Data Set Group2: UT-VGX Hepatocytes Affy Mouse Gene 1.0 ST (Oct14) RMA

Data Set: UT-VGX Hepatocytes Affy Mouse Gene 1.0 ST Gene Level (Oct14) RMA GN Accession: GN700 GEO Series: Title: Organism: Mouse (Mus musculus, mm10) Group: BXD Tissue: Liver 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 GN700_MeanDataAnnotated_rev081815.txt (N/A) GN700_StdError_rev081815.txt (N/A)

Specifics of this Data Set:

Summary:

mRNA levels in cryopreserved BXD strain hepatotcytes (males at 60 days of age) immediately after thawing to 4 deg C. This is the "frozen state" mRNA status.

About the cases used to generate this set of data:

Sample ID Varigenix Strain Sex RNA Concentrations ng/ul 260/280 260/230 Agilent Concentration(ng/ul) RIN V1 BXD32 M 1414.8 2.09 2.21 3,062 9.3 V2 BXD1 M 1608.9 2.11 2.24 3,102 9.3 V3 BXD5 M 1263.91 2.1 2.09 2,460 8.5 V4 BXD31 M 1793.95 2.1 2.22 3,387 8.5 V5 BXD8 M 1193.21 2.1 2.17 2,293 9.3 V6 BXD18 M 1041.05 2.13 2.17 2,115 9.2 V7 BXD42 M 398.28 1.99 2.28 1,519 8.3 V8 BXD29 M 477.37 2.02 2.24 1,301 8.1 V9 BXD21 M 414.6 2 2.27 1,174 8.3 V10 BXD27 M 438.61 2.02 2.27 1,100 8.1 V11 BXD16 M 436.21 2.01 2.27 868 8.5 V12 BXD19 M 489.12 2.01 2.26 1,277 8 V13 BXD22 M 1032.89 2.09 2.22 2,060 7.8 V14 BXD38 M 510.24 2.01 2.22 1,213 8 V15 BXD34 M 1021.26 2.09 2.24 1,514 8.2 V16 BXD20 M 330.85 2 2.27 901 8.1 V17 BXD15 M 1220.54 2.1 2.21 1,909 8.1 V18 BXD6 M 1001.04 2.09 2.2 1,523 8.3 V19 BXD13 M 1241.88 2.1 2.21 1,770 8.2 V20 BXD40 M 1032.04 2.08 2.22 1,985 8.2 V21 BXD14 M 881.62 2.11 2.19 481 8.7 V22 BXD2 M 1069.09 2.08 2.22 1,536 8.2 V23 BXD28 M 452.6 2 2.26 2,567 7.9 V24 BXD11 M 930.72 2.07 2.21 999 8.5 V25 BXD39 M 1177.27 2.07 2.23 838 8.7

About the tissue used to generate this set of data:

Hepatocytes prepared by Rob Kaiser at CRL Piedmont in Spring of 2011. Held in liquid nitrogen (vapor phase) until use Fall 2014 at UTHSC. One vial of hepatocytes in 1 ml of freeze media was wiped with 70% ETOH, quick thawed by swift agitation in a 37 degree C water bath until a small amount of ice remained in the vial. Contents of the vial were removed with a sterile 1000 ul pipette tip and added to a 5 ml sterile polypropylene tube on ice containing 3 ml of ice-cold sterile 1x PBS. sitting in ice. One ml of sterile ice-cold 1x PBS was added to the original vial to remove any remaining cells and added to the 5 ml tube on ice. This process was quickly repeated with three more vials of cells. Four 5 ml tubes were centrifuged at 8,000 rpm at 4 degrees C for 4 minutes to pellet hepatocytes. PBS diluted freeze media was completely removed from the cell pellet. Entire process for sets of vials took about 7 minutes until RNA lysis buffer was added.  The QIAgen AllPrep DNA/RNA mini kit was used in conjunction with the QIAcube for purification of DNA and RNA from the hepatocytes. 600 ul of kit lysis buffer was added to pelleted cells, along with one 5 mm sterile stainless steel bead and cells were completely disrupted using the TissueLyser. The QIAcube protocol was used first for DNA extraction (held at -80 deg C for future use) and the flow-through containing total RNA was then used for the second purification. Any residual DNA was removed from the RNA before Agilent quantification of concentration and RIN, using the QIAgen DNase I reagent, followed by ethanol precipitation and resuspension of DNA-free total  RNA in 50 ul RNAse free water.

About the array platform:

Affy Mouse Gene 1.0 ST (GPL6246)

About data values and data processing:

Standard 2z+8 of log2 data. RMA data were log2 transformed (adding an olffset of 1 to avoid negative values). Variance was stablized (i.e. each array was converted to a set of Z scores). Z scores were then multipled by 2.  Mean Z  was then shifted from 0 to to 8 units per array.

Notes:

Experiment Type:

Control hepatocyte mRNA expression data prior to any treatment for young adult male BXD strains. This is esssentially the mRNA state of frozen hepatocytes.

Contributor:

Robert W. Williams, Roberrt E. Scott and colleagues. Cells were donated to Williams group by Varigenix Inc. and CRL Inc.

Citation:

In progress.

Data source acknowledgment:

We thank Varigenix and Charle River Laboratory for their donation of BXD cyropreserved hepatcytes. We thank Jesse Ingels for preparing RNA samples. We thank Lorne Rose and the UTHSC Molecular Resource Center for processing RNA samples and generating array data. We thank Arthur Centeno for data entry. We thank the UTHSC CITG and the UT-ORNL Governor's chair for support of microarray analysis.

Study Id:

239

• 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)