HEI Retina Illumina V6.2 (April 2010) RankInv **

HEI Retina Illumina V6.2 (April 2010) RankInv (accession number: GN267)

Summary:

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 75 BXD strains, C57BL/6J, DBA/2J, both reciprocal F1s, and BALB/cByJ. A total of 80 strains were quantified. 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.

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.

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

About downloading this data set:

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.

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

Normalization:

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.

Funding Support for the HEI Retina Dataset:

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)

Information about this text file:

Dataset was uploaded to GeneNetwork by Arthur Centeno and Xiaodong Zhou, April 7, 2010. This text file was generated by Justin P. Templeton April 2010 from a previous version by RWW and EEG.

References

Rogojina AT, Orr WE, Song BK, Geisert EE, Jr.: Comparing the use of Affymetrix to spotted oligonucleotide microarrays using two retinal pigment epithelium cell lines. Molecular vision 2003, 9:482-496.(Link)
Vazquez-Chona F, Song BK, Geisert EE, Jr.: Temporal changes in gene expression after injury in the rat retina. Investigative ophthalmology & visual science 2004, 45(8):2737-2746.(Link)

GEO Series Data: This section to be used for GEO submission of the whole series of arrays

GSE Series No GEO series number
Status Private on April, 2010
Organism(s) Mus musculus
Experiment type Expression profiling by array
Overall design We used pooled RNA samples of retinas, usually two independent pools--two male, two female pool--for most lines of mice.
Contributor(s) Eldon E. Geisert, Lu Lu, Natalie E. Freeman-Anderson, Justin P. Templeton, Robert W. Williams

Submission date Not yet submitted to GEO.
Contact name Eldon E. Geisert
E-mails EGeisert@uthsc.edu
Phone 901-448-7740
FAX 901-448-5028
URL GeneNetwork BXD HEI RETINA
Organization name University of Tennessee Health Science Center
Department(s) Department of Ophthalmology
Laboratory(s) Geisert, Lu, Wiliams Labs
Street address 930 Madison Avenue
City Memphis
State/province TN
ZIP/Postal code 38163
Country USA
Platforms (1) GPLXXXX Illumina Mouse Whole Genome 6 version 2.0