Data Set Group2: DoD TATRC Retina Blast Affy MoGene 2.0 ST RMA

Data Set: DoD Retina After Blast Affy MoGene 2.0 ST (Mar16) RMA Gene Level ** GN Accession: GN785 GEO Series: No Geo series yet Title: Unpublished Organism: Mouse (Mus musculus, mm10) Group: BXD Tissue: Retina mRNA Dataset Status: Private Platforms: Affy Mouse Gene 2.0 ST Array Normalization: RMA

Contact Information Eldon Geisert Emory Eye Center B5600 Clinic B 1365B Clifton Road NE Atlanta, GA 30322 USA Tel. 404-778-4239 egeiser@emory.edu Website Download datasets and supplementary data files

Specifics of this Data Set:

None

Summary:

The DoD dataset was constructed using the Affymetrics GeneChip® Mouse Gene 2.0 ST microarrays. This relatively recent microarray was specifically designed to represent the whole-transcriptome. It includes probes to measure mRNA, long intergenic non-coding RNAs and microRNAs. Researchers have identified many transcripts in the mouse genome that do not have protein coding potential. Most of these non-coding RNAs have little functional annotation. There is considerable evidence that these non-coding RNAs play important roles in development of the retina and the progression of disease. The coverage in the new ST 2.0 array includes over 28,000 coding transcripts and over 7,000 non-coding transcripts. There are also probes on the array covering 590 microRNAs. This is RMA expression data that has been normalized using what we call a 2z+8 scale, but without special correction for batch effects. The data for each strains were computed as the mean of four samples per strain. Expression values on a log2 scale range from 3.77 to 14.62, a nominal range of approximately 3600-fold. After taking the log2 of the original non-logged expression estimates, we convert data within an array to a z score. We then multiply the z score by 2. Finally, we add 8 units to ensure that no values are negative. The result is a scale with a mean of 8 units and a standard deviation of 2 units. A two-fold difference in expression is equivalent roughly to 1 unit on this scale.

About the cases used to generate this set of data:

Almost all animals are young adults between 60 and 90 days of age (Table 1, minimum age is 50 and maximum age is 134 days). We measured expression in conventional inbred strains, BXD recombinant inbred (RI) strains, and reciprocal F1s between C57BL/6J and DBA/2J. BXD strains: The first 32 of these strains are from the Taylor series of BXD strains generated at the Jackson Laboratory by Benjamin A. Taylor. BXD1 through BXD32 were started in the late 1970s, whereas BXD33 through 42 were started in the 1990s. In 2004, BXD24/TyJ developed a spontaneous mutation, rd16 which resulted in retinal degeneration and was renamed BXD24b/TyJ (BXD24 in this database). The strain, BXD24a, was cryo-recovered in 2004 from 1988 embryo stocks (F80) and does not exhibit retinal degeneration. In 2009, BXD24b was renamed BXD24/TyJ-Cep290rd16/J by JAX Labs to reflect the discovery of the genetic basis of the mutation. At the same time BXD24a was then referred to just as BXD24/TyJ by Jax Labs, but still called BXD24a in this dataset. The other 36 BXD strains (BXD43 and higher) were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams starting in 1997 using B6D2 generation 10 advanced intercross progeny. This modified breeding protocol doubles the number of recombinations per BXD strain and improves mapping resolution (Peirce et al. 2004). All of the Taylor series of BXD strains and many of the new BXD strains are available from the Jackson Laboratory. All of the new BXD strains (BXD43 and higher) are also available directly from Lu Lu and colleagues at the University of Tennessee Health Science Center in Memphis, TN, USA. BXD24/TyJ is now known as BXD24b/TyJ and has nearly complete retinal degeneration. BXD24a/TyJ, a 1988 F80 inbred stock that has been rederived from cryogenic storage, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control, but is not included in the HEI data set. Index EIGC ID (LIMS ID) Strain Sex Age at harvest RIN Score 1 602 BXD9 F 133 9.1 2 603 BXD9 M 100 9.5 3 604 BXD40 F 100 9.4 4 605 BXD40 M 100 9.1 5 606 BXD48 F 75 9.1 6 607 BXD48 M 75 8.6 7 608 BXD63 F 75 9.2 8 609 BXD63 M 61 9.4 9 612 BXD73 M 108 10 10 614 BXD87 M 85 9.2 11 615 BXD87 F 85 9.9 12 616 BXD69 F 76 9.3 13 617 BXD69 M 100 10 14 618 BXD51 M 82 8.9 15 619 BXD92 (BXD65b) M 82 8.8 16 620 BXD92 (BXD65b) F 82 8.8 17 635 BXD100 M 70 9 18 636 BXD100 M 70 8.8 19 652 BXD92 (BXD65b) F 64 9 20 653 BXD87 F 67 9.7 21 654 BXD87 M 67 8.9 22 655 BXD63 M 71 9 23 660 BXD69 M 97 10 24 687 BXD6 M 85 7.7 25 688 BXD6 M 85 9.4 26 690 BXD12 F 83 10 27 691 BXD12 F 83 10 28 692 BXD12 M 83 10 29 695 BXD5 F 77 10 30 696 BXD5 M 77 10 31 698 BXD5 F 77 9.9 32 699 BXD5 F 77 10 33 701 BXD8 M 79 10 34 702 BXD8 M 79 10 35 705 BXD8 F 77 9.2 36 707 BXD15 F 77 9.4 37 708 BXD15 F 77 9.1 38 710 BXD15 M 77 9.1 39 713 BXD22 F 71 9.5 40 714 BXD22 F 71 9.7 41 716 BXD22 M 71 9.1 42 717 BXD22 M 71 9.1 43 719 BXD14 F 70 9.2 44 722 BXD14 M 70 8.9 45 723 BXD14 M 70 9.2 46 725 BXD18 F 70 9 47 726 BXD18 F 70 9.1 48 728 BXD18 M 70 9.1 49 729 BXD18 M 70 9.2 50 731 BXD19 F 66 9.3 51 732 BXD19 F 66 9.4 52 734 BXD19 M 66 9.8 53 735 BXD19 M 66 9.4 54 737 BXD21 F 71 9.7 55 738 BXD21 F 71 9.6 56 740 BXD21 M 71 9.1 57 741 BXD21 M 71 9.7 58 743 BXD2 F 70 8.3 59 744 BXD2 F 70 8.6 60 746 BXD2 M 70 7.5 61 747 BXD2 M 77 8.6 62 768 BXD48 M 121 9.4 63 770 BXD92 (BXD65b) M 65 10 64 771 BXD101 F 85 8.3 65 772 BXD101 F 85 9.3 66 773 BXD101 M 86 9.5 67 774 BXD101 M 86 9.8 68 775 BXD102 F 66 9.5 69 776 BXD102 F 66 10 70 777 BXD102 M 84 9.6 71 787 BXD60 M 86 9.9 72 788 BXD60 M 86 9.9 73 789 BXD63 F 115 9.7 74 790 BXD100 F 72 9.8 75 791 BXD100 F 72 10 76 818 BXD51 F 77 9.7 77 819 BXD51 F 77 9.6 78 820 BXD51 M 72 9.7 79 821 BXD65 M 72 9.6 80 822 BXD65 M 65 9.5 81 825 BXD65 F 72 9.5 82 827 BXD86 M 69 9.1 83 828 BXD86 M 69 9.4 84 829 BXD90 F 69 9.6 85 831 BXD9 M 127 9.7 86 832 BXD39 F 99 9.4 87 833 BXD39 F 107 9.3 88 834 BXD60 F 107 9.5 89 836 BXD84 M 103 9.7 90 846 BXD39 M 63 9.7 91 847 BXD39 M 63 9.8 92 849 BXD20 F 70 10 93 850 BXD20 M 70 10 94 851 BXD20 * 70 9.5 95 855 DBA/2J F 78 9.7 96 856 DBA/2J F 78 10 97 857 DBA/2J M 78 10 98 858 DBA/2J M 78 9.9 99 859 C57BL/6J F 78 10 100 860 C57BL/6J F 78 10 101 861 C57BL/6J M 78 10 102 862 C57BL/6J M 78 9.6 103 EGE10907-0172_890_20844 BXD28 M 75 10 104 EGE10907-0173_891_20845 BXD28 M 75 9.7 105 EGE10907-0174_892_20846 BXD28 F 75 9.7 106 EGE10907-0176_895_20848 BXD33 M 75 9.88 107 EGE10907-0177_896_20849 BXD33 F 75 10 108 EGE10907-0178_897_20850 BXD33 F 75 9.4 109 EGE10907-0179_898_20851 BXD36 M 75 9.4 110 EGE10907-0180_899_20852 BXD36 F 75 9.5 111 EGE10907-0181_900_20853 BXD36 F 75 9.1 112 EGE10907-0182_910_20854 BXD27 M 70 9.7 113 EGE10907-0183_990_20855 BXD9 F 98 9.4 114 EGE10907-0184_991_20856 BXD16 F 113 10 115 EGE10907-0185_992_20857 BXD16 M 113 9 116 EGE10907-0186_993_20858 BXD27 F 96 9.4 117 EGE10907-0187_994_20859 BXD27 F 96 9.4 118 EGE10907-0188_996_20860 BXD48 F 98 9.4 119 EGE10907-0189_997_20861 BXD73 M 106 10 120 EGE10907-0190_999_20862 BXD11 F 121 9.6 121 EGE10907-0191_100_20863 BXD11 F 121 9.9 122 EGE10907-0192_1010_21276 BXD13 M 69 9.8 123 EGE10907-0193_1011_21277 BXD13 M 69 9.8 124 EGE10907-0194_1012_21278 BXD16 F 65 10 125 EGE10907-0195_1015_21279 BXD16 M 65 10 126 EGE10907-0196_1019_21280 BXD33 M 75 10 127 EGE10907-0197_1020_21281 BXD36 M 78 10 128 EGE10907-0198_1021_21282 BXD38 F 70 9.8 129 EGE10907-0199_1022_21283 BXD38 F 70 10 130 EGE10907-0200_1023_21284 BXD38 M 70 9.7 131 EGE10907-0201_1047_21285 BXD11 M 65 10 132 EGE10907-0202_1048_21286 BXD11 M 65 10 133 EGE10907-0203_1049_21287 BXD38 M 77 10 134 EGE10907-0204_1050_21288 BXD73 F 70 10 135 EGE10907-0205_1051_21289 BXD73 F 70 10 136 EGE10907-0206_1052_21290 BXD86 F 69 10 137 EGE10907-0207_1053_21291 BXD86 F 69 10 138 EGE10907-0208_1054_21292 BXD90 F 71 10 139 EGE10907-0209_1055_21293 BXD90 M 71 10 140 EGE10907-0210_1056_21294 BXD90 M 71 10 141 EGE10907-0211_1148_21295 BXD31 F 90 10 142 EGE10907-0212_1149_21296 BXD31 F 90 10 143 EGE10907-0213_1150_21297 BXD31 M 90 10 144 EGE10907-0214_1151_21298 BXD31 M 90 9.9 145 EGE10907-0215_1152_21299 BXD42 F 83 10 146 EGE10907-0216_21429 BXD42 F 83 10 147 EGE10907-0217_21430 BXD42 M 83 10 148 EGE10907-0218_21431 BXD42 M 83 9.3 149 EGE10907-0219_21432 BXD50 F 92 9.6 150 EGE10907-0220_21433 BXD50 F 92 9.6 151 EGE10907-0221_21434 BXD50 F 92 10 152 EGE10907-0222_21435 BXD1 M 73 9.6 153 EGE10907-0223_21436 BXD13 F 71 9.7 154 EGE10907-0224_21437 BXD1 M 71 9.5 155 EGE10907-0225_21438 BXD13 F 71 9.6 156 EGE10907-0226_21439 BXD43 F 85 10 157 EGE10907-0227_21452 BXD43 F 85 9.6 158 EGE10907-0229_21442 BXD43 M 85 8.2 159 EGE10907-0230_21443 BXD50 M 69 9.4 160 EGE10907-0231_21444 BXD1 F 68 9.4 161 EGE10907-0232_21445 BXD1 F 68 9.6 162 EGE10907-0233_21446 BXD29 M 65 9.5 163 EGE10907-0234_21447 BXD29 M 65 10 164 EGE10907-0235_21448 BXD75 F 68 10 165 EGE10907-0236_21449 BXD75 M 68 10 166 EGE10907-0237_21450 BXD96 F 67 9.9 167 EGE10907-0238_21931 BXD99 M 71 7.9 168 EGE10907-0239_21932 BXD99 M 71 9.7 169 EGE10907-0240_21933 BXD67 F 68 8.8 170 EGE10907-0241_21934 BXD67 F 68 8.5 171 EGE10907-0242_21935 BXD67 M 68 9.5 172 EGE10907-0243_21936 BXD67 M 68 9.6 173 EGE10907-0244_21937 BXD6 F 68 9.6 174 EGE10907-0245_21938 BXD12 M 82 9.5 175 EGE10907-0246_21939 BXD60 F 72 9.6 176 EGE10907-0247_21940 BXD65 F 75 9.1 177 EGE10907-0248_21941 BXD75 F 69 8.8 178 EGE10907-0249_21942_(MoGene-2_0-st) BXD75 M 69 9.2 179 EGE10907-0250_21943 BXD8 F 97 9.1 180 EGE10907-0251_21944 BXD85 F 79 8.6 181 EGE10907-0252_21945 BXD85 M 79 9.1 182 EGE10907-0253_21946 BXD85 M 79 9.4 183 EGE10907-0254_21947 BXD102 M 94 8.6 184 EGE10907-0255_21948 BXD99 F 83 9 185 EGE10907-0256_21949 BXD69 F 68 9 186 EGE10907-0257_21950 BXD84 F 74 9.5 187 EGE10907-0258_21951 BXD84 F 74 9.4 188 EGE10907-0259_21952 BXD84 M 74 8.6 189 EGE10907-0260_21451 BXD96 M 67 9.2 190 EGE10907-0261_21452 BXD99 F 71 8.9 191 EGE10907-0262_21931 BXD6 F 66 9.4 192 EGE10907-0263_21932 BXD14 F 69 8.5 193 EGE10907-0264_21933 BXD34 M 79 9.1 194 EGE10907-0265_21934 BXD34 M 79 9.9 195 EGE10907-0266_21935 BXD40 F 75 9.6 196 EGE10907-0267_21936 BXD40 M 78 9.7 197 EGE10907-0268_21937 BXD56 F 72 9.7 198 EGE10907-0269_21938 BXD56 F 72 9.7 199 EGE10907-0270_21939 BXD56 M 72 9.6 200 EGE10907-0271_21940 BXD56 M 72 9.4 201 EGE10907-0272_21941 BXD71 F 72 9.9 202 EGE10907-0273_21942 BXD71 F 75 9.4 203 EGE10907-0274_21943 BXD71 M 75 10 204 EGE10907-0275_21944 BXD71 M 75 10 205 EGE10907-0276_21945 BXD27 M 65 10 206 EGE10907-0277_21946 BXD15 M 65 10 207 EGE10907-0278_21947 BXD20 F 125 10 208 EGE10907-0279_21948 BXD29 F 77 10 209 EGE10907-0280_21949 BXD29 F 77 10 210 EGE10907-0281_21950 BXD34 F 74 10 211 EGE10907-0282_21951 BXD34 F 74 10 212 EGE10907-0283_21952 BXD85 F 87 10 213 EGE10907-0284_21451 BXD43 M 75 9.8

About the tissue used to generate this set of data:

Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Retinas were removed immediately and placed in RiboLock (RiboLock: Thermo Scientific RiboLock RNase #EO0381 40U/µl 2500U) at room temperature. Individual retinas from the mouse were stored in each tube. RNA was isolated using a Qiacube with the resultant RIN scores ranging from 8.5 to 10.0.

About the array platform:

The Affymetrics GeneChip® Mouse Gene 2.0 ST microarrays. This relatively recent microarray was specifically designed to represent the whole-transcriptome. It includes probes to measure mRNA, long intergenic non-coding RNAs and microRNAs. Researchers have identified many transcripts in the mouse genome that do not have protein coding potential. Most of these non-coding RNAs have little functional annotation. Nonetheless, there is considerable evidence that these non-coding RNAs play important roles in development of the retina and the progression of disease. The coverage in the new ST 2.0 array includes over 28,000 coding transcripts and over 7,000 non-coding transcripts. There are also probes on the array covering 590 microRNAs.

About data values and data processing:

Replication, sex, and sample balance: Our goal was to obtain data for independent biological sample pools from both sexes for most lines of mice. The four batches of arrays included in this final data set, collectively represent a reasonably well-balanced sample of males and females, in general without within-strain-by-sex replication.

Notes:

Experiment Type:

Contributor:

Eldon E. Geisert, Lu Lu, XiangDi Wang, Justin P. Templeton and Robert W. Williams.

Citation:

Related Publications: Geisert EE, Lu L, Freeman-Anderson NE, Templeton JP, Nassr M, Wang X, Gu W, Jiao Y, Williams RW.:Gene expression in the mouse eye: an online resource for genetics using 103 strains of mice. Molecular Vision 2009 Aug 31;15:1730-63, (Link) Geisert EE, Jr., Williams RW: The Mouse Eye Transcriptome: Cellular Signatures, Molecular Networks, and Candidate Genes for Human Disease. In Eye, Retina, and Visual System of the Mouse. Edited by Chalupa LM, Williams RW. Cambridge: The MIT Press; 2008:659-674 Peirce JL, Lu L, Gu J, Silver LM, Williams RW: A new set of BXD recombinant inbred lines from advanced intercross populations in mice. BMC Genet 2004, 5:7. (Link) Templeton JP, Nassr M, Vazquez-Chona F, Freeman-Anderson NE, Orr WE, Williams RW, Geisert EE: Differential response of C57BL/6J mouse and DBA/2J mouse to optic nerve crush. BMC Neurosci. 2009, July 30;10:90. Other Data Sets Users of these mouse retina data may also find the following complementary resources useful: NEIBank collection of ESTs and SAGE data. RetNet: the Retinal Information Network--tables of genes and loci causing inherited retinal diseases.

Data source acknowledgment:

DoD funding (W81XWH-12-0255) Genetic Networks Activated by Blast Injury to the Eye (Eldon E. Geisert).

Study Id:

170

• 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)