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. --- .../INIA_PG_RMA_Ex_0612/acknowledgment.rtf | 1 - general/datasets/INIA_PG_RMA_Ex_0612/cases.rtf | 840 --------------------- .../INIA_PG_RMA_Ex_0612/experiment-design.rtf | 10 - general/datasets/INIA_PG_RMA_Ex_0612/platform.rtf | 1 - .../datasets/INIA_PG_RMA_Ex_0612/processing.rtf | 1 - general/datasets/INIA_PG_RMA_Ex_0612/summary.rtf | 3 - general/datasets/INIA_PG_RMA_Ex_0612/tissue.rtf | 1 - 7 files changed, 857 deletions(-) delete mode 100644 general/datasets/INIA_PG_RMA_Ex_0612/acknowledgment.rtf delete mode 100644 general/datasets/INIA_PG_RMA_Ex_0612/cases.rtf delete mode 100644 general/datasets/INIA_PG_RMA_Ex_0612/experiment-design.rtf delete mode 100644 general/datasets/INIA_PG_RMA_Ex_0612/platform.rtf delete mode 100644 general/datasets/INIA_PG_RMA_Ex_0612/processing.rtf delete mode 100644 general/datasets/INIA_PG_RMA_Ex_0612/summary.rtf delete mode 100644 general/datasets/INIA_PG_RMA_Ex_0612/tissue.rtf (limited to 'general/datasets/INIA_PG_RMA_Ex_0612') diff --git a/general/datasets/INIA_PG_RMA_Ex_0612/acknowledgment.rtf b/general/datasets/INIA_PG_RMA_Ex_0612/acknowledgment.rtf deleted file mode 100644 index f8bf764..0000000 --- a/general/datasets/INIA_PG_RMA_Ex_0612/acknowledgment.rtf +++ /dev/null @@ -1 +0,0 @@ -

NIAAA U01 support to RWW.

diff --git a/general/datasets/INIA_PG_RMA_Ex_0612/cases.rtf b/general/datasets/INIA_PG_RMA_Ex_0612/cases.rtf deleted file mode 100644 index faf8ab0..0000000 --- a/general/datasets/INIA_PG_RMA_Ex_0612/cases.rtf +++ /dev/null @@ -1,840 +0,0 @@ -

Young adult mice raised in specific pathogen-free vivarium at UTHSC.

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ERROR CHECKING by Mozhui, Centeno and Roy: The changes have been applied in GeneNetwork (GN389 - Pituitary) as follow:

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SampleId - New Strain Assignment
-R7087P (was BXD101) = BXD100
-R7138P_RW170 (was BXD85) = BXD95
-R7156P (was C57BL/6J) = B6D2F1
-R7141P = BXD65

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IndexSample IDStrainTissueAgeSex
1R7128PB6D2F1Pituitary69F
2R7156PB6D2F1Pituitary92M
3R7129PB6D2F1Pituitary69M
4R7134PD2B6F1Pituitary77F
5R7133PD2B6F1Pituitary77M
6R7160PC57BL/6JPituitary92F
7R7127PC57BL/6JPituitary77M
8R7126PDBA/2JPituitary77F
9R7157PDBA/2JPituitary75F
10R7125PDBA/2JPituitary68M
11R7155PDBA/2JPituitary75M
12R7058PBXD1Pituitary72F
13R7063PBXD1Pituitary86M
14R7079PBXD11Pituitary87F
15R7069PBXD11Pituitary76M
16R7051PBXD12Pituitary78F
17R7061PBXD12Pituitary78M
18R7064PBXD14Pituitary81F
19R7066PBXD14Pituitary81M
20R7052PBXD24Pituitary86M
21R7076PBXD27Pituitary76F
22R7071PBXD27Pituitary73M
23R7059PBXD29Pituitary72F
24R7060PBXD29Pituitary72M
25R7055PBXD31Pituitary74F
26R7062PBXD31Pituitary74M
27R7143PBXD32Pituitary81F
28R7135PBXD32Pituitary81M
29R7119PBXD34Pituitary77F
30R7054PBXD34Pituitary77M
31R7049PBXD39Pituitary79F
32R7065PBXD39Pituitary79M
33R7130PBXD40Pituitary85F
34R7132PBXD40Pituitary85M
35R7056PBXD42Pituitary87F
36R7044PBXD42Pituitary87M
37R7043PBXD43Pituitary81F
38R7047PBXD43Pituitary81M
39R7091PBXD44Pituitary83F
40R7050PBXD44Pituitary83M
41R7077PBXD45Pituitary77F
42R7078PBXD45Pituitary77F
43R7042PBXD45Pituitary77F
44R7092PBXD48Pituitary76F
45R7093PBXD48Pituitary76M
46R7045PBXD49Pituitary84F
47R7094PBXD49Pituitary84M
48R7095PBXD50Pituitary77F
49R7096PBXD50Pituitary77M
50R7142PBXD56Pituitary84F
51R7097PBXD56Pituitary77M
52R7080PBXD60Pituitary70F
53R7141P_RW204BXD60Pituitary76M
54R7075PBXD62Pituitary83F
55R7083PBXD62Pituitary83M
56R7084PBXD62Pituitary83M
57R7098PBXD63Pituitary77F
58R7100PBXD65Pituitary84M
59R7120PBXD66Pituitary257M
60R7140PBXD68Pituitary76F
61R7101PBXD68Pituitary76M
62R7074PBXD69Pituitary69F
63R7139PBXD69Pituitary81M
64R7141PBXD65Pituitary76F
65R7137P_RW112BXD70Pituitary76M
66R7124PBXD71Pituitary76F
67R7123PBXD71Pituitary76M
68R7068PBXD73Pituitary83M
69R7118PBXD74Pituitary69F
70R7117PBXD74Pituitary69M
71R7082PBXD75Pituitary76F
72R7048PBXD75Pituitary76M
73R7122PBXD77Pituitary223M
74R7103PBXD79Pituitary86F
75R7104PBXD79Pituitary86M
76R7073PBXD80Pituitary73F
77R7070PBXD80Pituitary73M
78R7139P_RW138BXD83Pituitary81F
79R7137PBXD83Pituitary76M
80R7085PBXD84Pituitary76F
81R7081PBXD84Pituitary76M
82R7105PBXD85Pituitary73M
83R7144PBXD87Pituitary83F
84R7136P_RW196BXD87Pituitary83M
85R7106PBXD89Pituitary82F
86R7107PBXD89Pituitary82M
87R7108PBXD90Pituitary82F
88R7109PBXD90Pituitary82M
89R7138P_RW170BXD95Pituitary73F
90R7111PBXD97Pituitary71F
91R7112PBXD97Pituitary71M
92R7113PBXD99Pituitary77F
93R7114PBXD99Pituitary77M
94R7072PBXD100Pituitary83F
95R7087PBXD100Pituitary88F
96R7086PBXD100Pituitary83M
97R7088PBXD101Pituitary88M
98R7053PBXD102Pituitary88F
99R7046PBXD102Pituitary88M
100R7090PBXD103Pituitary78F
101R7067PBXD103Pituitary78M
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diff --git a/general/datasets/INIA_PG_RMA_Ex_0612/experiment-design.rtf b/general/datasets/INIA_PG_RMA_Ex_0612/experiment-design.rtf deleted file mode 100644 index 13175b5..0000000 --- a/general/datasets/INIA_PG_RMA_Ex_0612/experiment-design.rtf +++ /dev/null @@ -1,10 +0,0 @@ -

Normative expression in the whole pituitary of young adult mice. In general, a sex-balanced samples (one array from male cases, one array from female cases) for BXD and parental strains.

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QUALITY CONTROL DATA

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  1. 737 probe sets with LRS of 46 or higher (LOD>10)
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  2. Highest LRS = 165.7
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  3. Review of top Mendelian transcripts consist with correct strain assignment
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  4. Final sex assignment is correct
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diff --git a/general/datasets/INIA_PG_RMA_Ex_0612/platform.rtf b/general/datasets/INIA_PG_RMA_Ex_0612/platform.rtf deleted file mode 100644 index 7057d48..0000000 --- a/general/datasets/INIA_PG_RMA_Ex_0612/platform.rtf +++ /dev/null @@ -1 +0,0 @@ -

The GeneChip® Mouse Gene 1.0 ST Array is the latest product in the family of Affymetrix expression arrays offering whole-transcript coverage. Each of the 28,853 genes is represented on the array by approximately 27 probes spread across the full length of the gene, providing a more complete and more accurate picture of gene expression than 3'-based expression array designs. The small format of the array makes it a cost-effective expression profiling solution for new microarray users. Sense DNA targets are generated from as little as 100ng of total RNA. The Gene 1.0 ST Array is part of a complete solution for gene expression analysis that includes Whole Transcript (WT) Sense Target Labeling and Control Reagents, fluidics and scanning instrumentation and basic analysis software. The array contains the most up-to-date content of well-annotated genes, and data is analyzed using a simple workflow. The Gene 1.0 ST Array uses a subset of probes from the Mouse Exon 1.0 ST Array and covers only well-annotated content. Like the Exon 1.0 ST Array, "gene-level" analysis of multiple probes on different exons is summarized into an expression value representing all transcripts from the same gene.

diff --git a/general/datasets/INIA_PG_RMA_Ex_0612/processing.rtf b/general/datasets/INIA_PG_RMA_Ex_0612/processing.rtf deleted file mode 100644 index 55aad2e..0000000 --- a/general/datasets/INIA_PG_RMA_Ex_0612/processing.rtf +++ /dev/null @@ -1 +0,0 @@ -

Conventional Affymetrix gene level probe summarization (RMA) followed by log2 transformation and standard GeneNetwork variance stabilization (2z +8). The z scores are multiplied by 2 and we then add a value of 8 to all values. This eliminates negative values and results in a scale of expression for which 1 unit is roughly equivalent to a two fold absolute difference in mRNA concentration.

diff --git a/general/datasets/INIA_PG_RMA_Ex_0612/summary.rtf b/general/datasets/INIA_PG_RMA_Ex_0612/summary.rtf deleted file mode 100644 index 14a715d..0000000 --- a/general/datasets/INIA_PG_RMA_Ex_0612/summary.rtf +++ /dev/null @@ -1,3 +0,0 @@ -

Gene expression data for the whole pituitary across 52 strains of mice. Sex Balance: Sex of samples has been double-checked. As of July 2012, for 42 strains we have separate data for both males and females (usually one array each). Three strains (BXD45, 63, and 95) are only represented by female samples and two strains (BXD65 and BXD77) are only represented by male samples. Five other strains (BXD24, 66, 73, 85, 101) are may represent combined male and female samples. These unpublished data are apparently error-free based on a review and analysis of transcripts with Mendelian segregation patterns (as of July 20, 2012). The data set contains 751 eQTLs with LOD scores above 10 (LRS>46). Peak LRS of 165.9 for Record ID 10513604. Data for BXD70 are somewhat problematic (see 10444135 and 10467784), perhaps due to a bad array, strain assignment error, or residual heterozygozity. S Roy double-checked (July 22) and thinks that Sample R7141P is more likely to be BXD65.

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Part of a systematic genetic analysis of the hypothalamus-pituitary-adrenal axis in the BXD family of strains.

diff --git a/general/datasets/INIA_PG_RMA_Ex_0612/tissue.rtf b/general/datasets/INIA_PG_RMA_Ex_0612/tissue.rtf deleted file mode 100644 index 3977f1e..0000000 --- a/general/datasets/INIA_PG_RMA_Ex_0612/tissue.rtf +++ /dev/null @@ -1 +0,0 @@ -

Whole pituitary gland dissected by hand. Dissections by Khyobeni Mozhui, Jesse Ingels, and Adrienne Adler at UTHSC.

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