From e34e7da50fc0ff5ed41e8bdaf2b1d41c9e9cf534 Mon Sep 17 00:00:00 2001 From: Bonface Date: Thu, 15 Feb 2024 06:09:54 -0600 Subject: Update dataset RTF Files. --- general/datasets/RTC_1106_R/cases.rtf | 914 ---------------------------------- 1 file changed, 914 deletions(-) delete mode 100644 general/datasets/RTC_1106_R/cases.rtf (limited to 'general/datasets/RTC_1106_R/cases.rtf') diff --git a/general/datasets/RTC_1106_R/cases.rtf b/general/datasets/RTC_1106_R/cases.rtf deleted file mode 100644 index 5ae01c7..0000000 --- a/general/datasets/RTC_1106_R/cases.rtf +++ /dev/null @@ -1,914 +0,0 @@ -
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Parental and 31 BXD lines were studied. Mice were received from The 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 were 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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Sex of samples is listed below in Table 1. In brief, data for BXD14 and 23 are male-only samples, whereas BXD12, 16, 31, 34, 36 and C57BL/6J are from female-only samples. All other samples (DBA/2J, BXD1, 2, 6, 9, 11, 18, 21 32, 33, 39, 40) consist of one male and one female array. The sex of samples can be independently validated using the Xist probe set (1427262_at).

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Figure 1: The expression of Xist can be used as an independent marker for sex. Xist is expressed at very low levels (noise) in male samples (far left) and at high values in females (far right). Sex-balanced samples (middle) have high variance due to the inclusion of one array per sex.

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    Table 1

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IndexProbeSet IDSample DescriptionSexStraincd25MicroarrayShort DescriptionAgePool No.Pool members (animal number)Date of preparation
1HZI1008BXD-06f (f1) CD25+FBXD6CD25+YesBXD-06f17f11,3,41-31-2006
2HZI1009BXD-06m (m2) CD25+MBXD6CD25+YesBXD-06m18m25,6,71-31-2006
3HZI1010BXD-14m (m3) CD25+MBXD14CD25+YesBXD-14m17m31,3,41-31-2006
4HZI1013BXD-40f (f6) CD25+FBXD40CD25+YesBXD-40f17f61,2,32-1-2006
5HZI1014BXD-40m (m7) CD25+MBXD40CD25+YesBXD-40m17m75,6,72-2-2006
6HZI1015BXD-02f (f8) CD25+FBXD2CD25+YesBXD-02f17f81,2,32-14-2006
7HZI1016BXD-02m (m20) CD25+MBXD2CD25+YesBXD-02m21m204,5,64-6-2006
8HZI1017BXD-11f (f30) CD25+FBXD11CD25+YesBXD-11f17f303,4,55-11-2006
9HZI1018BXD-11m (m9) CD25+MBXD11CD25+YesBXD-11m18m91,22-14-2006
10HZI1019BXD-12f (f10) CD25+FBXD12CD25+YesBXD-12f17f101,2,32-14-2006
11HZI1020BXD-39f (f23) CD25+FBXD39CD25+YesBXD-39f19f234,5,64-11-2006
12HZI1021BXD-33m (m11) CD25+MBXD33CD25+YesBXD-33m17m111,22-14-2006
13HZI1022BXD-18f (f14) CD25+FBXD18CD25+YesBXD-18f17f143,4,52-15-2006
14HZI1023BXD-18m (m13) CD25+MBXD18CD25+YesBXD-18m18m137,82-15-2006
15HZI1024BXD-23m (m15) CD25+MBXD23CD25+YesBXD-23m18m151,2,32-15-2006
16HZI1026BXD-09f (f17) CD25+FBXD9CD25+YesBXD-09f21f171,2,34-5-2006
17HZI1028BXD-09m (m35) CD25+MBXD9CD25+YesBXD-09m15m357,8,97-7-2006
18HZI1029BXD-32f (f18) CD25+FBXD32CD25+YesBXD-32f21f181,2,34-6-2006
19HZI1030BXD-32m (m19) CD25+MBXD32CD25+YesBXD-32m22m191,2,34-6-2006
20HZI1031BXD-33f (f22) CD25+FBXD33CD25+YesBXD-33f18f222,3,44-11-2006
21HZI1032BXD-39m (m29) CD25+MBXD39CD25+YesBXD-39m17m295,6,75-10-2006
22HZI1033BXD-01f (f32) CD25+FBXD1CD25+YesBXD-01f18f323,47-6-2006
23HZI1034BXD-01m (m31) CD25+MBXD1CD25+YesBXD-01m18m311,27-6-2006
24HZI1035BXD-16f (f26) CD25+FBXD16CD25+YesBXD-16f18f261,2,34-12-2006
25HZI1036BXD-21f (f25) CD25+FBXD21CD25+YesBXD-21f19f255,6,74-12-2006
26HZI1037BXD-21m (m24) CD25+MBXD21CD25+YesBXD-21m18m241,2,34-12-2006
27HZI1039BXD-31f (f34) CD25+FBXD31CD25+YesBXD-31f16f341,2,37-7-2006
28HZI1040C57BL/6Jf (f28) CD25+FC57BL/6JCD25+YesC57BL/6Jf16f281,2,35-10-2006
29HZI1041DBA/2Jf (f27) CD25+FDBA/2JCD25+YesDBA/2Jf16f275,6,75-10-2006
30HZI1042DBA/2Jm (m21) CD25+MDBA/2JCD25+YesDBA/2Jm21m211,2,34-11-2006
31HZI1487BXD-08f (f67) CD25+FBXD8CD25+YesBXD-08f11f674,5,66-25-2007
32HZI1488BXD-08m (m66) CD25+MBXD8CD25+YesBXD-08m17m661,2,36-25-2007
33HZI1489BXD-16m (m36) CD25+MBXD16CD25+YesBXD-16m20, 16m365,6,78-28-2006
34HZI1490BXD-12m (m42) CD25+MBXD12CD25+YesBXD-12m20m425,6,710-23-2006
35HZI1491BXD-13f (f44) CD25+FBXD13CD25+YesBXD-13f15f441,2,312-13-2006
36HZI1492BXD-13m (m45) CD25+MBXD13CD25+YesBXD-13m15m454,5,6,712-13-2006
37HZI1493BXD-14f (f48) CD25+FBXD14CD25+YesBXD-14f16f485,6,72-15-2007
38HZI1494BXD-19f (f64) CD25+FBXD19CD25+YesBXD-19f19f647,8,96-20-2007
39HZI1495BXD-19m (m46) CD25+MBXD19CD25+YesBXD-19m16m464,5,612-15-2006
40HZI1499BXD-28m (m43) CD25+MBXD28CD25+YesBXD-28m17,2m431,2,310-23-2006
41HZI1500BXD-42f (f49) CD25+FBXD42CD25+YesBXD-42f17f49??3-8-2007
42HZI1502F1 (BXD)m (f50) CD25+MB6D2F1CD25+YesF1 (BXD)m15m511,2,3,4-18-2007
43HZI1503F1 (BXD)m (m51) CD25+FB6D2F1CD25+YesF1 (BXD)f15f501,2,34-18-2007
44HZI1504BXD-86f (f52) CD25+FBXD86CD25+YesBXD-86f16f521,2,34-18-2007
45HZI1505BXD-43f (f53) CD25+FBXD43CD25+YesBXD-43f16f531,2,34-23-2007
46HZI1506BXD-44f (f54) CD25+FBXD44CD25+YesBXD-44f18f541,2,34-23-2007
47HZI1507BXD-45f (f55) CD25+FBXD45CD25+YesBXD-45f19f551,2,34-23-2007
48HZI1508BXD-62f (f56) CD25+FBXD62CD25+YesBXD-62f17f561,2,34-26-2007
49HZI1509BXD-73f (f57) CD25+FBXD73CD25+YesBXD-73f18f571,2,34-26-2007
50HZI1510BXD-51f (f59) CD25+FBXD51CD25+YesBXD-51f22f591,2,36-18-2007
51HZI1523BXD-75f (f58) CD25+FBXD75CD25+YesBXD-75f15,17f581,2,34-26-2007
52HZI1525BXD-29m (m37) CD25+MBXD29CD25+YesBXD-29m20, 16m371,2,38-29-2006
53HZI1526BXD-34f (f4) CD25+FBXD34CD25+YesBXD-34f17f41,2,32-1-2006
54HZI1940BXD-27m (m39) CD25+MBXD27CD25+YesBXD-27m18 - 20m391,3,49-1-2006
55HZI1941BXD-42m (m47) CD25+MBXD42CD25+YesBXD-42m15,16m471,2,312-15-2006
56HZI1942BXD-34m (m5) CD25+MBXD34CD25+YesBXD-34m17m55,7,82-1-2006
57HZI1943BXD-38f (f70) CD25+FBXD38CD25+YesBXD-38f13f704,5,6,72-1-2008
58HZI1944BXD-31m (m69) CD25+MBXD31CD25+YesBXD-31m14m694,5,62-1-2008
59HZI1945BXD-27f (f12) CD25+FBXD27CD25+YesBXD-27f18f121,22-15-2006
60HZI1946BXD-38m (m63) CD25+MBXD38CD25+YesBXD-38m18m631,2,36-20-2007
61HZI1947BXD-23f (f62) CD25+FBXD23CD25+YesBXD-23f21f621,2,36-20-2007
62HZI1948BXD-28f (f61) CD25+FBXD28CD25+YesBXD-28f22f611,2,36-18-2007
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