Data Set Group2: UTHSC B6D2 Glaucoma and Aged Retina Affy MoGene 1.0 ST (Sep16) RMA

Data Set: UTHSC B6D2 Retina Affy MoGene 1.0ST Exon Level (Sep16) RMA GN Accession: GN804 GEO Series: No Geo series yet Title: Organism: Mouse (Mus musculus, mm10) Group: B6D2 Tissue: Retina mRNA Dataset Status: Public Platforms: Affy Mouse Gene 1.0 ST (GPL6246) Normalization: RMA

Contact Information Lu Lu University of Tennessee Health Science Center 71 S. Manassas, Room 410K Memphis, TN 38163 USA Tel. 901 448-7557 lulu@uthsc.edu Website Download datasets and supplementary data files

Specifics of this Data Set:

Exon Level

Summary:

This is an array data set generated using the Affymetrix Genechip Mouse 1.0 ST array. Please see the companion microRNA (miRNA) data set. All of these data sets provides estimates of expression for 45 retinas from C57BL/6J (B6 cases B6.01 to B6.17), DBA/2J (cases D2.01 to D2.16), and DBA/2J with a wildtype Gpnmb allele (D2GP.01 to D2GP.12). Cases range in age from 30 to 576 days and include both sexes. We are using these data in combination with the micro RNA array 4.0 to study normal and glaucomatous changes in gene expression as a function of age.  Please contact Lu Lu (lulu@uthsc.edu), Robert W. Williams  (rwilliams@uthsc.edu), or Junming Yue (jyue@uthsc.edu). Supported in part by Research to Prevent Blindness.

About the cases used to generate this set of data:

Index Sample ID Case ID Strain Sex DOB Sac date Age group Age (days) Age (month) EarTag Number Tube ID Agilent RNA concentration (ng/ul) RIN Nanodrop RNA concentration (ng/ul) 260/280 260/230 Batch ID Notes 1 B6.01 071515.08 C57BL/6J M 06/15/15 07/15/15 1~2 30 1.0   R11 173 10.00 181.22 2.09 2.12 2 best 2 B6.02 071515.09 C57BL/6J M 06/15/15 07/15/15 1~2 30 1.0   R12 121 N/A 148.52 2.10 1.69 2 best 3 B6.03 052314.01 C57BL/6J F 03/23/14 05/23/14 2~4 61 2.0   Ret 32 68 10.0 48.53 2.02 1.93 1   4 B6.04 062514.01 C57BL/6J M 04/10/14 06/25/14 2~4 76 2.5   Ret 21 81 9.0 168.7 2.06 1.97 1   5 B6.05 040816.03 C57BL/6J M 02/04/16 04/08/16 2~4 64 2.1   R74 385 10.00 448.16 1.98 2.12 2   6 B6.06 040816.04 C57BL/6J M 02/04/16 04/08/16 2~4 64 2.1   R75 226 8.70 167.31 2.04 2.13 2   7 B6.07 041014.19 C57BL/6J F 10/20/13 04/10/14 5~7 172 5.7   Ret 10 22 10.0 36.97 2.22 0.051 1   8 B6.08 101813.27 C57BL/6J M 05/06/13 10/18/13 5~7 165 5.5   Ret 7 38 10.0 54.47 2.08 0.094 1   9 B6.09 050214.03 C57BL/6J F 08/14/13 05/02/14 7~9 261 8.7   Ret 27 20 10.0 54.45 2.11 1.14 1   10 B6.10 041014.24 C57BL/6J M 09/02/13 04/10/14 7~9 220 7.3   Ret 12 38 9.50 58.97 2.08 2.14 1   11 B6.11 101813.17 C57BL/6J F 12/07/12 10/18/13 10~12 315 10.5   Ret 2 59 9.40 83.86 2.17 1.87 1   12 B6.12 052116.01 C57BL/6J M 05/19/15 05/22/16 10~12 369 12.3   R102 293 8.30 179.69 2.06 2.11 2   13 B6.13 052116.02 C57BL/6J M 05/19/15 05/22/16 10~12 369 12.3   R103 255 8.40 194.24 2.04 1.82 2   14 B6.14 042114.19 C57BL/6J F 03/11/13 04/21/14 13~15 406 13.5 1252 Ret 26 28 10.0 39.95 2.22 1.71 1   15 B6.15 050214.07 C57BL/6J M 03/20/13 05/02/14 13~15 408 13.6   Ret 28 30 10.0 51.81 2.06 2.07 1   16 B6.16 041714.02 C57BL/6J M 09/18/12 04/17/14 19~21 576 19.2 1117 Ret 17 25 10.0 51.55 2.13 1.13 1   17 B6.17 041714.03 C57BL/6J M 09/18/12 04/17/14 19~21 576 19.2 1116 Ret 18 28 10.0 65.11 2.01 2.16 1   18 D2.01 030116.02 DBA/2J M 01/29/16 03/01/16 1~2 32 1.1   R63 107 8.80 119.02 2.05 1.79 2   19 D2.02 030116.04 DBA/2J M 01/29/16 03/01/16 1~2 32 1.1   R65 202 9.10 250.38 2.03 1.67 2   20 D2.03 062714.02 DBA/2J F 03/23/14 06/27/14 2~4 104 3.5   Ret 20a     189.3 1.95 1.81 1 No Agilent as of 6/27/2014 21 D2.04 062714.01 DBA/2J M 03/19/14 06/27/14 2~4 100 3.3   Ret 19a     154 2.05 1.89 1 No Agilent as of 6/27/2014 22 D2.05 032316.03 DBA/2J M 01/23/16 03/23/16 2~4 60 2.0   R70 99 9.30 99.17 2.04 1.63 2   23 D2.06 032316.04 DBA/2J M 01/23/16 03/23/16 2~4 60 2.0   R71 205 9.10 124.33 2.03 1.24 2   24 D2.07 050214.11 DBA/2J F 12/07/13 05/02/14 5~7 146 4.9   Ret 29 100 10.0 86.47 2.14 1.9 1   25 D2.08 101813.08 DBA/2J M 03/21/13 10/18/13 5~7 211 7.0   Ret 1 52 9.9 86.98 2.11 2.12 1   26 D2.09 041014.23 DBA/2J F 08/24/13 04/10/14 7~9 229 7.6   Ret 11 21 9.9 44.39 2.17 1.15 1   27 D2.10 050214.15 DBA/2J F 07/27/13 05/02/14 7~9 279 9.3   Ret 30 37 10.0 43.57 2.13 2.04 1   28 D2.11 101813.23 DBA/2J F 11/29/12 10/18/13 10~12 323 10.8   Ret 6 77 9.7 105.02 2.06 2.14 1   29 D2.12 101813.19 DBA/2J M 12/08/12 10/18/13 10~12 314 10.5   Ret 3 46 9.9 65.7 2.13 1.71 1   30 D2.13 042114.18 DBA/2J F 03/19/13 04/21/14 13~15 398 13.3 1148 Ret 25 26 9.9 65.53 2.17 2.43 1   31 D2.14 042114.17 DBA/2J M 03/19/13 04/21/14 13~15 398 13.3 1130 Ret 24 40 9.4 36.98 2.07 0.8 1   32 D2.15 041014.06 DBA/2J M 9/6/2012 04/10/14 19~21 581 19.4 1123 Ret 8 35 9.9 52.99 2.12 0.091 1   33 D2.16 041014.07 DBA/2J F 9/6/2012 04/10/14 19~21 581 19.4 1124 Ret 9 30 9.5 52.44 2.19 0.08 1   34 D2GP.01 041416.15 DBA-Gpmnb(wp) F 03/15/16 04/14/16 1~2 30 1.0   R92 334 9.10 135.79 1.87 2.23 2   35 D2GP.02 120715.02 DBA-Gpmnb(wp) M 11/05/15 12/07/15 1~2 32 1.1   R31 85 9.20 106.06 2.04 2.06 2   36 D2GP.03 041416.04 DBA-Gpmnb(wp) F 02/02/16 04/14/16 2~4 72 2.4   R81 112 9.40 94.79 1.94 2.19 2   37 D2GP.04 120815.04 DBA-Gpmnb(wp) M 10/08/15 12/08/15 2~4 61 2.0   R39 89 N/A 118.84 2.05 1.97 2   38 D2GP.05 101813.21 DBA-Gpmnb(wp) F 04/09/13 10/18/13 5~7 192 6.4   Ret 4 53 9.9 74.13 2.14 2.28 1   39 D2GP.06 101813.22 DBA-Gpmnb(wp) M 04/09/13 10/18/13 5~7 192 6.4   Ret 5 54 10.0 81.32 2.1 2.19 1   40 D2GP.07 041014.27 DBA-Gpmnb(wp) F 08/29/13 04/10/14 7~9 224 7.5   Ret 15 14 10.0 37.03 2.06 1.44 1   41 D2GP.08 041014.28 DBA-Gpmnb(wp) M 08/29/13 04/10/14 7~9 224 7.5   Ret 16 29 9.9 63.83 2.03 2.08 1   42 D2GP.09 041014.25 DBA-Gpmnb(wp) F 06/12/13 04/10/14 10~12 302 10.1   Ret 13 31 9.8 60.73 2.07 2.12 1   43 D2GP.10 041014.26 DBA-Gpmnb(wp) M 06/12/13 04/10/14 10~12 302 10.1   Ret 14 24 10.0 65.1 2.06 1.09 1   44 D2GP.11 042114.08 DBA-Gpmnb(wp) F 01/14/13 04/21/14 13~15 462 15.4 1021 Ret 22 87 9.0 150.69 2.09 2.02 1   45 D2GP.12 042114.09 DBA-Gpmnb(wp) F 01/14/13 04/21/14 13~15 462 15.4 1022 Ret 23 18 10.0 44.16 2.11 0.069 1

About the tissue used to generate this set of data:

About the array platform:

About data values and data processing:

Notes:

Experiment Type:

Contributor:

Citation:

Data source acknowledgment:

Study Id:

253

• 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)