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/B30_K_1206_Rn/acknowledgment.rtf | 3 + general/datasets/B30_K_1206_Rn/cases.rtf | 1748 ++++++++++++++++++++ .../datasets/B30_K_1206_Rn/experiment-design.rtf | 62 + general/datasets/B30_K_1206_Rn/notes.rtf | 14 + general/datasets/B30_K_1206_Rn/platform.rtf | 3 + general/datasets/B30_K_1206_Rn/processing.rtf | 49 + general/datasets/B30_K_1206_Rn/summary.rtf | 5 + general/datasets/B30_K_1206_Rn/tissue.rtf | 9 + 8 files changed, 1893 insertions(+) create mode 100644 general/datasets/B30_K_1206_Rn/acknowledgment.rtf create mode 100644 general/datasets/B30_K_1206_Rn/cases.rtf create mode 100644 general/datasets/B30_K_1206_Rn/experiment-design.rtf create mode 100644 general/datasets/B30_K_1206_Rn/notes.rtf create mode 100644 general/datasets/B30_K_1206_Rn/platform.rtf create mode 100644 general/datasets/B30_K_1206_Rn/processing.rtf create mode 100644 general/datasets/B30_K_1206_Rn/summary.rtf create mode 100644 general/datasets/B30_K_1206_Rn/tissue.rtf (limited to 'general/datasets/B30_K_1206_Rn') diff --git a/general/datasets/B30_K_1206_Rn/acknowledgment.rtf b/general/datasets/B30_K_1206_Rn/acknowledgment.rtf new file mode 100644 index 0000000..5d9cc73 --- /dev/null +++ b/general/datasets/B30_K_1206_Rn/acknowledgment.rtf @@ -0,0 +1,3 @@ +
+

Plant maintenance, tissue collection, RNA isolation, and data submission to ArrayExpress was done at SCRI by Arnis Druka with support from BBSRC/SEERAD grant SCR/910/04 The genetics of gene expression in barley' to Michael Kearsey (University of Birmingham, UK) and Robbie Waugh (SCRI, UK). Probe synthesis, labeling and hybridization were performed according to manufacturer’s protocols (Affymetrix, Santa Clara, CA) at the Iowa State University GeneChip Core facility (Rico Caldo and Roger Wise). ArrayExpress (EBI, UK) team members Tim Rayner, Helen Parkinson, and Alvis Brazma are acknowledged for excellent help with data submission to ArrayExpress.

+
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The SM cross was originally made to map barley grain quality traits; Steptoe is high-yielding barley cultivar used for animal feeding, but Morex has good malting barley characteristics (Hayes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   
+ +

 

+
diff --git a/general/datasets/B30_K_1206_Rn/experiment-design.rtf b/general/datasets/B30_K_1206_Rn/experiment-design.rtf new file mode 100644 index 0000000..e743086 --- /dev/null +++ b/general/datasets/B30_K_1206_Rn/experiment-design.rtf @@ -0,0 +1,62 @@ +
+

RNA Sample Processing:

+ +

Trizol RNA isolation and RNeasy clean up protocol for whole plants (embryo-derived tissue dissected from 4 days old germinating grains) and the seedling leaves (12 days after planting).

+ +


+☐ Grind tissue (9 embryos) with a mortar and pestle in liquid nitrogen
+☐ Add 5 ml TRIzol (pre-heated to 60oC) to all samples, vortex until all the tissue is thawed, place in the 60oC waterbath..
+☐ Incubate samples at 60oC for 10 minutes, vortexing three times.
+☐ Centrifuge @ 4000 x rpm @ 4C for 30 minutes (in Eppendorf 5810R).
+☐ While centrifuging, label new set of 15 ml tubes
+☐ Transfer supernatant to 15 ml centrifuge tube
+☐ Add 1 ml of chloroform. Vortex the sample until color shade is uniform at least 5
+seconds, and incubate at room temperature for 5 minutes.
+☐ Centrifuge @ 4000 x rpm for 30 minutes @ 4oC.
+☐ While centrifuging, label new 15 ml tubes
+☐ Collect the upper aqueous layer (there will be about 3 mls) and transfer to a new 15 ml tube.
+☐ Add 0.6 volumes (2 ml) of isopropanol, mix gently, incubate at room temperature for 20 minutes.
+☐ Centrifuge @ 4000 rpm for 30 minutes @ 4oC.
+☐ Wash the pellet with 10 ml of cold 75% ethanol. Swirl & centrifuge at
+4000 rpm for 15 minutes @ 4oC.
+☐ Discard supernatant, centrifuge for 5 min, remove the rest of the ethanol
+☐ Air-dry the pellet for 10 minutes, inverted on a kimwipe.
+☐ Dissolve pellet in 400 ul of DEPC-treated H2O. Resuspend by pipeting up & down a
+few times.
+☐ Add 2 ul SuperaseIn. Incubate at 60oC for 10 minutes to resuspend.
+☐ Set water bath to 37oC.
+☐ Add 50 ul 10X DnaseI Buffer, 45 ul H2O and 5 ul of DnaseI, incubate at 37oC for 1 hr.
+☐ Prepare Buffer RLT (Rneasy Clean-up Midi Kit) by adding b-mercaptoethanol (10ul/1ml RLT).
+☐ Add 2.0 ml Buffer RLT to the RNA prep and mix thoroughly.
+☐ Add 1.4 ml ethanol (96-100%) to the diluted RNA. Mix thoroughly.
+☐ Label 15 ml tubes from the kit and place midi columns in them
+☐ Apply sample to a Midi column, close tube gently and centrifuge for 20 min at 3000 rpm.
+☐ Discard the flow-through.
+☐ Add 2.5 ml Buffer RPE to the RNA easy column, close the centrifuge tube gently,
+incubate for 3 min
+☐ Centrifuge for 10 min at 3000 rpm. Discard the flow-through.
+☐ Add another 2.5 ml Buffer RPE to the RNeasy column. Close the centrifuge tube
+gently, incubate for 3 min
+☐ Centrifuge for 10 min at 3000 rpm, remove flow-through
+☐ Centrifuge again for another 5 min.
+☐ Label new 15 ml tubes from the kit.
+☐ Transfer the RNA easy column to a new tube and pipet 250 ul volume of
+RNase-free water directly onto the RNeasy silica-membrane incubate for 1 min
+☐ Centrifuge for 5 min at 3000 rpm.
+☐ To the same tube add again 250 ul H2O, incubate for 1 min.
+☐ Centrifuge for 5 min at 3000 rpm.
+☐ Label two sets of 1.5 ml Eppendorf tubes.
+☐ Transfer 490 ul to the one tube and 10 ul to another one. Use 10 ul tube for the RNA

+ +

Detailed descriptions of these procedures can be found under the ArrayExpress (http://www.ebi.ac.uk/aerep/?) protocol P-MEXP-4631 (Caldo et al. 2004).

+ +

Replication and Sample Balance:

+ +

3 independent replicates of both parental cultivars Steptoe and Morex were generated for both tissues, embryo and seedling leaf.

+ +

Experimental Design and Batch Structure:

+
+ +
+

The following are ArrayExpress (http://www.ebi.ac.uk/aerep/?) experiment IDs: E-TABM-111 (leaf, 41 chips) and E-TABM-112 (embryo derived, 156 chips).

+
diff --git a/general/datasets/B30_K_1206_Rn/notes.rtf b/general/datasets/B30_K_1206_Rn/notes.rtf new file mode 100644 index 0000000..46cff8f --- /dev/null +++ b/general/datasets/B30_K_1206_Rn/notes.rtf @@ -0,0 +1,14 @@ +
+

Arnis Druka
+Genetics Programme
+Scottish Crop Research Institute
+Invergowrie, Dundee DD2 5DA
+Angus, Scotland, United Kingdom
+Tel +44 01382 562731
+Fax +44 01382 568587
+adruka@scri.sari.ac.uk

+
+ +
+

This text file originally generated by Arnis Druka on May 8, 2006. Modified Aug1 by AD. Entered by RWW Aug 4, 2006. Modified by AD Jan 29, 2007, Feb 01, 2007.

+
diff --git a/general/datasets/B30_K_1206_Rn/platform.rtf b/general/datasets/B30_K_1206_Rn/platform.rtf new file mode 100644 index 0000000..a935318 --- /dev/null +++ b/general/datasets/B30_K_1206_Rn/platform.rtf @@ -0,0 +1,3 @@ +
+

Affymetrix 22K Barley1 GeneChip probe array (http://www.affymetrix.com/products/arrays/specific/barley.affx ; Affymetrix product #900515 GeneChip Barley Genome Array) representing 21,439 non-redundant Barley1 exemplar sequences was derived from worldwide contribution of 350,000 high-quality ESTs from 84 cDNA libraries, in addition to 1,145 barley gene sequences from the National Center for Biotechnology Information non-redundant database (Close et al 2004). Abbreviated annotations were created based on the exemplar sequence homology by Arnis Druka using data from the Harvest (http://harvest.ucr.edu/) data depository.

+
diff --git a/general/datasets/B30_K_1206_Rn/processing.rtf b/general/datasets/B30_K_1206_Rn/processing.rtf new file mode 100644 index 0000000..d8d039a --- /dev/null +++ b/general/datasets/B30_K_1206_Rn/processing.rtf @@ -0,0 +1,49 @@ +
+ + + + + + + + + + + + + + + + + + + +
+
Types of the expression data-sets
+ 		+
Data processing description
+
Barley1 Embryo gcRMA SCRI (Dec 06)
+ Barley1 Leaf gcRMA SCRI (Dec 06)		 +

 

+ +

The Affymetrix' CEL files that were generated using MAS 5.0 Suite were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) and processed using the RMA algorithm.

+ +

 

+
Barley1 Embryo MAS 5.0 SCRI (Dec 06)
+ Barley1 Leaf MAS 5.0 SCRI (Dec 06)		 +

 

+ +

The MAS 5.0 values were calculated from the DAT files using Affymetrix' MAS 5.0 Suite.

+ +

 

+
Barley1 Embryo0 gcRMA SCRI (Apr 06)
+ Barley1 Leaf gcRMAn SCRI (Dec 06)		 +

The Affymetrix' CEL files were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) software and processed using the RMA algorithm. Per-chip and per-gene normalization was done following the standard GeneSpring procedure (citation of the GeneSpring normalization description):

+ +
    +
  1. Values below 0.01 were set to 0.01.
    2. +
  2. Each measurement was divided by the 50.0th percentile of all measurements in that sample.
    3. +
  3. Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.
    4. +
+
+
diff --git a/general/datasets/B30_K_1206_Rn/summary.rtf b/general/datasets/B30_K_1206_Rn/summary.rtf new file mode 100644 index 0000000..67f4fab --- /dev/null +++ b/general/datasets/B30_K_1206_Rn/summary.rtf @@ -0,0 +1,5 @@ +

Barley1 Leaf MAS 5.0 SCRI (Dec 06) - integrated probe set value for each gene has been calculated using MAS 5.0 algorithm which uses pixel values from both, PM and MM probes. Descriptions of probe set signal calculation can be found on this page below, section 'About Data Processing'.

+ +
+

The SCRI barley data set provides estimates of mRNA abundance in doubled haploid recombinant lines of cultivated barley. Embryo-derived tissues at four days after imbibition (150 lines) and seedling leaves at 12 days after imbibition (subset of 34 lines) and three biological replicates of each parental cultivar (Steptoe and Morex) for each tissue were used for the isolation of total RNA and hybridization to the Barley1 22K GeneChip (GEO GPL1340).

+
diff --git a/general/datasets/B30_K_1206_Rn/tissue.rtf b/general/datasets/B30_K_1206_Rn/tissue.rtf new file mode 100644 index 0000000..a8351e8 --- /dev/null +++ b/general/datasets/B30_K_1206_Rn/tissue.rtf @@ -0,0 +1,9 @@ +
+

Plant material according to the current plant ontologies: Embryo-derived tissues: whole plant (PO:0000003) at the development stage 1.05-coleoptile emerged from seed (GRO:0007056); Seedling leaves: primary shoot (PO:0006341) at the developmental stage 2.02-first leaf unfolded (GRO:0007060) (Druka et al. 2006).

+ +

To obtain embryo-derived tissue, growth room#2, AN building, SCRI, with the standard laboratory bench positioned in the middle of the room was used to germinate sterilized seeds. Seeds were placed between three layers of wet 3MM filter paper in the 156 10 mm Petri plates. Thirty to fifty seeds per line (per Petri plate) were used. Germination was in the dark, 16 hours at 17 deg C and 8 hours at 12 deg C. After 96 hours, embryo-derived tissue (mesocotyl, coleoptile, and seminal roots) from three grains was dissected and flash frozen in the liquid nitrogen. Germination and collection was repeated two more times. Complete randomization of the Petri plates was done for each germination event. Tissues from all three germinations (collections) were bulked before RNA isolation. Three replicates of the parental cultivars were germinated for each collection.

+ +

To obtain seedling leaves, three Microclima 1000 growth chambers (Snijders Scientific B.V., Tilburg, Holland) were used for the experiment. Each cabinet accomodated 40 (13x13 cm) pots. Humidity was set to 70%, with light conditions for 16 hours light at 17C and 8 hours dark at 12C. The cycle started at 10 am with lights on. Light intensity was 337-377 mmol m-2 s-1, measured at the beginning of the experiment, 11 cm from the light source. Measurement was done using Sky Quantium light sensor at 15oC. Plants were placed 55 cm from the light source (from the bulb to the surface of the vermiculite). Ten sterilized seeds per pot were planted and 3 pots per genotype / per cabinet were used. After 12 days, leaf blade and sheath from 5-7 the same size plants was cut off, bulked and flash frozen in the liquid nitrogen.

+ +

 

+
-- cgit v1.2.3