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. --- .../datasets/Hc_m2_1205_r/experiment-design.rtf | 3252 ++++++++++++++++++++ 1 file changed, 3252 insertions(+) create mode 100644 general/datasets/Hc_m2_1205_r/experiment-design.rtf (limited to 'general/datasets/Hc_m2_1205_r/experiment-design.rtf') diff --git a/general/datasets/Hc_m2_1205_r/experiment-design.rtf b/general/datasets/Hc_m2_1205_r/experiment-design.rtf new file mode 100644 index 0000000..68713a4 --- /dev/null +++ b/general/datasets/Hc_m2_1205_r/experiment-design.rtf @@ -0,0 +1,3252 @@ +
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Sample Processing: Samples were processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center for Genomic Research, The University of Memphis, led by Thomas R. Sutter. All processing steps were performed by Shirlean Goodwin. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8. The majority of samples were 1.9 to 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. We required an RNA integrity number (RIN) of greater than 8. This RIN value is based on the intensity ratio and amplitude of 18S and 28S rRNA signals. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using Superscript II reverse transcriptase (Invitrogen Inc.). The Enzo Life Sciences, Inc., BioArray High Yield RNA Transcript Labeling Kit (T7, Part No. 42655) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 2.0 or 2.1 are acceptable) and the Bioanalyzer output (a dark cRNA smear on the 2100 output centered roughly between 600 and 2000 nucleotides is required). Those samples that passed both QC steps (10% usually failed and new RNA samples had to be acquired and processed) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No. 900371). Fragmented cRNA samples were either stored at -80 deg. C until use or were immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.

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Replication and Sample Balance: We obtained a male sample pool and female sample pool from each isogenic group. While all strains were orginally represented by matched male and female samples, not all data sets passed the final quality control steps. Seventy-seven of 99 strains are represented by pairs or (rarely) trios of arrays. The first and last samples are technical replicates of a B6D2F1 hippocampal pool (aliquotes R1291H3 and R1291H4).

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Experimental Design and Batch Structure: This data set consists arrays processed in six groups over a three month period (May 2005 to August 2005). Each group consists of 32 to 34 arrays.Sex, strain, and strain type (BXD, CXB, and MDP) were interleaved among groups to ensure reasonable balance and to minimize group-by-strain statistical confounds in group normalization. The two independent samples from a single strain were always run in different groups. All arrays were processed using a single protocol by a single operator, Shirlean Goodwin.

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All samples in a group were labeled on one day, except for a few cases that failed QC on their first pass. The hybridization station accommodates up to 20 samples, and for this reason each group was split into a large first set of 20 samples and a second set of 12 to 14 samples. Samples were washed in groups of four and then held in at 4 deg C until all 20 (or 12-14) arrays were ready to scan. The last four samples out of the wash stations were scanned directly. Samples were scanned in sets of four.

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    Data Table 1:

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This table lists all arrays by order of processing (Run), Sample ID, Strain, Sex, Age, number of animals in each sample pool (Pool), F generation number when less than 30 (GenN, and the Source of animals. SampleID is the ID number of the pooled RNA sample with a H1 through H3 suffix to indicate the actual hippocampal RNA aliquot used to prepare cRNA. Grp is the sequential group processing number (1 - 6).
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indextube IDstrainagesexbatch IDpool sizelRMA outlierscale factorback ground averagepresentabsentmarginalAFFX-b-ActinMur (3'/5')AFFX-GapdhMur (3'/5')source
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99R1948H2BXD7681F230.011.50768.850.5530.4280.021.30.75UTM RW
100R2094H1BXD7661M540.013.29942.690.5190.4620.0191.390.88UTM RW
101R2262H1BXD7762F340.024.31747.160.4930.4880.0191.320.74UTM RW
102R1423H1BXD7762M230.023.07154.150.510.4710.0191.260.74UTM RW
103R1947H1BXD79108F220.012.59951.520.5240.4570.0191.350.74UTM RW
104R2092H1BXD7986M540.063.73542.250.5140.4680.0182.941.06UTM RW
105R1880H1BXD8068F530.064.85542.220.5010.4810.0182.171.36UTM RW
106R1881H2BXD8068M230.022.07348.930.5240.4580.0191.340.83UTM RW
107R2075H1BXD8360F230.012.45455.10.5020.480.0181.270.77UTM RW
108R2076H2BXD8360M630.032.62455.650.4950.4880.0182.210.94UTM RW
109R2077H2BXD8462F6202.171.870.5220.4590.0181.680.81UTM RW
110R2135H3BXD8475M220.012.46764.460.5050.4760.0191.20.74UTM RW
111R1473H1BXD8579F230.023.38455.340.4780.5020.021.240.77UTM RW
112R1474H1BXD8557M130.012.83155.240.5220.4610.0181.041.29UTM RW
113R1597H1BXD8586M440.092.02853.950.4870.4920.0211.280.83UTM RW
114R1415H1BXD8677F430.022.52553.160.4950.4850.021.660.91UTM RW
115R1710H1BXD8784M240.012.69756.40.5120.4690.0191.280.79UTM RW
116R1872H2BXD8990F220.023.01363.530.4920.4880.0211.220.72UTM RW
117R1850H3BXD8982M440.032.73644.890.4980.4830.0191.50.83UTM RW
118R2058H1BXD9061F230.013.38948.050.5020.4780.021.530.76UTM RW
119R1301H2BXD9258F230.023.54341.970.5220.460.0181.50.79UTM RW
120R1309H1BXD9259M430.051.65566.340.4980.4810.0211.520.82UTM RW
121R2057H1BXD9392F530.024.03344.410.5090.4710.021.220.78UTM RW
122R2059H1BXD9358M1303.05860.290.4930.4880.0191.181.37UTM RW
123R2313H1BXD9459F3303.09159.450.4870.4950.0181.340.73UTM RW
124R1915H1BXD9665F520.045.14546.190.5020.4810.0171.370.74UTM RW
125R1846H2BXD9663M1303.15955.850.4870.4930.020.921.26UTM RW
126R1927H2BXD9767M130.042.62257.810.5390.4440.0171.451.32UTM RW
127R1942H1BXD9862F530.043.10448.420.5280.4540.0192.221.08UTM RW
128R1943H2BXD9862M330.024.0456.850.4840.4970.0191.180.76UTM RW
129R2197H1BXD9970F330.024.28851.750.490.4920.0181.350.81UTM RW
130R2315H1BXD9984M520.036.03643.050.4840.4970.0181.70.96UTM RW
131R2038H3C3H/HeJ63F630.022.67166.740.4760.5040.021.410.77UTM RW
132R2039H1C3H/HeJ63M530.13.38444.150.5280.4540.0172.160.88UTM RW
133R2137H1C57BL/6ByJ55F530.024.74647.010.4880.4930.0181.230.79JAX
134R1361H1C57BL/6J69F640.013.05851.870.4770.5030.021.670.76UTM RW
135R2041H2C57BL/6J65M140.043.34149.260.5270.4560.0181.141.45UTM RW
136R1449H2C57BL/6J71M530.093.59244.320.470.510.021.680.77UTM DG
137R2619H1CAST/Ei64F530.144.07751.870.4550.5280.0182.741.2JAX
138R2116H1CXB155F330.075.79251.590.4590.5210.021.170.8JAX
139R2096H1CXB155M420.013.43553.780.4950.4850.021.220.79JAX
140R2124H1CXB1053F420.114.86739.880.4510.5280.021.550.8JAX
141R2125H1CXB1158F330.033.25654.950.4610.5190.021.460.77JAX
142R2128H1CXB1158M420.064.98654.130.4650.5150.021.110.83JAX
143R2126H1CXB1247F430.113.93554.110.4690.5110.0211.50.79JAX
144R2109H1CXB1247M330.074.51849.260.4880.4920.021.230.77JAX
145R2110H1CXB1356M430.213.47848.080.4610.5170.0221.210.78JAX
146R2117H2CXB262F420.043.3945.970.5330.450.0172.050.89JAX
147R2098H1CXB268M330.022.57254.220.4960.4850.0191.380.86JAX
148R2118H1CXB347F330.033.64663.160.4780.5030.0191.220.77JAX
149R2100H1CXB347M430.025.7651.380.480.5030.0171.240.81JAX
150R2119H1CXB458F430.023.89749.210.4880.4940.0181.310.79JAX
151R2101H1CXB458M330.137.37253.770.4330.5480.0191.20.97JAX
152R2505H1CXB580F630.022.8349.60.4990.480.021.330.76UTM RW
153R2131H1CXB542M430.15.57751.150.4340.5470.0191.70.89JAX
154R0129H2CXB570M330.074.82945.420.4880.4930.0191.230.83UTM RW
155R2102H1CXB649M430.075.14851.630.4530.5290.0181.430.87JAX
156R2121H1CXB763F420.064.90448.710.4640.5170.0191.190.92JAX
157R2104H2CXB758M320.063.38948.790.5020.4790.0191.741.48JAX
158R2122H1CXB854F330.044.12859.770.4510.5290.021.120.76JAX
159R2105H1CXB841M430.163.14661.040.4510.530.0191.340.84JAX
160R2123H1CXB954F330.085.70855.940.4380.5430.0191.320.78JAX
161R2106H1CXB954M430.065.86846.550.4690.5120.0191.180.82JAX
162R2045H2D2B6F165F120.014.40347.990.4970.4850.0181.091.53UTM RW
163R1595H2D2B6F163F530.062.57958.490.5060.4750.0192.491.21UTM RW
164R1551H1D2B6F172F630.022.6253.760.5060.4760.0181.370.76UTM RW
165R1468H1DBA/2J64F530.032.92953.80.5150.4650.0191.280.79UTM RW
166R1683H1KK/HIJ72F630.023.91954.230.4910.4890.021.310.83JAX
167R1687H3KK/HIJ72M530.043.88840.860.4990.4830.0191.860.88JAX
168R2046H1LG/J63F520.032.82259.180.5140.4680.0181.680.8UTM RW
169R2047H2LG/J63M630.072.03860.340.5090.4710.022.160.95UTM RW
170R2048H1NOD/LtJ77F620.144.04550.210.4890.490.0212.890.95UTM RW
171R2049H3NOD/LtJ76M530.12.32852.780.5190.4620.0193.091.35UTM RW
172R2200H1NZO/HlLtJ62F520.032.64854.290.5430.4380.0191.270.8JAX
173R2350H1NZO/HlLtJ96M620.192.39150.520.5180.4630.023.712.21JAX
174R2051H3PWD/PhJ64M530.073.26651.50.4750.5060.0192.81.01UTM RW
175R2322H1PWK/PhJ63F520.092.9454.910.5110.470.0192.321.02JAX
176R2349H1PWK/PhJ83M620.153.30654.930.4590.5220.0194.651.45JAX
177R2198H2WSB/EiJ58F610.022.92257.970.5020.4790.0191.440.76JAX
178R2199H1WSB/EiJ58M530.043.17154.950.4750.5050.021.320.81JAX
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