From d029d5d7f8ead1f1de8d318045004a4a6f68f5fb Mon Sep 17 00:00:00 2001 From: Bonface Date: Fri, 9 Feb 2024 09:41:28 -0600 Subject: Update dataset RTF Files. --- general/datasets/HC_M2CB_1205_R/cases.rtf | 56 +++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 general/datasets/HC_M2CB_1205_R/cases.rtf (limited to 'general/datasets/HC_M2CB_1205_R/cases.rtf') diff --git a/general/datasets/HC_M2CB_1205_R/cases.rtf b/general/datasets/HC_M2CB_1205_R/cases.rtf new file mode 100644 index 0000000..15e6cda --- /dev/null +++ b/general/datasets/HC_M2CB_1205_R/cases.rtf @@ -0,0 +1,56 @@ +

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.

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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
    +     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/HlJ
    +     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/HlLtJ
    +     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 mitochondrial 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 strains are available from Lu Lu and colleagues at UTHSC.

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