22) CD25FBXD33CD25-YesBXD-33f18f222,3,44-11-2006
22HZI1200BXD-39m (m29) CD25MBXD39CD25-YesBXD-39m17m295,6,75-10-2006
23HZI1201BXD-01f (f32) CD25FBXD1CD25-YesBXD-01f18f323,47-6-2006
24HZI1202BXD-01m (m31) CD25MBXD1CD25-YesBXD-01m18m311,27-6-2006
25HZI1203BXD-16f (f26) CD25FBXD16CD25-YesBXD-16f18f261,2,34-12-2006
26HZI1204BXD-21f (f25) CD25FBXD21CD25-YesBXD-21f19f255,6,74-12-2006
27HZI1205BXD-21m (m24) CD25MBXD21CD25-YesBXD-21m18m241,2,34-12-2006
28HZI1208C57BL/6Jf (f28) CD25FC57BL/6JCD25-YesC57BL/6Jf16f281,2,35-10-2006
29HZI1209DBA/2Jf (f27) CD25FDBA/2JCD25-YesDBA/2Jf16f275,6,75-10-2006
30HZI1210DBA/2Jm (m21) CD25MDBA/2JCD25-YesDBA/2Jm21m211,2,34-11-2006
31HZI2473BXD-13 m 45MBXD13CD25-YesBXD-13m15m454,5,6,712-13-2006
32HZI2474BXD-19 m 46MBXD19CD25-YesBXD-19m16m464,5,612-15-2006
33HZI2475BXD-28 m 43MBXD28CD25-YesBXD-28m17,2m431,2,310-23-2006
34HZI2476BXD-29 m 37MBXD29CD25-YesBXD-29m20, 16m371,2,38-29-2006
35HZI2477BXD-31 m 69MBXD31CD25-YesBXD-31m14m694,5,62-1-2008
36HZI2478BXD-33 m 11MBXD33CD25-YesBXD-33m17m111,22-14-2006
37HZI2479BXD-38 m 63MBXD38CD25-YesBXD-38m18m631,2,36-20-2007
38HZI2480BXD-42 m 47MBXD42CD25-YesBXD-42m15,16m471,2,312-15-2006
39HZI2481BXD-42 m 65MBXD42CD25-YesBXD-42m15,16m471,2,312-15-2006
40HZI2482BXD-13 f 44FBXD13CD25-YesBXD-13f15f441,2,312-13-2006
41HZI2483BXD-18 F 14FBXD18CD25-YesBXD-18f17f143,4,52-15-2006
42HZI2484BXD-19 f 38FBXD19CD25-YesBXD-19f221f381,2,39-1-2006
43HZI2485BXD-19 f 64FBXD19CD25-YesBXD-19f19f647,8,96-20-2007
44HZI2486BXD-28 f 61FBXD28CD25-YesBXD-28f22f611,2,36-18-2007
45HZI2487BXD-29 f 40FBXD29CD25-YesBXD-29f15 - 16f404,5,69-25-2006
46HZI2488BXD-31 f 34FBXD31CD25-YesBXD-31f16f341,2,37-7-2006
47HZI2489BXD-38 f 70FBXD38CD25-YesBXD-38f13f704,5,6,72-1-2008
48HZI2490BXD-42 f 49FBXD42CD25-YesBXD-42f17f49??3-8-2007
49HZI2491BXD-43 f 53FBXD43CD25-YesBXD-43f16f531,2,34-23-2007
50HZI2492BXD-44 f 54FBXD44CD25-YesBXD-44f18f541,2,34-23-2007
51HZI2493BXD-45 f 55FBXD45CD25-YesBXD-45f19f551,2,34-23-2007
52HZI2494BXD-51 f 59FBXD51CD25-YesBXD-51f22f591,2,36-18-2007
53HZI2495BXD-62 f 56FBXD62CD25-YesBXD-62f17f561,2,34-26-2007
54HZI2496BXD-73 f 57FBXD73CD25-YesBXD-73f18f571,2,34-26-2007
55HZI2497BXD-75 f 58FBXD75CD25-YesBXD-75f15,17f581,2,34-26-2007
56HZI2498BXD-86 f 52FBXD86CD25-YesBXD-86f16f521,2,34-18-2007
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