Data Set Group2: Normal HEI Retina (April 2010)

Data Set: HEI Retina Normal Illumina V6.2 (Apr10) RankInv GN Accession: GN302 GEO Series: No Geo series yet Title: Organism: Mouse (Mus musculus, mm10) Group: BXD Tissue: Retina mRNA Dataset Status: Public Platforms: Illumina Mouse WG-6 v2.0 (GPL6887) Normalization: RankInv

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 GN302_MeanDataAnnotated_rev081815.txt (N/A) GN302_StdError_rev081815.txt (N/A)

Specifics of this Data Set:

None

Summary:

This is a subtractive dataset. The Normal retina dataset was subtracted from the ONC data set probe by probe to create a data set of the changes occurring following ONC. This data set can be used to define gene changes following ONC. It is not compatible with most of the bioinformatic tools available on GeneNetwork. HEI Retina Illumina V6.2 (April 2010) RankInv was normalized and scaled by William E. Orr and uploaded by Arthur Centeno and Xiaodong Zhou on April 7, 2010. This data set consists of either 69 BXD strains (Normal data set) or 75 BXD strains (Full data set), C57BL/6J, DBA/2J, both reciprocal F1s, and BALB/cByJ. A total of either 74 strains (Normal data set) or 80 strains (Full data set) were quantified. COMMENT on  FULL versus NORMAL data sets: For many general uses there is no significant difference between FULL and NORMAL data sets. However, the FULL data set includes strains with high endogenous Gfap mRNA expression, indicative of reactive gliosis. For that reason, and to compare to OPTIC NERVE CRUSH (ONC), we removed data from six strains to make the NORMAL data set. The NORMAL data set exludes data from BXD24, BXD32, BXD49, BXD70, BXD83, and BXD89. BXD24 has known retinal degeneration and is now known officially as  BXD24/TyJ-Cep290/J, JAX Stock number 000031. BXD32 has mild retinal degeneration. The NORMAL data set does include BXD24a, now also known as BXD24/TyJ (JAX Stock number 005243). The data are now open and available for analysis. Please cite: Freeman NE, Templeton JP, Orr WE, Lu L, Williams RW, Geisert EE (2011) Genetic networks in the mouse retina: Growth Associated Protein 43 and Phosphate Tensin Homology network. Molecular Vision 17:1355-1372. Full Text PDF or HTML This is rank invariant 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 6.25 to 18.08 (11.83 units), 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. The lowest level of expression is 6.254 for ILMN_2747167 (Arhgap11a) from HEI Retina Illumina V6.2 (April 2010) RankInv **. Lowest single data about 5.842. The highest level of expression is 18.077 for ILMN_2516699 (Ubb). Highest single value is about 18.934.   Other 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.(Link)     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 Mouse Retina SAGE Library from the Cepko laboratory. This site provides extensive developmental data from as early as embryonic day E12.5. Digital reference of ophthalmology from Columbia provides high quality photographs of human ocular diseases, case studies, and short explanations. This reference does not have a molecular focus. Mouse Retinal Developmental Gene Expression data sets from the Friedlander laboratory. This site provides extensive developmental data using the Affymetrix U74 v 2 array (predecessor of the M430). Data sets on differential gene expression in anatomical compartments of the human eye from Pat Brown's lab. View expression signatures for different ocular tissues using the geneXplorer 2.0.

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 48 and maximum age is 118 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. What Makes the G2 HEI Retina Database different from the HEI Retina Database Examination of Gfap expression across all of the strains in the HEI Retinal Dataset, reveals that some strains express very high levels of Gfap relative to others. For example, BXD24 expresses Gfap at a 9-fold higher level, than BXD22. It has been established that BXD24 acquired a mutation in Cep290 that results in early onset photoreceptor degeneration (Chang et al., 2006). This degeneration results in reactive gliosis throughout the retina. In addition to BXD24, other BXD strains expressed very high levels of Gfap including: BXD32, BXD49, BXD70, BXD83 and BXD89. For the G2 dataset all of these strains with potential reactive gliosis were removed from the dataset.

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 RNAlater at room temperature. Two retinas from one mouse were stored in a single tube. Each array was hybridized with a pool of cRNA from 2 retinas (1 mouse). Natalie Freeman-Anderson extracted RNA at UTHSC.   Dissecting and preparing eyes for RNA extraction   Retinas for RNA extraction were placed in RNA STAT-60 (Tel-Test Inc.) and processed per manufacturer’s instructions (in brief form below). Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:   Homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue via syringe) Allow the homogenate to stand for 5-10 min at room temperature Add 0.2 ml of chloroform per 1 ml RNA STAT-60 Mix the sample vigorously for 15 sec and let the sample incubate at room temperature for 5-10 min Centrifuge at 12,000 g for 1 hr at 4°C Transfer the aqueous phase to a clean centrifuge tube Add 0.5 ml of isopropanol per 1 ml RNA STAT-60 Vortex and incubate the sample at -20°C for 1 hr or overnight Centrifuge at 12,000 g for 1 hr Remove the supernatant and wash the RNA pellet with 75% ethanol Remove ethanol, let air dry (5-10 min) Dissolve the pellet in 50 μl of nuclease free water.

About the array platform:

Illumina MouseWG-6 v2.0 arrays: The Illumina Sentrix Mouse-6 BeadChip uses 50-nucleotide probes to interrogate approximately 46,000 sequences from the mouse transcriptome. For each array, the RNA was pooled from two retinas.

About data values and data processing:

Values of all 45,281 probe sets in this data set range from a low of 6.25 (Rho GTPase activating protein 11A, Arhgap11a, probe ID ILMN_2747167) to a high of 18.08 (Ubiquitin B, Ubb, probe ID ILMN_2516699). This corresponds to 11.83 units or a 1 to 3641 dynamic range of expression (2^11.83). We normalized raw signal values using Beadstudio’s rank invariant normalization algorithm. BXD62 was the strain used as the control group   Sample Processing: Drs. Natalie E. Freeman-Anderson and Justin P. Templeton extracted the retinas from the mice and Dr. Natalie Freeman-Anderson processed all samples in the HEI Vision Core Facility. The tissue was homogenized and extracted according to the RNA-Stat-60 protocol as described by the manufacturer (Tel-Test, Friendswood, TX) listed above. The quality and purity of RNA was assessed using an Agilent Bioanalyzer 2100 system. The RNA from each sample was processed with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX) to produce labeled cRNA. The cRNA for each sample was then hybridized to an Illumina Sentrix® Mouse-6-V2 BeadChip (Illumina, San Diego, CA)     Quality control analysis of the raw image data was performed using the Illumina BeadStudio software. MIAME standards were used for all microarray data. Rank invariant normalization with BeadStudio software was used to calculate the data. Once this data was collected, the data was globally normalized across all samples using the formula 2 (z-score of log2 [intensity]) + 8. 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. Table 1: HEI Retina case IDs, including sample tube ID, strain, age, sex, and source of mice   Index Sample ID Strain Age Sex Source of Animal 1 121608_11-C57BL/6JcFA C57BL/6J 69 F JAX 2 121608_12-C57BL/6JcFB C57BL/6J 69 F JAX 3 KA7444-C57BL/6JcMC C57BL/6J 97 M UTHSC RW 4 KA7444-C57BL/6JcMD C57BL/6J 97 M UTHSC RW 5 31209.05-DBA2JcFA DBA2J 75 F UTHSC RW 6 31209.05-DBA2JcFB DBA2J 75 F UTHSC RW 7 121608_13-DBA/2JcMA DBA/2J 89 M UTHSC RW 8 121608_14-DBA/2JcMB DBA/2J 89 M UTHSC RW 9 KA7446-B6D2F1cFA B6D2F1 92 F UTHSC RW 10 KA7446-B6D2F1cFB B6D2F1 92 F UTHSC RW 11 KA7446-B6D2F1cMC B6D2F1 92 M UTHSC RW 12 KA7446-B6D2F1cMD B6D2F1 92 M UTHSC RW 13 KA7466-D2B6F1cFA D2B6F1 70 F UTHSC RW 14 KA7466-D2B6F1cFB D2B6F1 70 F UTHSC RW 15 KA7466-D2B6F1cMC D2B6F1 70 M UTHSC RW 16 KA7466-D2B6F1cMD D2B6F1 70 M UTHSC RW 17 82609.13-1cFA BXD01 62 F JAX 18 82609.14-1cFB BXD01 62 F JAX 19 KA7389-1cFA BXD01 51 F UTHSC RW 20 KA7389-1cFB BXD01 51 F UTHSC RW 21 KA7389-1cMC BXD01 51 M UTHSC RW 22 KA7389-1cMD BXD01 51 M UTHSC RW 23 KA7300-2cFA BXD02 75 F UTHSC RW 24 KA7300-2cFB BXD02 75 F UTHSC RW 25 100909.01-2cMA BXD02 65 M JAX 26 100909.02-2cMB BXD02 65 M JAX 27 KA6699-5cFA BXD05 62 F UTHSC RW 28 KA6699-5cFB BXD05 62 F UTHSC RW 29 KA6699-5cFC BXD05 62 F UTHSC RW 30 KA6699-5cFD BXD05 62 F UTHSC RW 31 82609.09-5cMA BXD05 60 M JAX 32 82609.1-5cMB BXD05 60 M JAX 33 KA6763-6cFA BXD06 48 F UTHSC RW 34 KA6763-6cFB BXD06 48 F UTHSC RW 35 81209.06-6cMA BXD06 69 M VAMC 36 81209.07-6cMB BXD06 69 M VAMC 37 82609.07-8cFA BXD08 68 F JAX 38 82609.08-8cFB BXD08 68 F JAX 39 JAX-8cMA BXD08 76 M JAX 40 JAX-8cMB BXD08 76 M JAX 41 KA7289-9cFA BXD09 87 F UTHSC RW 42 KA7289-9cFB BXD09 87 F UTHSC RW 43 KA7289-9cMC BXD09 87 M UTHSC RW 44 KA7289-9cMD BXD09 87 M UTHSC RW 45 JAX-11cFA BXD11 84 F JAX 46 JAX-11cFB BXD11 84 F JAX 47 JAX-11cMC BXD11 71 M JAX 48 JAX-11cMD BXD11 71 M JAX 49 40209.07-12cFA BXD12 65 F VAMC 50 40209.08-12cFB BXD12 65 F VAMC 51 011309.01-12cMA BXD12 65 M UTHSC RW 52 011309.02-12cMB BXD12 65 M UTHSC RW 53 KA7286-13cFA BXD13 89 F UTHSC RW 54 KA7286-13cFB BXD13 89 F UTHSC RW 55 KA7286-13cMC BXD13 89 M UTHSC RW 56 KA7286-13cMD BXD13 89 M UTHSC RW 57 KA7302-14cFA BXD14 73 F UTHSC RW 58 KA7302-14cFB BXD14 73 F UTHSC RW 59 100909.05-14cMA BXD14 66 M JAX 60 100909.06-14cMB BXD14 66 M JAX 61 KA7288-15cFA BXD15 89 F UTHSC RW 62 KA7288-15cFB BXD15 89 F UTHSC RW 63 KA7288-15cMC BXD15 89 M UTHSC RW 64 KA7288-15cMD BXD15 89 M UTHSC RW 65 062509.01-16cFA BXD16 68 F UTHSC RW 66 KA7267-16cMA BXD16 91 M UTHSC RW 67 KA7267-16cMB BXD16 91 M UTHSC RW 68 KA6686-18cFB BXD18 65 F UTHSC RW 69 KA6686-18cFC BXD18 65 F UTHSC RW 70 KA6686-18cME BXD18 65 M UTHSC RW 71 KA6686-18cMF BXD18 65 M UTHSC RW 72 KA6676-19cFB BXD19 63 F UTHSC RW 73 KA6676-19cFC BXD19 63 F UTHSC RW 74 KA6676-19cME BXD19 63 M UTHSC RW 75 KA6676-19cMF BXD19 63 M UTHSC RW 76 060409.05-20cFA BXD20 67 F UTHSC RW 77 060409.06-20cFB BXD20 67 F UTHSC RW 78 021909.03-20cMA BXD20 64 M UTHSC RW 79 021909.04-20cMB BXD20 64 M UTHSC RW 80 82609.02-21cFC BXD21 65 F JAX 81 82609.03-21cFD BXD21 65 F JAX 82 121709.01-21cMA BXD21 80 M JAX 83 121709.02-21cMB BXD21 80 M JAX 84 121709.03-22cFA BXD22 62 F JAX 85 121709.04-22cFB BXD22 62 F JAX 86 092308_03-22cMA BXD22 118 M UTHSC RW 87 092308_04-22cMB BXD22 118 M UTHSC RW 88 80409.01-24AcFA BXD24A 72 F UTHSC RW 89 080409_02_24AcFB BXD24A 72 F UTHSC RW 90 82609.26-24AcFC BXD24A 64 F UTHSC RW 91 81209.03-24AcMC BXD24A 62 M UTHSC RW 92 KA6678-24cFA BXD24 62 F UTHSC RW 93 KA6678-24cFB BXD24 62 F UTHSC RW 94 KA6678-24cME BXD24 62 M UTHSC RW 95 KA6678-24cMF BXD24 62 M UTHSC RW 96 060409.07-27cFA BXD27 63 F UTHSC RW 97 060409.08-27cFB BXD27 63 F UTHSC RW 98 80409.03-27cMA BXD27 74 M UTHSC RW 99 80409.04-27cMB BXD27 74 M UTHSC RW 100 JAX-28cFA BXD28 67 F JAX 101 JAX-28cFB BXD28 67 F JAX 102 JAX-28cMC BXD28 67 M JAX 103 JAX-28cMD BXD28 67 M JAX 104 82609.11-29cFA BXD29 66 F JAX 105 82609.12-29cFB BXD29 66 F JAX 106 82609.04-29cMA BXD29 66 M JAX 107 82609.05-29cMB BXD29 66 M JAX 108 JAX-31cMB BXD 31 56 M JAX 109 JAX-31cFC BXD 31 69 F JAX 110 JAX-31cFD BXD 31 69 F JAX 111 011309.03-32cFA BXD32 62 F UTHSC RW 112 011309.04-32cFB BXD32 62 F UTHSC RW 113 KA7318-32cFC BXD32 71 F UTHSC RW 114 KA7319-32cMA BXD32 74 M UTHSC RW 115 KA7319-32cMB BXD32 74 M UTHSC RW 116 100909.07-33cFA BXD33 65 F JAX 117 100909.08-33cFB BXD33 65 F JAX 118 022609.01-33cMA BXD33 92 M UTHSC RW 119 022609.02-33cMB BXD33 92 M UTHSC RW 120 KA7416-34cFA BXD34 97 F UTHSC RW 121 KA7416-34cFB BXD34 97 F UTHSC RW 122 KA6321-34cMA BXD34 66 M UTHSC RW 123 KA6321-34cMB BXD34 66 M UTHSC RW 124 060409.01-36cFA BXD36 63 F UTHSC RW 125 060409.02-36cFB BXD36 63 F UTHSC RW 126 060409.03-36cMC BXD36 63 M UTHSC RW 127 KA6702-38cFA BXD38 63 F UTHSC RW 128 KA6702-38cFB BXD38 63 F UTHSC RW 129 82609.24-38cFA BXD38 85 F UTHSC RW 130 82609.25-38cFB BXD38 85 F UTHSC RW 131 100909.03-38cMA BXD38 61 M JAX 132 100909.04-38cMB BXD38 61 M JAX 133 022609.05-39cFA BXD39 65 F UTHSC RW 134 022609.06-39cFB BXD39 65 F UTHSC RW 135 31209.01-39cMC BXD39 67 M UTHSC RW 136 92409.01-40cFA BXD40 64 F UTHSC RW 137 92409.02-40cFB BXD40 64 F UTHSC RW 138 KA6173-40cMA BXD40 59 M UTHSC RW 139 KA6173-40cMB BXD40 59 M UTHSC RW 140 KA6173-40cMC BXD40 59 M UTHSC RW 141 091809.01-42cFA BXD42 73 F UTHSC RW 142 091809.02-42cFB BXD42 73 F UTHSC RW 143 021909.01-42cFA BXD42 89 F UTHSC RW 144 011309.06-42cMA BXD42 67 M UTHSC RW 145 011309.07-42cMB BXD42 67 M UTHSC RW 146 110408_02-43cFA BXD43 61 F UTHSC RW 147 110408_03-43cFB BXD43 61 F UTHSC RW 148 KA6158-43cMA BXD43 66 M UTHSC RW 149 KA6158-43cMB BXD43 66 M UTHSC RW 150 100308_01-44cFA BXD44 67 F UTHSC RW 151 102208_02-44cMD BXD44 64 M UTHSC RW 152 103009.03-45cFA BXD45 68 F UTHSC RW 153 103009.04-45cFB BXD45 68 F UTHSC RW 154 022609.03-45cFA BXD45 78 F UTHSC RW 155 022609.04-45cFB BXD45 78 F UTHSC RW 156 40309.05-45cMB BXD45 65 M UTHSC RW 157 40209.05-48cFB BXD48 58 F VAMC 158 40209.06-48cFC BXD48 58 F VAMC 159 81209.04-48cMA BXD48 82 M UTHSC RW 160 81209.05-48cMB BXD48 82 M UTHSC RW 161 81209.08-49cFA BXD49 70 F VAMC 162 81209.09-49cFB BXD49 70 F VAMC 163 40209.01-49cMA BXD49 87 M VAMC 164 40209.02-49cMB BXD49 87 M VAMC 165 40209.03-49cMC BXD49 87 M VAMC 166 KA737850cFA BXD50 50 F UTHSC RW 167 KA737850cFB BXD50 50 F UTHSC RW 168 121908_01-50cMA BXD50 49 M UTHSC RW 169 121908_02-50cMB BXD50 49 M UTHSC RW 170 111208_01-51cFA BXD51 99 F UTHSC RW 171 102208_03-51cMA BXD51 56 M UTHSC RW 172 102208_04-51cMB BXD51 56 M UTHSC RW 173 090208_14-53BcFA BXD53B 93 F UTHSC RW 174 090208_15-53BcFB BXD53B 93 F UTHSC RW 175 090208_16-53BcMC BXD53B 93 M UTHSC RW 176 090208_17-53BcMD BXD53B 93 M UTHSC RW 177 111208_05-55cFB BXD55 70 F UTHSC RW 178 KA6183-55cMA BXD55 63 M UTHSC RW 179 KA6183-55cMB BXD55 63 M UTHSC RW 180 KA7362-56cFB BXD 56 54 F UTHSC RW 181 KA6088-56cMA BXD56 87 M UTHSC RW 182 KA6088-56cMB BXD56 87 M UTHSC RW 183 KA6088-56cMC BXD56 87 M UTHSC RW 184 21810.01-60RFA BXD 60 67 F UTHSC RW 185 21810.02-60RFB BXD 60 67 F UTHSC RW 186 21810.02-60RFC BXD 60 67 F UTHSC RW 187 SQ7325-60cMA BXD60 85 M UTHSC RW 188 SQ7325-60cMB BXD60 85 M UTHSC RW 189 092308_10-61cFA BXD61 110 F UTHSC RW 190 092308_11-61cFB BXD61 110 F UTHSC RW 191 31909.01-61cMA BXD61 67 M UTHSC RW 192 31909.02-61cMB BXD61 67 M UTHSC RW 193 KA7462-62cFA BXD62 76 F UTHSC RW 194 KA7462-62cFB BXD62 76 F UTHSC RW 195 KA5996-62cMA BXD62 113 M UTHSC RW 196 KA5996-62cMB BXD62 113 M UTHSC RW 197 KA5996-62cMC BXD62 113 M UTHSC RW 198 090309.01-63cFA BXD63 69 F UTHSC RW 199 090309.02-63cFB BXD63 69 F UTHSC RW 200 110609.01-63cMA BXD63 66 M UTHSC RW 201 110609.02-63cMB BXD63 66 M UTHSC RW 202 091809.03-65cFA BXD65 65 F UTHSC RW 203 091809.04-65cFB BXD65 65 F UTHSC RW 204 103009.01-65cMA BXD65 74 M UTHSC RW 205 103009.02-65cMB BXD65 74 M UTHSC RW 206 110408_05-66cFB BXD66 59 F UTHSC RW 207 KA7165-66cMA BXD66 95 M UTHSC RW 208 KA7165-66cMB BXD66 95 M UTHSC RW 209 90809.01-67cMA BXD67 61 M UTHSC RW 210 90809.02-67cMB BXD67 61 M UTHSC RW 211 110609.03-67cFA BXD67 68 F UTHSC RW 212 110609.04-67cFB BXD67 68 F UTHSC RW 213 120408_01-68cFA BXD68 67 F UTHSC RW 214 120408_02-68cFB BXD68 67 F UTHSC RW 215 SQ7205-68cMA BXD68 87 M UTHSC RW 216 SQ7205-68cMB BXD68 87 M UTHSC RW 217 KA6316-68cMA BXD68 76 M UTHSC RW 218 KA6316-68cMB BXD68 76 M UTHSC RW 219 KA6316-68cMC BXD68 76 M UTHSC RW 220 KA76-69cFA BXD69 48 F UTHSC RW 221 KA76-69cFB BXD69 48 F UTHSC RW 222 KA6074-69cMA BXD69 90 M UTHSC RW 223 KA6074-69cMB BXD69 90 M UTHSC RW 224 121608_01-70cFA BXD70 80 F UTHSC RW 225 121608_02-70cFB BXD70 80 F UTHSC RW 226 KA7394-70cMA BXD70 51 M UTHSC RW 227 81209.08-70cMA BXD70 71 M VAMC 228 81209.09-70cMB BXD70 71 M VAMC 229 052809.01-71cFA BXD71 70 F UTHSC RW 230 060409.09-71cMA BXD71 62 M UTHSC RW 231 060409.10-71cMB BXD71 62 M UTHSC RW 232 40809.01-73cFA BXD73 83 F UTHSC RW 233 40809.02-73cFB BXD73 83 F UTHSC RW 234 111708_01-73cFA BXD73 55 F UTHSC RW 235 111708_01-73cFB BXD73 55 F UTHSC RW 236 KA6164-73cMB BXD73 59 M UTHSC RW 237 KA6164-73cMC BXD73 59 M UTHSC RW 238 82609.22-74cFA BXD74 68 F VAMC 239 82609.23-74cFB BXD74 68 F VAMC 240 82609.20-74cMA BXD74 68 M VAMC 241 82609.21-74cMB BXD74 68 M VAMC 242 KA733675cFA BXD75 59 F UTHSC RW 243 KA733675cFB BXD75 59 F UTHSC RW 244 KA38-75cMB BXD75 62 M UTHSC RW 245 KA38-75cMC BXD75 62 M UTHSC RW 246 41509.01-77cFA BXD77 70 F UTHSC RW 247 41509.02-77cFB BXD77 70 F UTHSC RW 248 41509.03-77cMC BXD77 70 M UTHSC RW 249 41509.04-77cMD BXD77 70 M UTHSC RW 250 121608_03-80cFA BXD80 77 F UTHSC RW 251 121608_05-80cMC BXD80 70 M UTHSC RW 252 KA23-80cMC BXD80 77 M UTHSC RW 253 KA7305-81cFA BXD81 51 F UTHSC RW 254 KA7305-81cFB BXD81 51 F UTHSC RW 255 KA7305-81cMD BXD81 51 M UTHSC RW 256 060409.11-83cFA BXD83 65 F UTHSC RW 257 KA24-83cFA BXD83 78 F UTHSC RW 258 121608_07-83cMA BXD83 78 M UTHSC RW 259 121608_08-83cMB BXD83 78 M UTHSC RW 260 KA24-83cMD BXD83 78 M UTHSC RW 261 090409.05-84cFA BXD84 65 F VAMC 262 090409.06-84cFB BXD84 65 F VAMC 263 KA6203-84cMA BXD84 59 M UTHSC RW 264 KA6203-84cMB BXD84 59 M UTHSC RW 265 40309.02-85cFD BXD85 58 F UTHSC RW 266 40309.03-85cFE BXD85 58 F UTHSC RW 267 32609.01-85cMA BXD85 67 M UTHSC RW 268 32609.02-85cMB BXD85 67 M UTHSC RW 269 41509.05-86cFA BXD86 73 F UTHSC RW 270 41509.06-86cFB BXD86 73 F UTHSC RW 271 KA6101-86cMA BXD86 82 M UTHSC RW 272 KA6101-86cMC BXD86 82 M UTHSC RW 273 070909.02-87cFA BXD87 86 F UTHSC RW 274 070909.03-87cFB BXD87 86 F UTHSC RW 275 KA7407-87cMA BXD87 113 M UTHSC RW 276 KA7407-87cMB BXD87 113 M UTHSC RW 277 102208_05-89cFA BXD89 82 F UTHSC RW 278 KA5974-89cMA BXD89 113 M UTHSC RW 279 KA5974-89cMB BXD89 113 M UTHSC RW 280 102208_06-89cMC BXD89 82 M UTHSC RW 281 72309.01-90cFA BXD90 67 F UTHSC RW 282 72309.02-90cFB BXD90 67 F UTHSC RW 283 090409.03-90cMA BXD90 64 M VAMC 284 090409.04-90cMB BXD90 64 M VAMC 285 KA6094-92cMA BXD92 85 M UTHSC RW 286 020609.01-95cFA BXD95 71 F UTHSC RW 287 020609.02-95cFB BXD95 71 F UTHSC RW 288 KA6181-95cMA BXD95 61 M UTHSC RW 289 KA6181-95cMB BXD95 61 M UTHSC RW 290 31209.03-96cFA BXD96 62 F UTHSC RW 291 31209.04-96cFB BXD96 62 F UTHSC RW 292 KA7246-96cMA BXD96 73 M UTHSC RW 293 KA7246-96cMB BXD96 73 M UTHSC RW 294 81209.10-97cFA BXD97 83 F VAMC 295 81209.11-97cFB BXD97 83 F VAMC 296 81209.1-97cMA BXD97 83 M VAMC 297 81209.11-97cMB BXD97 83 M VAMC 298 SQ7520-98cFA BXD98 59 F UTHSC RW 299 SQ7520-98cFB BXD98 59 F UTHSC RW 300 SQ7520-98cMC BXD98 59 M UTHSC RW 301 SQ7520-98cMD BXD98 59 M UTHSC RW 302 82609.17-99cFA BXD99 64 F VAMC 303 82609.18-99cFB BXD99 64 F VAMC 304 81409.01-99cMA BXD99 66 M UTHSC RW 305 81409.02-99cMB BXD99 66 M UTHSC RW 306 121608_09-100cFA BXD100 81 F UTHSC RW 307 121608_10-100cFB BXD100 81 F UTHSC RW 308 KA6001-100cMA BXD100 111 M UTHSC RW 309 KA6001-100cMB BXD100 111 M UTHSC RW 310 81209.12-101cFA BXD101 72 F VAMC 311 81209.13-101cFB BXD101 72 F VAMC 312 KA7296-101cMA BXD101 75 M UTHSC RW 313 KA7296-101cMB BXD101 75 M UTHSC RW 314 92409.03-102cFA BXD102 71 F VAMC 315 92409.04-102cFB BXD102 71 F VAMC 316 KA7380-102cMA BXD102 115 M UTHSC RW 317 43009.01-103cFA BXD103 68 F UTHSC RW 318 43009.02-103cFB BXD103 68 F UTHSC RW 319 KA79-103cFA BXD103 48 F UTHSC RW 320 KA79-103cFB BXD103 48 F UTHSC RW 321 KA79-103cMC BXD103 48 M UTHSC RW 322 82609.15-103cMA BXD103 69 M VAMC 323 82609.16-103cMB BXD103 69 M VAMC 324 102909.01-BALBCcFA BALB/cByJ 78 F JAX 325 102909.02-BALBCcFB BALB/cByJ 78 F JAX 326 102909.03-BALBCcMA BALB/cByJ 78 M JAX 327 102909.04-BALBCcMB BALB/cByJ 78 M JAX

Notes:

This data set is available as a bulk download in several formats. The data are available as either strain means or the individual arrays. Due to the involved normalization procedures required to correct for batch effects we strongly recommend not using the raw CEL files without special statistical procedures.

Experiment Type:

Expression profiling by array We used pooled RNA samples of retinas, usually two independent pools--two male, two female pool--for most lines of mice. All normalization was performed by William E. Orr in the HEI Vision Core Facility Computed the log base 2 of each raw signal value Calculated the mean and standard Deviation of each Mouse WG-6 v2.0 array Normalized each array using the formula, 2 (z-score of log2 [intensity]) The result is to produce arrays that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage is that a two-fold difference in expression level corresponds approximately to a 1 unit difference. computed the mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.

Contributor:

Eldon E. Geisert, Lu Lu, Natalie E. Freeman-Anderson, Justin P. Templeton, Robert W. Williams

Citation:

Data source acknowledgment:

The HEI Retinal Database is supported by National Eye Institute Grants:   R01EY017841 (Dr. Eldon E. Geisert, PI)   P030EY13080 (NEI Vision Core Grant), and   A Unrestricted Grand from Research to Prevent Blindness (Dr. Barrett Haik, PI)

Study Id:

92

• 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)