Eye AXBXA Illumina V6.2(Oct08) RankInv Beta

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FINAL RECOMMENDED AXB/BXA EYE DATA SET. The Eye AXBXA Illumina Illumina V6.2 (Oct08) data set provides estimates of mRNA expression for whole eyes of 28 strains of mice, including 26 AXB/BXA recombinant inbred strains, and two parental strains, A/J and C57BL/6J. All eye samples were obtained from normal adult control animals raised in a standard laboratory environment at the Jackson Laboratory. We used the Illumina Sentrix MouseWG-6 v2 BeadChip (despite the nomenclature, this is actually the third version of the Illumina Mouse-6 platform).

Users of these mouse eye data may also find the following complementary resources extremely useful:

  1. NEIBank collection of ESTs and SAGE data
  2. RetNet: the Retinal Information Network--tables of genes and loci causing inherited retinal diseases
  3. Mouse Retina SAGE Library from the Cepko laboratory. This site provides extensive developmental data from as early as embryonic day E12.5.
  4. 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:


A total of 54 pooled whole eye samples were processed using approximately 10 Illumina Sentrix Mouse WG-6 v2 oligomer BeadChip slides. All 10 slides and a total of 54 samples passed stringent quality control and error checking. This particular data set was processed using the Illumina "Rank Invariant" protocol. Values were log2 transformed. Variance of each array was stabilized to 4 units (SD of 2 units) and recentered to a mean of 8. values range from a low of 6.3 (e.g., ILMN_1225143, no expression) to a high of about 19.7 for ILMN_2772482 (Crygd, extremely highly expressed). Data were entered by Arthur Centeno, Hongqiang Li, Robert W. Williams, and Lu Lu, October 1, 2008.

As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10. In this data set, 255 probes have LRS values >46 (LOD >10). The maximum LOD score achieved in this data set is 27.7 for Zfp330 (LRS of 127.9 using ILMN_2825109).

The probe ILMN_2475156 can be used to check sex assignment. With three exceptions, all 28 strains are represented by one male sample and one female sample. The three exceptions are are follows: both AXB13/14 cases are males, BXA25 is represented by a single male sample or a mixed sex sample, and BXA11 is represented by a single female sample.

Legend: Bar chart of the expression of Xist probe ILMN_2475156 in the AXB/BXA eye data set. This probe is used to check sex. Strains represented by equal numbers of male and female arrays (usually one of each) should have intermediate values and a high error term. Strains represented only by males will have very low values (for example, AXB13/14 is represented by only one male) and strains represented by only females will have very high expression (for example, BXA11 is represented by only one female).

    About the animals and tissue used to generate this set of data:

AXB/BXA animals were obtained directly from The Jackson Laboratory. Animals were housed at UTHSC before sacrifice. Mice were killed by cervical dislocation and eyes and brains were removed and placed in RNAlater.

Animals used in this study were between 51 and 90 days of age (see Table 1 below). All animals were sacrifice between 9 AM and 5 PM during the light phase.

Experimental Design and Batch Structure: This data set consists arrays processed September 2008 and all arrays in this data set were processed using a single protocol by a single operator. Processing was supervised directly by Dr. Lu Lu. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute in September 2008. Details on sample assignment to slides and batches is provide in the table below.

    Data Table 1:

This table lists all arrays by order of strain (index) and includes data on tube ID, strain, age, sex, number of animals in each sample pool (pool size), slide ID, slide position (A through F), batch by slide number (1 or 2), and Source of animals.

Index Tube ID Strain Age Sex Pool size Slide Id Slide Position Batch Id Source
1 R4893E1 A/J 59 F 0 4252491010 A 1 JAX
2 R4982E1 A/J 79 M 2 4252491006 A 1 JAX
3 R4894E1 A/J 59 M 0 4252491011 A 1 JAX
4 R3655E1 A/J 86 M 0 4252491031 A 2 JAX
5 R4897E1 AXB1 90 F 0 4252491005 C 1 JAX
6 R5005E1 AXB1 56 M 0 4252491008 A 1 JAX
7 R5001E1 AXB10 63 F 2 4252491008 B 1 JAX
8 R5002E1 AXB10 63 M 2 4252491021 B 1 JAX
9 R4891E1 AXB12 63 F 0 4252491009 A 1 JAX
10 R4999E1 AXB12 57 M 2 4252491005 D 1 JAX
11 R5000E1 AXB13 57 M 2 4252491008 C 1 JAX
12 R5003E1 AXB15 63 F 2 4252491005 E 1 JAX
13 R4963E1 AXB15 63 M 2 4252491031 B 1 JAX
14 R3661E1 AXB19 89 F 0 4252491008 D 1 JAX
15 R4962E1 AXB19 62 M 0 4252491005 F 1 JAX
16 R4975E1 AXB2 79 F 2 4252491006 C 1 JAX
17 R4976E1 AXB2 79 M 2 4252491021 C 1 JAX
18 R4973E1 AXB23 66 F 2 4252491009 E 1 JAX
19 R4972E1 AXB23 66 M 2 4252491006 D 1 JAX
20 R4959E1 AXB24 100 F 2 4252491006 E 1 JAX
21 R4960E1 AXB24 100 M 2 4252491019 A 1 JAX
22 R4994E1 AXB4 54 F 2 4252491031 C 1 JAX
23 R5007E1 AXB4 54 M 2 4252491006 F 1 JAX
24 R4995E1 AXB5 61 F 2 4252491021 F 1 JAX
25 R4996E1 AXB5 61 M 2 4252491009 F 1 JAX
26 R4997E1 AXB6 60 F 2 4252491010 C 1 JAX
27 R4998E1 AXB6 60 M 2 4252491021 D 1 JAX
28 R4958E1 AXB8 52 F 2 4252491019 D 1 JAX
29 R4957E1 AXB8 52 M 2 4252491010 D 1 JAX
30 R4991E1 BXA1 54 F 2 4252491010 E 1 JAX
31 R4990E1 BXA1 54 M 2 4252491009 B 1 JAX
32 R4980E1 BXA11 52 F 0 4252491020 A 1 JAX
33 R5006E1 BXA12 48 F 2 4252491011 C 2 JAX
34 R4993E1 BXA12 48 M 2 4252491031 D 1 JAX
35 R4968E1 BXA13 61 F 2 4252491011 D 1 JAX
36 R4969E1 BXA13 61 M 2 4252491008 E 1 JAX
37 R4966E1 BXA14 56 F 2 4252491031 E 1 JAX
38 R4967E1 BXA14 56 M 2 4252491011 E 1 JAX
39 R4970E1 BXA16 51 F 2 4252491011 F 1 JAX
40 R5004E1 BXA16 51 M 2 4252491031 F 1 JAX
41 R4981E1 BXA2 50 F 2 4252491008 F 1 JAX
42 R4965E1 BXA2 54 M 0 4252491020 B 1 JAX
43 R4984E1 BXA24 54 F 2 4252491021 E 1 JAX
44 R4974E1 BXA24 54 M 2 4252491019 C 1 JAX
45 R4988E1 BXA25 70 M 0 4252491020 F 1 JAX
46 R4964E1 BXA26 54 F 0 4252491019 B 1 JAX
47 R3636E1 BXA26 87 M 0 4252491009 D 1 JAX
48 R4977E1 BXA4 65 F 0 4252491020 C 1 JAX
49 R3638E1 BXA4 87 M 0 4252491019 E 1 JAX
50 R4978E1 BXA7 65 F 2 4252491019 F 1 JAX
51 R4979E1 BXA7 65 M 2 4252491021 A 1 JAX
52 R5008E1 BXA8 52 F 2 4252491020 E 1 JAX
53 R4983E1 BXA8 52 M 2 4252491020 D 1 JAX
54 R5012E1 C57BL/6J 87 F 2 4252491006 B 1 UTHSC RW
55 R5010E1 C57BL/6J 87 F 2 4252491011 B 1 UTHSC RW
56 R5011E1 C57BL/6J 79 M 2 4252491005 B 1 UTHSC RW
57 R5009E1 C57BL/6J 79 M 2 4252491010 B 1 UTHSC RW

    Downloading all data:

All data links (right-most column above) will be made active as soon as the global analysis of these data has been accepted for publication. Please see text on Data Sharing Policies, and Conditions and Limitations, and Contacts. Following publication, download a summary text file or Excel file of data. Please contact RW Williams if you have any questions on the use of these open data.

    About data processing:

This data set uses the standard Rank Invariant method developed by Illumina and described in their BeadStation Studio documentation.

About cases

The AXB/BXA genetic reference panel of recombinant inbred strains consists of just about 26 fully independent strains. All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. All of these strains were been genotyped at 13,377 SNPs in 2005 (Shifman et al., 2006).

About platform

Illumina Sentrix MouseWG-6 v2 BeadChip: This array consists of 45,281 unique probe sequences, each 50 nucleotides in length, that have been arrayed on glass slides using a novel bead technology.

ANNOTATION: In the summer of 2008, Xusheng Wang and Robert W. Williams reannotated all three Illumina Mouse 6 BeadChips, including the array used to process the AXB/BXA eye samples. This new annotation is now incorporated into GeneNetwork. The annotation file can be accessed at http://www.genenetwork.org/share/annotations/, by selecting "Illumina Mouse WG-6 v2.0 (GPL6887)".

Position data for the 50-mer Illumina probe sequences were aligned to the mm8 mouse genome build by Xusheng Wang as part of his master annotation of all Illumina mouse arrays. Manual annotation of this array was usually done by RW Williams.

About data processing

Sample Processing: Samples were processed by Lu Lu and colleagues in the Illumina Core at UTHSC between August 2008 and September 2008. All processing steps were performed by Dr. David Li. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8 to pass our quality control (QC). The majority of samples had values between 1.9 and 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using the Ambion/Illumina (http://www.ambion.com/catalog/CatNum.php?AMIL1791) TotalPrep RNA amplication kit (Cat#IL1791). The biotin labeled cRNA was then evaluated using both the 260/280 ratio (values of 2.0-2.3 are acceptable) using a NanoDrop ND-1000 (http://www.nanodrop.com/nd-1000-overview.html). Those samples that passed QC steps (approximately 10% failed and new RNA samples had to be acquired and processed) were immediately used on BeadChips. The slides were hybridized and washed following standard Illumina protocols.

Replication and Sample Balance: We obtained a male sample pool and female sample pool from 25 of the 28 strains. Three strains are represented by samples from a single sex.


A QTL on chromosome 10 modulates cone photoreceptor number in the mouse retina.

Whitney IE, Raven MA, Lu L, Williams RW, Reese BE.
Invest Ophthalmol Vis Sci. 2011 May 16;52(6):3228-36. 

Pituitary tumor-transforming gene 1 regulates the patterning of retinal mosaics.

Keeley PW, Zhou C, Lu L, Williams RW, Melmed S, Reese BE.
Proc Natl Acad Sci U S A. 2014 Jun 24;111(25):9295-300.


All array data were generated with funds from Dr. Benjamin Reese to RW Williams and Lu Lu as part of NIH NEI grant EY011087 (Dispersion Patterns for Retinal Neuroblasts). Arrays were scanned in the UTHSC NEI Vision Core with support from P30 EY013080. Some informatics support, including annotation of the array, was provided by NIDA and NIAAA grants to RWW and LL (NIH U01AA13499, U24AA13513 Lu Lu, PI).

    About this text file:

Data uploaded by Arthur Centeno, Oct 1, 2008. This text file originally generated by RWW on Oct 10, 2008. Updated by RWW, May 11, 2009, May 26, 2009.


Specifics of this data set