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/B30_k_1206_rn/cases.rtf | 1748 ++++++++++++++++++++++++++++++ 1 file changed, 1748 insertions(+) create mode 100644 general/datasets/B30_k_1206_rn/cases.rtf (limited to 'general/datasets/B30_k_1206_rn/cases.rtf') diff --git a/general/datasets/B30_k_1206_rn/cases.rtf b/general/datasets/B30_k_1206_rn/cases.rtf new file mode 100644 index 0000000..1425413 --- /dev/null +++ b/general/datasets/B30_k_1206_rn/cases.rtf @@ -0,0 +1,1748 @@ +
+

The SM cross was originally made to map barley grain quality traits; Steptoe is high-yielding barley cultivar used for animal feeding, but Morex has good malting barley characteristics (Hayes et al 1993). Many agronomic quality traits have been mapped using this population (for the lists see BeerGenes web-site http://gnome.agrenv.mcgill.ca/bg/).

+ +

The sample used in this study consists of 150 Steptoe x Morex doubled haploid recombinant lines (Kleinhofs et al. 1993) was used to obtain embryo-derived tissue. For the seedling leaf tissue a subset of 35 lines was used. This subset was selected based on evenly spaced crossovers along each of seven barley chromosomes. The expression data of 11 DH lines has been removed from both, embryo and leaf, leaving for the analysis 129 lines with embryo expression data and a subset of 30 lines with seedling leaf expression data. The lines were removed from the analysis after error checking; discrepancies with genotyping data were found. We left all 150 lines in the embryo Apr06 data set and the full data set is available from the ArrayExpress. The following table lists line IDs and corresponding CEL file IDs, also indicating:
+1) pedigree; shows the direction of the cross that was used to produce the original F1. The parental plants were given letter codes of A - Z. For example, SM1 was derived from an F1 that was generated by crossing Steptoe plant "B" as a female with Morex plant "F" as a male.
+2) 'minimapper' subset - MINI;
+3) lines that have expression data removed - ERROR:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Order #Line IDPermanent Oregon IDCross direction +
CEL file names
+ 		Mini-mapper setError check
embryo data-setleaf data-setembryo data-setleaf data-set
1SM0012907001Steptoe/Morex(BxF)AD_SCRI_82.CEL  OK 
2SM0022907002Steptoe/Morex(BxF)AD_SCRI_1.CEL  OK 
3SM0032907003Morex/Steptoe(CxF)AD_SCRI_19.CEL  OK 
4SM0042907004Morex/Steptoe(CxF)AD_SCRI_3.CEL0521-1_SetA1.CELSMminiOKOK
5SM0052907005Steptoe/Morex(BxH)AD_SCRI_88.CEL  OK 
6SM0062907006Morex/Steptoe(CxF)AD_SCRI_48.CEL  OK 
7SM0072907007Steptoe/Morex(BxH)AD_SCRI_35.CEL0521-2_SetA2.CELSMminiOKOK
8SM0092907009Steptoe/Morex(BxF)AD_SCRI_2.CEL  OK 
9SM0102907010Morex/Steptoe(IxE)AD_SCRI_42.CEL  OK 
10SM0112907011Steptoe/Morex(QxG)AD_SCRI_10.CEL  OK 
11SM0122907012Morex/Steptoe(CxF)AD_SCRI_45.CEL0521-3_SetA3.CELSMminiERRORERROR
12SM0132907013Morex/Steptoe(IxE)AD_SCRI_78.CEL0521-4_SetA4.CELSMminiERRORERROR
13SM0142907014Steptoe/Morex(BxH)AD_SCRI_18.CEL  OK 
14SM0152907015Steptoe/Morex(BxH)AD_SCRI_5.CEL  OK 
15SM0162907016Steptoe/Morex(BxH)AD_SCRI_21.CEL  OK 
16SM0202907020Steptoe/Morex(OxJ)AD_SCRI_77.CEL  OK 
17SM0212907021Morex/Steptoe(IxE)AD_SCRI_30.CEL  OK 
18SM0222907022Morex/Steptoe(IxE)AD_SCRI_31.CEL0521-5_SetA5.CELSMminiOKOK
19SM0232907023Steptoe/Morex(BxH)AD_SCRI_32.CEL  OK 
20SM0242907024Morex/Steptoe(IxE)AD_SCRI_33.CEL0521-6_SetA6.CELSMminiOKOK
21SM0252907025Morex/Steptoe(CxF)AD_SCRI_34.CEL  OK 
22SM0272907027Steptoe/Morex(OxJ)AD_SCRI_12.CEL0521-7_SetA7.CELSMminiOKOK
23SM0302907030Morex/Steptoe(IxE)AD_SCRI_79.CEL  OK 
24SM0312907031Steptoe/Morex(OxJ)AD_SCRI_16.CEL  OK 
25SM0322907032Morex/Steptoe(IxE)AD_SCRI_13.CEL  OK 
26SM0352907035Morex/Steptoe(CxF)AD_SCRI_15.CEL  ERROR 
27SM0392907039Morex/Steptoe(CxF)AD_SCRI_41.CEL  OK 
28SM0402907040Steptoe/Morex(BxH)AD_SCRI_83.CEL  OK 
29SM0412907041Steptoe/Morex(OxJ)AD_SCRI_11_redo.CEL0521-8_SetA8.CELSMminiOKOK
30SM0422907042Morex/Steptoe(CxF)AD_SCRI_57.CEL  OK 
31SM0432907043Morex/Steptoe(JxE)AD_SCRI_49.CEL0521-9_SetA9.CELSMminiOKOK
32SM0442907044Steptoe/Morex(OxJ)AD_SCRI_50.CEL0521-10_SetA10.CELSMminiOKOK
33SM0452907045Steptoe/Morex(BxH)AD_SCRI_51.CEL  OK 
34SM0462907046Steptoe/Morex(OxJ)AD_SCRI_52.CEL0521-11_SetA11.CELSMminiOKOK
35SM0482907048Steptoe/Morex(BxF)AD_SCRI_53.CEL  ERROR 
36SM0502907050Morex/Steptoe(IxE)AD_SCRI_46.CEL  OK 
37SM0542907054Morex/Steptoe(CxF)AD_SCRI_60.CEL  OK 
38SM0552907055Steptoe/Morex(OxJ)AD_SCRI_55.CEL  OK 
39SM0562907056Steptoe/Morex(BxH)AD_SCRI_23.CEL  OK 
40SM0572907057Morex/Steptoe(CxF)AD_SCRI_24.CEL  OK 
41SM0582907058Steptoe/Morex(BxF)AD_SCRI_22.CEL  OK 
42SM0592907059Steptoe/Morex(BxH)AD_SCRI_27.CEL  OK 
43SM0612907061Morex/Steptoe(LxF)AD_SCRI_81.CEL0521-12_SetA12.CELSMminiOKOK
44SM0622907062Morex/Steptoe(CxF)AD_SCRI_44.CEL  OK 
45SM0632907063Steptoe/Morex(OxJ)AD_SCRI_40.CEL0521-13_SetA13.CELSMminiOKOK
46SM0642907064Morex/Steptoe(CxF)AD_SCRI_87_redo.CEL  OK 
47SM0652907065Morex/Steptoe(CxF)AD_SCRI_54.CEL  OK 
48SM0672907067Steptoe/Morex(OxJ)AD_SCRI_73.CEL  OK 
49SM0682907068Steptoe/Morex(OxG)AD_SCRI_56.CEL  ERROR 
50SM0692907069Steptoe/Morex(BxH)AD_SCRI_71.CEL  OK 
51SM0702907070Steptoe/Morex(BxF)AD_SCRI_64.CEL  OK 
52SM0712907071Steptoe/Morex(BxH)AD_SCRI_58.CEL  OK 
53SM0722907072Morex/Steptoe(CxF)AD_SCRI_59.CEL  OK 
54SM0732907073Steptoe/Morex(BxF)AD_SCRI_74.CEL0521-14_SetA14.CELSMminiOKERROR
55SM0742907074Morex/Steptoe(CxF)AD_SCRI_25.CEL0521-15_SetA15.CELSMminiOKOK
56SM0752907075Steptoe/Morex(QxG)AD_SCRI_120.CEL  OK 
57SM0762907076Steptoe/Morex(BxF)AD_SCRI_112.CEL  OK 
58SM0772907077Morex/Steptoe(CxF)AD_SCRI_142.CEL  OK 
59SM0782907078Steptoe/Morex(BxF)AD_SCRI_86.CEL  OK 
60SM0792907079Morex/Steptoe(CxF)AD_SCRI_153.CEL0521-16_SetA16.CELSMminiOKERROR
61SM0802907080Steptoe/Morex(BxF)AD_SCRI_107.CEL  OK 
62SM0812907081Morex/Steptoe(CxF)AD_SCRI_105.CEL  OK 
63SM0822907082Steptoe/Morex(BxF)AD_SCRI_97.CEL  OK 
64SM0832907083Steptoe/Morex(BxF)AD_SCRI_89.CEL  OK 
65SM0842907084Morex/Steptoe(CxF)AD_SCRI_155.CEL  OK 
66SM0852907085Morex/Steptoe(IxE)AD_SCRI_149.CEL0521-17_SetA17.CELSMminiOKOK
67SM0872907087Steptoe/Morex(OxJ)AD_SCRI_113.CEL  OK 
68SM0882907088Morex/Steptoe(CxF)AD_SCRI_93.CEL0521-18_SetA18.CELSMminiOKOK
69SM0892907089Steptoe/Morex(OxJ)AD_SCRI_148.CEL0521-19_SetA19.CELSMminiOKOK
70SM0912907091Morex/Steptoe(CxF)AD_SCRI_110.CEL  OK 
71SM0922907092Steptoe/Morex(OxJ)AD_SCRI_7.CEL  OK 
72SM0932907093Steptoe/Morex(BxF)AD_SCRI_122.CEL  OK 
73SM0942907094Morex/Steptoe(CxF)AD_SCRI_150.CEL  OK 
74SM0972907097Morex/Steptoe(CxF)AD_SCRI_158.CEL  OK 
75SM0982907098Morex/Steptoe(CxF)AD_SCRI_121.CEL  OK 
76SM0992907099Steptoe/Morex(QxG)AD_SCRI_137.CEL  OK 
77SM1032907103Morex/Steptoe(IxE)AD_SCRI_156.CEL  OK 
78SM1042907104Steptoe/Morex(BxH)AD_SCRI_70.CEL  ERROR 
79SM1052907105Morex/Steptoe(IxE)AD_SCRI_69.CEL  OK 
80SM1102907110Morex/Steptoe(CxF)AD_SCRI_75.CEL  ERROR 
81SM1122907112Steptoe/Morex(BxF)AD_SCRI_84.CEL  OK 
82SM1162907116Morex/Steptoe(CxF)AD_SCRI_117.CEL0521-20_SetA20.CELSMminiOKOK
83SM1202907120Steptoe/Morex(OxJ)AD_SCRI_138.CEL  OK 
84SM1242907124Steptoe/Morex(BxF)AD_SCRI_146.CEL  OK 
85SM1252907125Morex/Steptoe(IxE)AD_SCRI_43.CEL  OK 
86SM1262907126Steptoe/Morex(OxJ)AD_SCRI_144_redo.CEL  OK 
87SM1272907127Steptoe/Morex(BxH)AD_SCRI_129.CEL  OK 
88SM1292907129Steptoe/Morex(OxJ)AD_SCRI_132.CEL  OK 
89SM1302907130Morex/Steptoe(CxF)AD_SCRI_101.CEL0521-21_SetA21.CELSMminiOKOK
90SM1312907131Steptoe/Morex(OxJ)AD_SCRI_102.CEL  OK 
91SM1322907132Steptoe/Morex(QxG)AD_SCRI_4_redo.CEL  OK 
92SM1332907133Morex/Steptoe(CxF)AD_SCRI_157.CEL  OK 
93SM1342907134Morex/Steptoe(IxE)AD_SCRI_159.CEL  OK 
94SM1352907135Steptoe/Morex(BxF)AD_SCRI_72.CEL0521-22_SetA22.CELSMminiOKOK
95SM1362907136Steptoe/Morex(QxG)AD_SCRI_123.CEL0521-23_SetA23.CELSMminiOKOK
96SM1372907137Steptoe/Morex(BxH)AD_SCRI_39.CEL  OK 
97SM1392907139Morex/Steptoe(CxF)AD_SCRI_133.CEL  OK 
98SM1402907140Morex/Steptoe(CxF)AD_SCRI_134.CEL0521-24_SetA24.CELSMminiOKOK
99SM1412907141Steptoe/Morex(BxH)AD_SCRI_136.CEL0521-25_SetA25.CELSMminiOKOK
100SM1422907142Morex/Steptoe(IxE)AD_SCRI_6.CEL  OK 
101SM1432907143Steptoe/Morex(BxH)AD_SCRI_145.CEL  OK 
102SM1442907144Steptoe/Morex(BxF)AD_SCRI_103.CEL  OK 
103SM1452907145Steptoe/Morex(QxG)AD_SCRI_108.CEL  OK 
104SM1462907146Morex/Steptoe(BxF)AD_SCRI_91.CEL0521-26_SetA26.CELSMminiOKOK
105SM1472907147Steptoe/Morex(OxJ)AD_SCRI_139.CEL  OK 
106SM1492907149Steptoe/Morex(BxF)AD_SCRI_131.CEL  ERROR 
107SM1502907150Morex/Steptoe(CxF)AD_SCRI_37.CEL  OK 
108SM1512907151Morex/Steptoe(IxE)AD_SCRI_28.CEL  OK 
109SM1522907152Steptoe/Morex(BxH)AD_SCRI_9_redo.CEL0521-27_SetA27.CELSMminiOKOK
110SM1532907153Steptoe/Morex(BxH)AD_SCRI_135.CEL  OK 
111SM1542907154Steptoe/Morex(BxH)AD_SCRI_114.CEL  OK 
112SM1552907155Steptoe/Morex(BxH)AD_SCRI_119.CEL0521-28_SetA28.CELSMminiOKOK
113SM1562907156Steptoe/Morex(BxH)AD_SCRI_140.CEL  OK 
114SM1572907157Morex/Steptoe(CxF)AD_SCRI_106_redo.CEL  OK 
115SM1582907158Morex/Steptoe(CxF)AD_SCRI_65.CEL  OK 
116SM1592907159Morex/Steptoe(IxE)AD_SCRI_168.CEL  OK 
117SM1602907160Steptoe/Morex(OxJ)AD_SCRI_47.CEL0521-29_SetA29.CELSMminiOKERROR
118SM1612907161Steptoe/Morex(BxH)AD_SCRI_76.CEL  ERROR 
119SM1622907162Morex/Steptoe(CxF)AD_SCRI_147.CEL  OK 
120SM1642907164Steptoe/Morex(OxJ)AD_SCRI_128.CEL  OK 
121SM1652907165Steptoe/Morex(BxH)AD_SCRI_143.CEL  OKOK
122SM1662907166Morex/Steptoe(CxF)AD_SCRI_115.CEL  OK 
123SM1672907167Steptoe/Morex(BxH)AD_SCRI_127.CEL0521-30_SetA30.CELSMminiOKOK
124SM1682907168Steptoe/Morex(BxH)AD_SCRI_130.CEL  OK 
125SM1692907169Morex/Steptoe(CxF)AD_SCRI_118.CEL0521-31_SetA31.CELSMminiOKOK
126SM1702907170Steptoe/Morex(BxF)AD_SCRI_151.CEL  OK 
127SM1712907171Steptoe/Morex(BxF)AD_SCRI_165.CEL  ERROR 
128SM1722907172Steptoe/Morex(OxJ)AD_SCRI_152.CEL  ERROR 
129SM1732907173Steptoe/Morex(OxJ)AD_SCRI_104.CEL0521-32_SetA32.CELSMminiOKOK
130SM1742907174Steptoe/Morex(BxH)AD_SCRI_154.CEL  OK 
131SM1762907176Morex/Steptoe(CxF)AD_SCRI_141.CEL  OK 
132SM1772907177Morex/Steptoe(CxF)AD_SCRI_111.CEL0521-33_SetA33.CELSMminiOKOK
133SM1792907179Morex/Steptoe(CxF)AD_SCRI_166.CEL  OK 
134SM1802907180Morex/Steptoe(IxE)AD_SCRI_161.CEL  OK 
135SM1812907181Morex/Steptoe(IxE)AD_SCRI_162.CEL  OK 
136SM1822907182Morex/Steptoe(CxF)AD_SCRI_163.CEL  OK 
137SM1832907183Morex/Steptoe(CxF)AD_SCRI_164.CEL  OK 
138SM1842907184Morex/Steptoe(IxE)AD_SCRI_160.CEL0521-34_SetA34.CELSMminiOKOK
139SM1852907185Morex/Steptoe(IxE)AD_SCRI_167.CEL  OK 
140SM1862907186Morex/Steptoe(IxE)AD_SCRI_62.CEL  OK 
141SM1872907187Morex/Steptoe(IxE)AD_SCRI_61.CEL  OK 
142SM1882907188Morex/Steptoe(CxF)AD_SCRI_63.CEL  OK 
143SM1892907189Steptoe/Morex(QxG)AD_SCRI_80.CEL  OK 
144SM1932907193Morex/Steptoe(IxE)AD_SCRI_36.CEL  OK 
145SM1942907194Steptoe/Morex(OxJ)AD_SCRI_29.CEL  OK 
146SM1962907196Steptoe/Morex(BxF)AD_SCRI_26.CEL  OK 
147SM1972907197Steptoe/Morex(BxF)AD_SCRI_85.CEL  OK 
148SM1982907198Morex/Steptoe(IxE)AD_SCRI_8.CEL  OK 
149SM1992907199Steptoe/Morex(BxF)AD_SCRI_20.CEL  OK 
150SM2002907200Morex/Steptoe(IxE)AD_SCRI_38.CEL0521-35_SetA35.CELSMminiOKOK
parentSteptoe  AD_SCRI_17.CEL0521-36_SetA36.CEL   
parentSteptoe  AD_SCRI_66.CEL0521-37_SetA37.CEL   
parentSteptoe  AD_SCRI_68.CEL0521-38_SetA38.CEL   
parentMorex  AD_SCRI_116.CEL0521-39_SetA39.CEL   
parentMorex  AD_SCRI_14.CEL0521-40_SetA40.CEL   
parentMorex  AD_SCRI_67.CEL0521-41_SetA41.CEL   
+ +

 

+
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