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.
---
.../HQFNeoc_1210_RankInv/experiment-design.rtf | 937 +++++++++++++++++++++
1 file changed, 937 insertions(+)
create mode 100644 general/datasets/HQFNeoc_1210_RankInv/experiment-design.rtf
(limited to 'general/datasets/HQFNeoc_1210_RankInv/experiment-design.rtf')
diff --git a/general/datasets/HQFNeoc_1210_RankInv/experiment-design.rtf b/general/datasets/HQFNeoc_1210_RankInv/experiment-design.rtf
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index 0000000..322268a
--- /dev/null
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@@ -0,0 +1,937 @@
+This data set consists arrays processed in XX groups over a XX month period (from Month Year to Month Year). Most groups consisted of XX samples. All arrays in this data set were processed using a single protocol by a single operator, NAME HERE. Processing was supervised directly by Dr. Lu Lu. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between Month Day and Month Day, Year. Details on sample assignment to slides and batches is provide in the table below.
+
+Error checking
+
+
+ - Checked for genotypes of BXD strains on all chromosomes using a battery of test Mendelian transcripts (transcripts with a Mendelian segregation pattern in the BXDs). Peak LRS of 260.2 for Prdx2 using Illumina probe ILM5340577. There are no errors in the strain assignment but there are possible genotyping errors, such as:
+ Thumpd1 (ILM7510148) in BXD34 using marker rs6271956
+ H2-D2 (ILM2190725) in BXD69 using marker gnf17.035.152
+ Fcer1g (ILM5550020) in BXD100 using marker rs3722740 (incorrectly scored as a heterozygote).
+
+ These genotype discrepancies are either due to recombination between the marker and the probe or a genotyping errors. (RWW, Feb 27, 2008)
+ - Total count of transcripts/probes with LOD greater than 10 is 1564 with 52 BXD strains (BXD1 through BXD43 from (n = 27) from JAX, and BXD43 through 100 (n = 25) from UTHSC).
+ - Sex assignment checked using Xist probe ILM104280446.
+ All female samples: Strains BXD43, BXD42, BXD68, BXD77, NZW/LacJ, and NZO/HlLtJ
+ All male samples: Strains BXD1, PWK/PhJ, BXD66, BXD97, BXD10, BXD75, BXD44, BXD89, BXD86, BXD80, BXD69
+
+
+Data Table 1:
+
+This table lists all arrays by order of strain (index) and includes data on strain, sex, slide ID and slide position (A through F).
+
+
+
+
+
+
+
+
+ | Index |
+ Strain |
+ Sex |
+ Slide ID |
+ Slide
+ Position |
+
+
+ | 1 |
+ B6D2F1 |
+ F |
+ 1848071018 |
+ D |
+
+
+ | 2 |
+ B6D2F1 |
+ M |
+ 1957998076 |
+ B |
+
+
+ | 3 |
+ C57BL/6J |
+ F |
+ 1957998083 |
+ A |
+
+
+ | 4 |
+ C57BL/6J |
+ M |
+ 1833451021 |
+ A |
+
+
+ | 5 |
+ DBA/2J |
+ F |
+ 1957998083 |
+ C |
+
+
+ | 6 |
+ DBA/2J |
+ M |
+ 1833451021 |
+ C |
+
+
+ | 7 |
+ BXD1 |
+ M |
+ 4051964030 |
+ B |
+
+
+ | 8 |
+ BXD5 |
+ F |
+ 1736925307 |
+ A |
+
+
+ | 9 |
+ BXD5 |
+ M |
+ 4051964028 |
+ C |
+
+
+ | 10 |
+ BXD6 |
+ F |
+ 4051964028 |
+ F |
+
+
+ | 11 |
+ BXD6 |
+ M |
+ 1736925307 |
+ D |
+
+
+ | 12 |
+ BXD8 |
+ F |
+ 4060001025 |
+ A |
+
+
+ | 13 |
+ BXD8 |
+ M |
+ 1957998111 |
+ E |
+
+
+ | 14 |
+ BXD9 |
+ F |
+ 4060001025 |
+ D |
+
+
+ | 15 |
+ BXD9 |
+ M |
+ 1736925359 |
+ B |
+
+
+ | 16 |
+ BXD11 |
+ F |
+ 4051964030 |
+ D |
+
+
+ | 17 |
+ BXD11 |
+ M |
+ 1848071017 |
+ B |
+
+
+ | 18 |
+ BXD12 |
+ F |
+ 4051964030 |
+ E |
+
+
+ | 19 |
+ BXD12 |
+ M |
+ 1848071017 |
+ C |
+
+
+ | 20 |
+ BXD13 |
+ F |
+ 4051964030 |
+ F |
+
+
+ | 21 |
+ BXD13 |
+ M |
+ 1848071017 |
+ D |
+
+
+ | 22 |
+ BXD14 |
+ F |
+ 4051964065 |
+ A |
+
+
+ | 23 |
+ BXD14 |
+ M |
+ 1848071017 |
+ E |
+
+
+ | 24 |
+ BXD15 |
+ F |
+ 4051964065 |
+ B |
+
+
+ | 25 |
+ BXD15 |
+ M |
+ 1848071017 |
+ F |
+
+
+ | 26 |
+ BXD16 |
+ F |
+ 1848071024 |
+ A |
+
+
+ | 27 |
+ BXD16 |
+ M |
+ 4051964065 |
+ C |
+
+
+ | 28 |
+ BXD18 |
+ F |
+ 4051964065 |
+ D |
+
+
+ | 29 |
+ BXD18 |
+ M |
+ 1848071024 |
+ B |
+
+
+ | 30 |
+ BXD19 |
+ F |
+ 4051964065 |
+ E |
+
+
+ | 31 |
+ BXD19 |
+ M |
+ 1848071024 |
+ C |
+
+
+ | 32 |
+ BXD21 |
+ F |
+ 1848071024 |
+ D |
+
+
+ | 33 |
+ BXD21 |
+ M |
+ 4051964065 |
+ F |
+
+
+ | 34 |
+ BXD23 |
+ F |
+ 1848071024 |
+ E |
+
+
+ | 35 |
+ BXD23 |
+ M |
+ 4051964022 |
+ A |
+
+
+ | 36 |
+ BXD27 |
+ F |
+ 1848071024 |
+ F |
+
+
+ | 37 |
+ BXD27 |
+ M |
+ 4051964022 |
+ B |
+
+
+ | 38 |
+ BXD28 |
+ F |
+ 1848071025 |
+ A |
+
+
+ | 39 |
+ BXD28 |
+ M |
+ 4051964022 |
+ C |
+
+
+ | 40 |
+ BXD31 |
+ F |
+ 4051964022 |
+ D |
+
+
+ | 41 |
+ BXD31 |
+ M |
+ 1848071025 |
+ B |
+
+
+ | 42 |
+ BXD32 |
+ F |
+ 4051964022 |
+ E |
+
+
+ | 43 |
+ BXD32 |
+ M |
+ 1848071025 |
+ C |
+
+
+ | 44 |
+ BXD33 |
+ F |
+ 4051964022 |
+ F |
+
+
+ | 45 |
+ BXD33 |
+ M |
+ 1848071025 |
+ D |
+
+
+ | 46 |
+ BXD34 |
+ F |
+ 4051964023 |
+ A |
+
+
+ | 47 |
+ BXD34 |
+ M |
+ 1848071025 |
+ E |
+
+
+ | 48 |
+ BXD36 |
+ F |
+ 1848071025 |
+ F |
+
+
+ | 49 |
+ BXD36 |
+ M |
+ 4051964023 |
+ B |
+
+
+ | 50 |
+ BXD38 |
+ F |
+ 4051964023 |
+ C |
+
+
+ | 51 |
+ BXD38 |
+ M |
+ 1957998101 |
+ A |
+
+
+ | 52 |
+ BXD39 |
+ F |
+ 4051964023 |
+ D |
+
+
+ | 53 |
+ BXD39 |
+ M |
+ 1957998101 |
+ B |
+
+
+ | 54 |
+ BXD40 |
+ F |
+ 4051964023 |
+ E |
+
+
+ | 55 |
+ BXD40 |
+ M |
+ 1957998101 |
+ C |
+
+
+ | 56 |
+ BXD42 |
+ F |
+ 4060001026 |
+ B |
+
+
+ | 57 |
+ BXD43 |
+ F |
+ 1957998101 |
+ D |
+
+
+ | 58 |
+ BXD43 |
+ F |
+ 4051964023 |
+ F |
+
+
+ | 59 |
+ BXD44 |
+ F |
+ 1957998101 |
+ E |
+
+
+ | 60 |
+ BXD44 |
+ M |
+ 4051964028 |
+ A |
+
+
+ | 61 |
+ BXD45 |
+ F |
+ 4051964028 |
+ B |
+
+
+ | 62 |
+ BXD45 |
+ M |
+ 1957998101 |
+ F |
+
+
+ | 63 |
+ BXD51 |
+ F |
+ 4051964028 |
+ D |
+
+
+ | 64 |
+ BXD51 |
+ M |
+ 1736925307 |
+ B |
+
+
+ | 65 |
+ BXD55 |
+ F |
+ 1736925307 |
+ C |
+
+
+ | 66 |
+ BXD55 |
+ M |
+ 4051964028 |
+ E |
+
+
+ | 67 |
+ BXD60 |
+ F |
+ 4060001014 |
+ A |
+
+
+ | 68 |
+ BXD60 |
+ M |
+ 1736925307 |
+ E |
+
+
+ | 69 |
+ BXD61 |
+ F |
+ 4060001014 |
+ B |
+
+
+ | 70 |
+ BXD61 |
+ M |
+ 1736925307 |
+ F |
+
+
+ | 71 |
+ BXD62 |
+ F |
+ 4060001014 |
+ C |
+
+
+ | 72 |
+ BXD62 |
+ M |
+ 1957998111 |
+ A |
+
+
+ | 73 |
+ BXD65 |
+ F |
+ 1957998111 |
+ B |
+
+
+ | 74 |
+ BXD65 |
+ M |
+ 4060001014 |
+ D |
+
+
+ | 75 |
+ BXD66 |
+ M |
+ 4060001026 |
+ C |
+
+
+ | 76 |
+ BXD68 |
+ F |
+ 4060001026 |
+ D |
+
+
+ | 77 |
+ BXD69 |
+ M |
+ 1957998111 |
+ C |
+
+
+ | 78 |
+ BXD69 |
+ M |
+ 4060001014 |
+ E |
+
+
+ | 79 |
+ BXD70 |
+ M |
+ 4060001026 |
+ E |
+
+
+ | 80 |
+ BXD73 |
+ F |
+ 1957998111 |
+ D |
+
+
+ | 81 |
+ BXD73 |
+ M |
+ 4060001014 |
+ F |
+
+
+ | 82 |
+ BXD75 |
+ M |
+ 4060001026 |
+ F |
+
+
+ | 83 |
+ BXD77 |
+ F |
+ 4060001027 |
+ A |
+
+
+ | 84 |
+ BXD80 |
+ M |
+ 4060001027 |
+ B |
+
+
+ | 85 |
+ BXD84 |
+ F |
+ 1957998111 |
+ F |
+
+
+ | 86 |
+ BXD84 |
+ M |
+ 4060001025 |
+ B |
+
+
+ | 87 |
+ BXD86 |
+ M |
+ 4060001027 |
+ C |
+
+
+ | 88 |
+ BXD87 |
+ F |
+ 4060001027 |
+ F |
+
+
+ | 89 |
+ BXD87 |
+ M |
+ 4060001025 |
+ C |
+
+
+ | 90 |
+ BXD89 |
+ M |
+ 4060001027 |
+ D |
+
+
+ | 91 |
+ BXD90 |
+ F |
+ 1736925359 |
+ C |
+
+
+ | 92 |
+ BXD90 |
+ M |
+ 4060001025 |
+ E |
+
+
+ | 93 |
+ BXD96 |
+ F |
+ 4060001025 |
+ F |
+
+
+ | 94 |
+ BXD96 |
+ M |
+ 1736925359 |
+ D |
+
+
+ | 95 |
+ BXD97 |
+ M |
+ 4060001027 |
+ E |
+
+
+ | 96 |
+ BXD100 |
+ F |
+ 1848071017 |
+ A |
+
+
+ | 97 |
+ BXD100 |
+ M |
+ 4051964030 |
+ C |
+
+
+ | 98 |
+ 129S1/SvImJ |
+ F |
+ 1736925359 |
+ E |
+
+
+ | 99 |
+ 129S1/SvImJ |
+ M |
+ 1848071018 |
+ A |
+
+
+ | 100 |
+ A/J |
+ F |
+ 1848071018 |
+ B |
+
+
+ | 101 |
+ A/J |
+ M |
+ 1736925359 |
+ F |
+
+
+ | 102 |
+ AKR/J |
+ F |
+ 1848071018 |
+ C |
+
+
+ | 103 |
+ AKR/J |
+ M |
+ 1957998076 |
+ A |
+
+
+ | 104 |
+ BALB/cByJ |
+ F |
+ 1957998076 |
+ C |
+
+
+ | 105 |
+ BALB/cByJ |
+ M |
+ 1953348019 |
+ A |
+
+
+ | 106 |
+ C3H/HeJ |
+ F |
+ 1953348019 |
+ D |
+
+
+ | 107 |
+ C3H/HeJ |
+ M |
+ 1957998076 |
+ F |
+
+
+ | 108 |
+ CAST/EiJ |
+ F |
+ 1833451021 |
+ B |
+
+
+ | 109 |
+ CAST/EiJ |
+ M |
+ 1957998083 |
+ B |
+
+
+ | 110 |
+ KK/HlJ |
+ F |
+ 1957998083 |
+ E |
+
+
+ | 111 |
+ KK/HlJ |
+ M |
+ 1848071023 |
+ F |
+
+
+ | 112 |
+ BXSB/MpJ |
+ F |
+ 1957998076 |
+ E |
+
+
+ | 113 |
+ BXSB/MpJ |
+ M |
+ 1953348019 |
+ C |
+
+
+ | 114 |
+ FVB/NJ |
+ F |
+ 1833451021 |
+ D |
+
+
+ | 115 |
+ FVB/NJ |
+ M |
+ 1957998083 |
+ D |
+
+
+ | 116 |
+ MOLF/EiJ |
+ F |
+ 1957998083 |
+ F |
+
+
+ | 117 |
+ MOLF/EiJ |
+ M |
+ 1848071001 |
+ B |
+
+
+ | 118 |
+ NOD/LtJ |
+ F |
+ 1848071001 |
+ C |
+
+
+ | 119 |
+ NOD/LtJ |
+ M |
+ 4060001004 |
+ A |
+
+
+ | 120 |
+ NZB/BlNJ |
+ F |
+ 4060001004 |
+ B |
+
+
+ | 121 |
+ NZB/BlNJ |
+ M |
+ 1848071001 |
+ D |
+
+
+ | 122 |
+ NZO/HlLtJ |
+ F |
+ 4060001004 |
+ C |
+
+
+ | 123 |
+ NZW/LacJ |
+ F |
+ 4060001004 |
+ D |
+
+
+ | 124 |
+ PWD/PhJ |
+ F |
+ 4060001004 |
+ E |
+
+
+ | 125 |
+ PWK/PhJ |
+ M |
+ 4060001004 |
+ F |
+
+
+ | 126 |
+ WSB/EiJ |
+ F |
+ 4051964030 |
+ A |
+
+
+ | 127 |
+ BTBRT<+>tf/J |
+ F |
+ 1957998076 |
+ D |
+
+
+ | 128 |
+ BTBRT<+>tf/J |
+ M |
+ 1953348019 |
+ B |
+
+
+
+ |
+
+
+
--
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