From d029d5d7f8ead1f1de8d318045004a4a6f68f5fb Mon Sep 17 00:00:00 2001 From: Bonface Date: Fri, 9 Feb 2024 09:41:28 -0600 Subject: Update dataset RTF Files. --- .../G2NEI_ILM_Retina_BXD_RI0410/acknowledgment.rtf | 13 + .../datasets/G2NEI_ILM_Retina_BXD_RI0410/cases.rtf | 14 + .../experiment-design.rtf | 12 + .../datasets/G2NEI_ILM_Retina_BXD_RI0410/notes.rtf | 1 + .../G2NEI_ILM_Retina_BXD_RI0410/platform.rtf | 1 + .../G2NEI_ILM_Retina_BXD_RI0410/processing.rtf | 2654 ++++++++++++++++++++ .../G2NEI_ILM_Retina_BXD_RI0410/summary.rtf | 50 + .../G2NEI_ILM_Retina_BXD_RI0410/tissue.rtf | 32 + 8 files changed, 2777 insertions(+) create mode 100644 general/datasets/G2NEI_ILM_Retina_BXD_RI0410/acknowledgment.rtf create mode 100644 general/datasets/G2NEI_ILM_Retina_BXD_RI0410/cases.rtf create mode 100644 general/datasets/G2NEI_ILM_Retina_BXD_RI0410/experiment-design.rtf create mode 100644 general/datasets/G2NEI_ILM_Retina_BXD_RI0410/notes.rtf create mode 100644 general/datasets/G2NEI_ILM_Retina_BXD_RI0410/platform.rtf create mode 100644 general/datasets/G2NEI_ILM_Retina_BXD_RI0410/processing.rtf create mode 100644 general/datasets/G2NEI_ILM_Retina_BXD_RI0410/summary.rtf create mode 100644 general/datasets/G2NEI_ILM_Retina_BXD_RI0410/tissue.rtf (limited to 'general/datasets/G2NEI_ILM_Retina_BXD_RI0410') diff --git a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/acknowledgment.rtf b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/acknowledgment.rtf new file mode 100644 index 0000000..a41ff76 --- /dev/null +++ b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/acknowledgment.rtf @@ -0,0 +1,13 @@ +

The HEI Retinal Database is supported by National Eye Institute Grants:

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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.

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BXD strains: + + +
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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.

diff --git a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/experiment-design.rtf b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/experiment-design.rtf new file mode 100644 index 0000000..4fff707 --- /dev/null +++ b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/experiment-design.rtf @@ -0,0 +1,12 @@ +

Expression profiling by array

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We used pooled RNA samples of retinas, usually two independent pools--two male, two female pool--for most lines of mice.

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All normalization was performed by William E. Orr in the HEI Vision Core Facility

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  1. Computed the log base 2 of each raw signal value
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  2. Calculated the mean and standard Deviation of each Mouse WG-6 v2.0 array
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  3. 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.
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  4. 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.
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diff --git a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/notes.rtf b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/notes.rtf new file mode 100644 index 0000000..13ff99a --- /dev/null +++ b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/notes.rtf @@ -0,0 +1 @@ +

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.

diff --git a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/platform.rtf b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/platform.rtf new file mode 100644 index 0000000..2c52707 --- /dev/null +++ b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/platform.rtf @@ -0,0 +1 @@ +

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.

diff --git a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/processing.rtf b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/processing.rtf new file mode 100644 index 0000000..97cc2be --- /dev/null +++ b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/processing.rtf @@ -0,0 +1,2654 @@ +

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

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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)

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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.

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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.

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Table 1: HEI Retina case IDs, including sample tube ID, strain, age, sex, and source of mice

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+ + + + + + + +
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IndexSample IDStrainAgeSexSource of Animal
1121608_11-C57BL/6JcFAC57BL/6J69FJAX
2121608_12-C57BL/6JcFBC57BL/6J69FJAX
3KA7444-C57BL/6JcMCC57BL/6J97MUTHSC RW
4KA7444-C57BL/6JcMDC57BL/6J97MUTHSC RW
531209.05-DBA2JcFADBA2J75FUTHSC RW
631209.05-DBA2JcFBDBA2J75FUTHSC RW
7121608_13-DBA/2JcMADBA/2J89MUTHSC RW
8121608_14-DBA/2JcMBDBA/2J89MUTHSC RW
9KA7446-B6D2F1cFAB6D2F192FUTHSC RW
10KA7446-B6D2F1cFBB6D2F192FUTHSC RW
11KA7446-B6D2F1cMCB6D2F192MUTHSC RW
12KA7446-B6D2F1cMDB6D2F192MUTHSC RW
13KA7466-D2B6F1cFAD2B6F170FUTHSC RW
14KA7466-D2B6F1cFBD2B6F170FUTHSC RW
15KA7466-D2B6F1cMCD2B6F170MUTHSC RW
16KA7466-D2B6F1cMDD2B6F170MUTHSC RW
1782609.13-1cFABXD0162FJAX
1882609.14-1cFBBXD0162FJAX
19KA7389-1cFABXD0151FUTHSC RW
20KA7389-1cFBBXD0151FUTHSC RW
21KA7389-1cMCBXD0151MUTHSC RW
22KA7389-1cMDBXD0151MUTHSC RW
23KA7300-2cFABXD0275FUTHSC RW
24KA7300-2cFBBXD0275FUTHSC RW
25100909.01-2cMABXD0265MJAX
26100909.02-2cMBBXD0265MJAX
27KA6699-5cFABXD0562FUTHSC RW
28KA6699-5cFBBXD0562FUTHSC RW
29KA6699-5cFCBXD0562FUTHSC RW
30KA6699-5cFDBXD0562FUTHSC RW
3182609.09-5cMABXD0560MJAX
3282609.1-5cMBBXD0560MJAX
33KA6763-6cFABXD0648FUTHSC RW
34KA6763-6cFBBXD0648FUTHSC RW
3581209.06-6cMABXD0669MVAMC
3681209.07-6cMBBXD0669MVAMC
3782609.07-8cFABXD0868FJAX
3882609.08-8cFBBXD0868FJAX
39JAX-8cMABXD0876MJAX
40JAX-8cMBBXD0876MJAX
41KA7289-9cFABXD0987FUTHSC RW
42KA7289-9cFBBXD0987FUTHSC RW
43KA7289-9cMCBXD0987MUTHSC RW
44KA7289-9cMDBXD0987MUTHSC RW
45JAX-11cFABXD1184FJAX
46JAX-11cFBBXD1184FJAX
47JAX-11cMCBXD1171MJAX
48JAX-11cMDBXD1171MJAX
4940209.07-12cFABXD1265FVAMC
5040209.08-12cFBBXD1265FVAMC
51011309.01-12cMABXD1265MUTHSC RW
52011309.02-12cMBBXD1265MUTHSC RW
53KA7286-13cFABXD1389FUTHSC RW
54KA7286-13cFBBXD1389FUTHSC RW
55KA7286-13cMCBXD1389MUTHSC RW
56KA7286-13cMDBXD1389MUTHSC RW
57KA7302-14cFABXD1473FUTHSC RW
58KA7302-14cFBBXD1473FUTHSC RW
59100909.05-14cMABXD1466MJAX
60100909.06-14cMBBXD1466MJAX
61KA7288-15cFABXD1589FUTHSC RW
62KA7288-15cFBBXD1589FUTHSC RW
63KA7288-15cMCBXD1589MUTHSC RW
64KA7288-15cMDBXD1589MUTHSC RW
65062509.01-16cFABXD1668FUTHSC RW
66KA7267-16cMABXD1691MUTHSC RW
67KA7267-16cMBBXD1691MUTHSC RW
68KA6686-18cFBBXD1865FUTHSC RW
69KA6686-18cFCBXD1865FUTHSC RW
70KA6686-18cMEBXD1865MUTHSC RW
71KA6686-18cMFBXD1865MUTHSC RW
72KA6676-19cFBBXD1963FUTHSC RW
73KA6676-19cFCBXD1963FUTHSC RW
74KA6676-19cMEBXD1963MUTHSC RW
75KA6676-19cMFBXD1963MUTHSC RW
76060409.05-20cFABXD2067FUTHSC RW
77060409.06-20cFBBXD2067FUTHSC RW
78021909.03-20cMABXD2064MUTHSC RW
79021909.04-20cMBBXD2064MUTHSC RW
8082609.02-21cFCBXD2165FJAX
8182609.03-21cFDBXD2165FJAX
82121709.01-21cMABXD2180MJAX
83121709.02-21cMBBXD2180MJAX
84121709.03-22cFABXD2262FJAX
85121709.04-22cFBBXD2262FJAX
86092308_03-22cMABXD22118MUTHSC RW
87092308_04-22cMBBXD22118MUTHSC RW
8880409.01-24AcFABXD24A72FUTHSC RW
89080409_02_24AcFBBXD24A72FUTHSC RW
9082609.26-24AcFCBXD24A64FUTHSC RW
9181209.03-24AcMCBXD24A62MUTHSC RW
92KA6678-24cFABXD2462FUTHSC RW
93KA6678-24cFBBXD2462FUTHSC RW
94KA6678-24cMEBXD2462MUTHSC RW
95KA6678-24cMFBXD2462MUTHSC RW
96060409.07-27cFABXD2763FUTHSC RW
97060409.08-27cFBBXD2763FUTHSC RW
9880409.03-27cMABXD2774MUTHSC RW
9980409.04-27cMBBXD2774MUTHSC RW
100JAX-28cFABXD2867FJAX
101JAX-28cFBBXD2867FJAX
102JAX-28cMCBXD2867MJAX
103JAX-28cMDBXD2867MJAX
10482609.11-29cFABXD2966FJAX
10582609.12-29cFBBXD2966FJAX
10682609.04-29cMABXD2966MJAX
10782609.05-29cMBBXD2966MJAX
108JAX-31cMBBXD 3156MJAX
109JAX-31cFCBXD 3169FJAX
110JAX-31cFDBXD 3169FJAX
111011309.03-32cFABXD3262FUTHSC RW
112011309.04-32cFBBXD3262FUTHSC RW
113KA7318-32cFCBXD3271FUTHSC RW
114KA7319-32cMABXD3274MUTHSC RW
115KA7319-32cMBBXD3274MUTHSC RW
116100909.07-33cFABXD3365FJAX
117100909.08-33cFBBXD3365FJAX
118022609.01-33cMABXD3392MUTHSC RW
119022609.02-33cMBBXD3392MUTHSC RW
120KA7416-34cFABXD3497FUTHSC RW
121KA7416-34cFBBXD3497FUTHSC RW
122KA6321-34cMABXD3466MUTHSC RW
123KA6321-34cMBBXD3466MUTHSC RW
124060409.01-36cFABXD3663FUTHSC RW
125060409.02-36cFBBXD3663FUTHSC RW
126060409.03-36cMCBXD3663MUTHSC RW
127KA6702-38cFABXD3863FUTHSC RW
128KA6702-38cFBBXD3863FUTHSC RW
12982609.24-38cFABXD3885FUTHSC RW
13082609.25-38cFBBXD3885FUTHSC RW
131100909.03-38cMABXD3861MJAX
132100909.04-38cMBBXD3861MJAX
133022609.05-39cFABXD3965FUTHSC RW
134022609.06-39cFBBXD3965FUTHSC RW
13531209.01-39cMCBXD3967MUTHSC RW
13692409.01-40cFABXD4064FUTHSC RW
13792409.02-40cFBBXD4064FUTHSC RW
138KA6173-40cMABXD4059MUTHSC RW
139KA6173-40cMBBXD4059MUTHSC RW
140KA6173-40cMCBXD4059MUTHSC RW
141091809.01-42cFABXD4273FUTHSC RW
142091809.02-42cFBBXD4273FUTHSC RW
143021909.01-42cFABXD4289FUTHSC RW
144011309.06-42cMABXD4267MUTHSC RW
145011309.07-42cMBBXD4267MUTHSC RW
146110408_02-43cFABXD4361FUTHSC RW
147110408_03-43cFBBXD4361FUTHSC RW
148KA6158-43cMABXD4366MUTHSC RW
149KA6158-43cMBBXD4366MUTHSC RW
150100308_01-44cFABXD4467FUTHSC RW
151102208_02-44cMDBXD4464MUTHSC RW
152103009.03-45cFABXD4568FUTHSC RW
153103009.04-45cFBBXD4568FUTHSC RW
154022609.03-45cFABXD4578FUTHSC RW
155022609.04-45cFBBXD4578FUTHSC RW
15640309.05-45cMBBXD4565MUTHSC RW
15740209.05-48cFBBXD4858FVAMC
15840209.06-48cFCBXD4858FVAMC
15981209.04-48cMABXD4882MUTHSC RW
16081209.05-48cMBBXD4882MUTHSC RW
16181209.08-49cFABXD4970FVAMC
16281209.09-49cFBBXD4970FVAMC
16340209.01-49cMABXD4987MVAMC
16440209.02-49cMBBXD4987MVAMC
16540209.03-49cMCBXD4987MVAMC
166KA737850cFABXD5050FUTHSC RW
167KA737850cFBBXD5050FUTHSC RW
168121908_01-50cMABXD5049MUTHSC RW
169121908_02-50cMBBXD5049MUTHSC RW
170111208_01-51cFABXD5199FUTHSC RW
171102208_03-51cMABXD5156MUTHSC RW
172102208_04-51cMBBXD5156MUTHSC RW
173090208_14-53BcFABXD53B93FUTHSC RW
174090208_15-53BcFBBXD53B93FUTHSC RW
175090208_16-53BcMCBXD53B93MUTHSC RW
176090208_17-53BcMDBXD53B93MUTHSC RW
177111208_05-55cFBBXD5570FUTHSC RW
178KA6183-55cMABXD5563MUTHSC RW
179KA6183-55cMBBXD5563MUTHSC RW
180KA7362-56cFBBXD 5654FUTHSC RW
181KA6088-56cMABXD5687MUTHSC RW
182KA6088-56cMBBXD5687MUTHSC RW
183KA6088-56cMCBXD5687MUTHSC RW
18421810.01-60RFABXD 6067FUTHSC RW
18521810.02-60RFBBXD 6067FUTHSC RW
18621810.02-60RFCBXD 6067FUTHSC RW
187SQ7325-60cMABXD6085MUTHSC RW
188SQ7325-60cMBBXD6085MUTHSC RW
189092308_10-61cFABXD61110FUTHSC RW
190092308_11-61cFBBXD61110FUTHSC RW
19131909.01-61cMABXD6167MUTHSC RW
19231909.02-61cMBBXD6167MUTHSC RW
193KA7462-62cFABXD6276FUTHSC RW
194KA7462-62cFBBXD6276FUTHSC RW
195KA5996-62cMABXD62113MUTHSC RW
196KA5996-62cMBBXD62113MUTHSC RW
197KA5996-62cMCBXD62113MUTHSC RW
198090309.01-63cFABXD6369FUTHSC RW
199090309.02-63cFBBXD6369FUTHSC RW
200110609.01-63cMABXD6366MUTHSC RW
201110609.02-63cMBBXD6366MUTHSC RW
202091809.03-65cFABXD6565FUTHSC RW
203091809.04-65cFBBXD6565FUTHSC RW
204103009.01-65cMABXD6574MUTHSC RW
205103009.02-65cMBBXD6574MUTHSC RW
206110408_05-66cFBBXD6659FUTHSC RW
207KA7165-66cMABXD6695MUTHSC RW
208KA7165-66cMBBXD6695MUTHSC RW
20990809.01-67cMABXD6761MUTHSC RW
21090809.02-67cMBBXD6761MUTHSC RW
211110609.03-67cFABXD6768FUTHSC RW
212110609.04-67cFBBXD6768FUTHSC RW
213120408_01-68cFABXD6867FUTHSC RW
214120408_02-68cFBBXD6867FUTHSC RW
215SQ7205-68cMABXD6887MUTHSC RW
216SQ7205-68cMBBXD6887MUTHSC RW
217KA6316-68cMABXD6876MUTHSC RW
218KA6316-68cMBBXD6876MUTHSC RW
219KA6316-68cMCBXD6876MUTHSC RW
220KA76-69cFABXD6948FUTHSC RW
221KA76-69cFBBXD6948FUTHSC RW
222KA6074-69cMABXD6990MUTHSC RW
223KA6074-69cMBBXD6990MUTHSC RW
224121608_01-70cFABXD7080FUTHSC RW
225121608_02-70cFBBXD7080FUTHSC RW
226KA7394-70cMABXD7051MUTHSC RW
22781209.08-70cMABXD7071MVAMC
22881209.09-70cMBBXD7071MVAMC
229052809.01-71cFABXD7170FUTHSC RW
230060409.09-71cMABXD7162MUTHSC RW
231060409.10-71cMBBXD7162MUTHSC RW
23240809.01-73cFABXD7383FUTHSC RW
23340809.02-73cFBBXD7383FUTHSC RW
234111708_01-73cFABXD7355FUTHSC RW
235111708_01-73cFBBXD7355FUTHSC RW
236KA6164-73cMBBXD7359MUTHSC RW
237KA6164-73cMCBXD7359MUTHSC RW
23882609.22-74cFABXD7468FVAMC
23982609.23-74cFBBXD7468FVAMC
24082609.20-74cMABXD7468MVAMC
24182609.21-74cMBBXD7468MVAMC
242KA733675cFABXD7559FUTHSC RW
243KA733675cFBBXD7559FUTHSC RW
244KA38-75cMBBXD7562MUTHSC RW
245KA38-75cMCBXD7562MUTHSC RW
24641509.01-77cFABXD7770FUTHSC RW
24741509.02-77cFBBXD7770FUTHSC RW
24841509.03-77cMCBXD7770MUTHSC RW
24941509.04-77cMDBXD7770MUTHSC RW
250121608_03-80cFABXD8077FUTHSC RW
251121608_05-80cMCBXD8070MUTHSC RW
252KA23-80cMCBXD8077MUTHSC RW
253KA7305-81cFABXD8151FUTHSC RW
254KA7305-81cFBBXD8151FUTHSC RW
255KA7305-81cMDBXD8151MUTHSC RW
256060409.11-83cFABXD8365FUTHSC RW
257KA24-83cFABXD8378FUTHSC RW
258121608_07-83cMABXD8378MUTHSC RW
259121608_08-83cMBBXD8378MUTHSC RW
260KA24-83cMDBXD8378MUTHSC RW
261090409.05-84cFABXD8465FVAMC
262090409.06-84cFBBXD8465FVAMC
263KA6203-84cMABXD8459MUTHSC RW
264KA6203-84cMBBXD8459MUTHSC RW
26540309.02-85cFDBXD8558FUTHSC RW
26640309.03-85cFEBXD8558FUTHSC RW
26732609.01-85cMABXD8567MUTHSC RW
26832609.02-85cMBBXD8567MUTHSC RW
26941509.05-86cFABXD8673FUTHSC RW
27041509.06-86cFBBXD8673FUTHSC RW
271KA6101-86cMABXD8682MUTHSC RW
272KA6101-86cMCBXD8682MUTHSC RW
273070909.02-87cFABXD8786FUTHSC RW
274070909.03-87cFBBXD8786FUTHSC RW
275KA7407-87cMABXD87113MUTHSC RW
276KA7407-87cMBBXD87113MUTHSC RW
277102208_05-89cFABXD8982FUTHSC RW
278KA5974-89cMABXD89113MUTHSC RW
279KA5974-89cMBBXD89113MUTHSC RW
280102208_06-89cMCBXD8982MUTHSC RW
28172309.01-90cFABXD9067FUTHSC RW
28272309.02-90cFBBXD9067FUTHSC RW
283090409.03-90cMABXD9064MVAMC
284090409.04-90cMBBXD9064MVAMC
285KA6094-92cMABXD9285MUTHSC RW
286020609.01-95cFABXD9571FUTHSC RW
287020609.02-95cFBBXD9571FUTHSC RW
288KA6181-95cMABXD9561MUTHSC RW
289KA6181-95cMBBXD9561MUTHSC RW
29031209.03-96cFABXD9662FUTHSC RW
29131209.04-96cFBBXD9662FUTHSC RW
292KA7246-96cMABXD9673MUTHSC RW
293KA7246-96cMBBXD9673MUTHSC RW
29481209.10-97cFABXD9783FVAMC
29581209.11-97cFBBXD9783FVAMC
29681209.1-97cMABXD9783MVAMC
29781209.11-97cMBBXD9783MVAMC
298SQ7520-98cFABXD9859FUTHSC RW
299SQ7520-98cFBBXD9859FUTHSC RW
300SQ7520-98cMCBXD9859MUTHSC RW
301SQ7520-98cMDBXD9859MUTHSC RW
30282609.17-99cFABXD9964FVAMC
30382609.18-99cFBBXD9964FVAMC
30481409.01-99cMABXD9966MUTHSC RW
30581409.02-99cMBBXD9966MUTHSC RW
306121608_09-100cFABXD10081FUTHSC RW
307121608_10-100cFBBXD10081FUTHSC RW
308KA6001-100cMABXD100111MUTHSC RW
309KA6001-100cMBBXD100111MUTHSC RW
31081209.12-101cFABXD10172FVAMC
31181209.13-101cFBBXD10172FVAMC
312KA7296-101cMABXD10175MUTHSC RW
313KA7296-101cMBBXD10175MUTHSC RW
31492409.03-102cFABXD10271FVAMC
31592409.04-102cFBBXD10271FVAMC
316KA7380-102cMABXD102115MUTHSC RW
31743009.01-103cFABXD10368FUTHSC RW
31843009.02-103cFBBXD10368FUTHSC RW
319KA79-103cFABXD10348FUTHSC RW
320KA79-103cFBBXD10348FUTHSC RW
321KA79-103cMCBXD10348MUTHSC RW
32282609.15-103cMABXD10369MVAMC
32382609.16-103cMBBXD10369MVAMC
324102909.01-BALBCcFABALB/cByJ78FJAX
325102909.02-BALBCcFBBALB/cByJ78FJAX
326102909.03-BALBCcMABALB/cByJ78MJAX
327102909.04-BALBCcMBBALB/cByJ78MJAX
+
diff --git a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/summary.rtf b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/summary.rtf new file mode 100644 index 0000000..44e98a7 --- /dev/null +++ b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/summary.rtf @@ -0,0 +1,50 @@ +
+

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.

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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.

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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.

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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).

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The data are now open and available for analysis.

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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.

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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.

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The highest level of expression is 18.077 for ILMN_2516699 (Ubb). Highest single value is about 18.934.

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+ +

Other Related Publications

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+

 

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  1. 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)
    2. +
  2. 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
    3. +
  3. 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)
    4. +
  4. 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) +

     

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    5. +
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+ +
Other Data Sets Users of these mouse retina data may also find the following complementary resources useful: + +
    +
  1. NEIBank collection of ESTs and SAGE data.
    2. +
  2. RetNet: the Retinal Information Network--tables of genes and loci causing inherited retinal diseases
    3. +
  3. Mouse Retina SAGE Library from the Cepko laboratory. This site provides extensive developmental data from as early as embryonic day E12.5.
    4. +
  4. 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.
    5. +
  5. 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).
    6. +
  6. 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.
    7. +
+
diff --git a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/tissue.rtf b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/tissue.rtf new file mode 100644 index 0000000..766ab59 --- /dev/null +++ b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/tissue.rtf @@ -0,0 +1,32 @@ +
+

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.

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Each array was hybridized with a pool of cRNA from 2 retinas (1 mouse). Natalie Freeman-Anderson extracted RNA at UTHSC.

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+ +

Dissecting and preparing eyes for RNA extraction

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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:

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