Data Set Group2: INIA Pituitary Affy MoGene 1.0ST (Jun12)

Data Set: INIA Pituitary Affy MoGene 1.0ST (Jun12) RMA Males GN Accession: GN428 GEO Series: Title: Organism: Mouse (Mus musculus, mm10) Group: BXD Tissue: Pituitary Gland mRNA Dataset Status: Public Platforms: Affy Mouse Gene 1.0 ST (GPL6246) Normalization: RMA

Contact Information Robert Williams University of Tennessee Health Science Center 71 S Manassas St, Room 405 TSRB Memphis, TN 38163 USA Tel. 901 448-7050 rwilliams@uthsc.edu Website Download datasets and supplementary data files GN428_MeanDataAnnotated_rev081815.txt (N/A) GN428_StdError_rev081815.txt (N/A)

Specifics of this Data Set:

None

Summary:

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 These unpublished data are apparently error-free based on a review and analysis of transcripts with Mendelian segregation patterns (as of July 20, 2012).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. Part of a systematic genetic analysis of the hypothalamus-pituitary-adrenal axis in the BXD family of strains.

About the cases used to generate this set of data:

Young adult mice raised in specific pathogen-free vivarium at UTHSC. ERROR CHECKING by Mozhui, Centeno and Roy: The changes have been applied in GeneNetwork (GN389 - Pituitary) as follow: SampleId - New Strain Assignment R7087P (was BXD101) = BXD100 R7138P_RW170 (was BXD85) = BXD95 R7156P (was C57BL/6J) = B6D2F1 R7141P = BXD65   Index Sample ID Strain Tissue Age Sex 1 R7128P B6D2F1 Pituitary 69 F 2 R7156P B6D2F1 Pituitary 92 M 3 R7129P B6D2F1 Pituitary 69 M 4 R7134P D2B6F1 Pituitary 77 F 5 R7133P D2B6F1 Pituitary 77 M 6 R7160P C57BL/6J Pituitary 92 F 7 R7127P C57BL/6J Pituitary 77 M 8 R7126P DBA/2J Pituitary 77 F 9 R7157P DBA/2J Pituitary 75 F 10 R7125P DBA/2J Pituitary 68 M 11 R7155P DBA/2J Pituitary 75 M 12 R7058P BXD1 Pituitary 72 F 13 R7063P BXD1 Pituitary 86 M 14 R7079P BXD11 Pituitary 87 F 15 R7069P BXD11 Pituitary 76 M 16 R7051P BXD12 Pituitary 78 F 17 R7061P BXD12 Pituitary 78 M 18 R7064P BXD14 Pituitary 81 F 19 R7066P BXD14 Pituitary 81 M 20 R7052P BXD24 Pituitary 86 M 21 R7076P BXD27 Pituitary 76 F 22 R7071P BXD27 Pituitary 73 M 23 R7059P BXD29 Pituitary 72 F 24 R7060P BXD29 Pituitary 72 M 25 R7055P BXD31 Pituitary 74 F 26 R7062P BXD31 Pituitary 74 M 27 R7143P BXD32 Pituitary 81 F 28 R7135P BXD32 Pituitary 81 M 29 R7119P BXD34 Pituitary 77 F 30 R7054P BXD34 Pituitary 77 M 31 R7049P BXD39 Pituitary 79 F 32 R7065P BXD39 Pituitary 79 M 33 R7130P BXD40 Pituitary 85 F 34 R7132P BXD40 Pituitary 85 M 35 R7056P BXD42 Pituitary 87 F 36 R7044P BXD42 Pituitary 87 M 37 R7043P BXD43 Pituitary 81 F 38 R7047P BXD43 Pituitary 81 M 39 R7091P BXD44 Pituitary 83 F 40 R7050P BXD44 Pituitary 83 M 41 R7077P BXD45 Pituitary 77 F 42 R7078P BXD45 Pituitary 77 F 43 R7042P BXD45 Pituitary 77 F 44 R7092P BXD48 Pituitary 76 F 45 R7093P BXD48 Pituitary 76 M 46 R7045P BXD49 Pituitary 84 F 47 R7094P BXD49 Pituitary 84 M 48 R7095P BXD50 Pituitary 77 F 49 R7096P BXD50 Pituitary 77 M 50 R7142P BXD56 Pituitary 84 F 51 R7097P BXD56 Pituitary 77 M 52 R7080P BXD60 Pituitary 70 F 53 R7141P_RW204 BXD60 Pituitary 76 M 54 R7075P BXD62 Pituitary 83 F 55 R7083P BXD62 Pituitary 83 M 56 R7084P BXD62 Pituitary 83 M 57 R7098P BXD63 Pituitary 77 F 58 R7100P BXD65 Pituitary 84 M 59 R7120P BXD66 Pituitary 257 M 60 R7140P BXD68 Pituitary 76 F 61 R7101P BXD68 Pituitary 76 M 62 R7074P BXD69 Pituitary 69 F 63 R7139P BXD69 Pituitary 81 M 64 R7141P BXD65 Pituitary 76 F 65 R7137P_RW112 BXD70 Pituitary 76 M 66 R7124P BXD71 Pituitary 76 F 67 R7123P BXD71 Pituitary 76 M 68 R7068P BXD73 Pituitary 83 M 69 R7118P BXD74 Pituitary 69 F 70 R7117P BXD74 Pituitary 69 M 71 R7082P BXD75 Pituitary 76 F 72 R7048P BXD75 Pituitary 76 M 73 R7122P BXD77 Pituitary 223 M 74 R7103P BXD79 Pituitary 86 F 75 R7104P BXD79 Pituitary 86 M 76 R7073P BXD80 Pituitary 73 F 77 R7070P BXD80 Pituitary 73 M 78 R7139P_RW138 BXD83 Pituitary 81 F 79 R7137P BXD83 Pituitary 76 M 80 R7085P BXD84 Pituitary 76 F 81 R7081P BXD84 Pituitary 76 M 82 R7105P BXD85 Pituitary 73 M 83 R7144P BXD87 Pituitary 83 F 84 R7136P_RW196 BXD87 Pituitary 83 M 85 R7106P BXD89 Pituitary 82 F 86 R7107P BXD89 Pituitary 82 M 87 R7108P BXD90 Pituitary 82 F 88 R7109P BXD90 Pituitary 82 M 89 R7138P_RW170 BXD95 Pituitary 73 F 90 R7111P BXD97 Pituitary 71 F 91 R7112P BXD97 Pituitary 71 M 92 R7113P BXD99 Pituitary 77 F 93 R7114P BXD99 Pituitary 77 M 94 R7072P BXD100 Pituitary 83 F 95 R7087P BXD100 Pituitary 88 F 96 R7086P BXD100 Pituitary 83 M 97 R7088P BXD101 Pituitary 88 M 98 R7053P BXD102 Pituitary 88 F 99 R7046P BXD102 Pituitary 88 M 100 R7090P BXD103 Pituitary 78 F 101 R7067P BXD103 Pituitary 78 M

About the tissue used to generate this set of data:

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

About the array platform:

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.

About data values and data processing:

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.

Notes:

Experiment Type:

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. QUALITY CONTROL DATA 737 probe sets with LRS of 46 or higher (LOD>10) Highest LRS = 165.7 Review of top Mendelian transcripts consist with correct strain assignment Final sex assignment is correct

Contributor:

Mozhui K, Lu L, Adler A, Ingels J, Williams RW

Citation:

Contact RW Williams

Data source acknowledgment:

NIAAA U01 support to RWW.

Study Id:

148

• The UT Center for Integrative and Translational Genomics
• NIGMS Systems Genetics and Precision Medicine project (R01 GM123489, 2017-2021)
• NIDA NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022)
• NIA Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
• NIAAA Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
• NIDA, NIMH, and NIAAA (P20-DA 21131, 2001-2012)
• NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)