From b2feda451ccfbeaed02dce9088d6dd228cf15861 Mon Sep 17 00:00:00 2001 From: Bonface Date: Tue, 13 Feb 2024 23:52:26 -0600 Subject: Update dataset RTF Files. --- general/datasets/Eye_m2_0908_r_nd/tissue.rtf | 2058 ++++++++++++++++++++++++++ 1 file changed, 2058 insertions(+) create mode 100644 general/datasets/Eye_m2_0908_r_nd/tissue.rtf (limited to 'general/datasets/Eye_m2_0908_r_nd/tissue.rtf') diff --git a/general/datasets/Eye_m2_0908_r_nd/tissue.rtf b/general/datasets/Eye_m2_0908_r_nd/tissue.rtf new file mode 100644 index 0000000..9b6ee0f --- /dev/null +++ b/general/datasets/Eye_m2_0908_r_nd/tissue.rtf @@ -0,0 +1,2058 @@ +

Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Eyes were removed immediately and placed in RNAlater at room temperature. Usually six eyes from animals with a common sex, age, and strain were stored in a single tube.

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Each array was hybridized with a pool of cRNA from 4 to 8 eyes from 2 to 4 animals. RNA was extracted at UTHSC by Zhiping Jia. If tissue was saved for RNA extraction at a later time, eyes were placed directly in RNAlater (Ambion, Inc.) and treated per the manufacturer’s directions. If eyes were used for immediate RNA extraction then we proceeded immediately to the next steps.

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Dissecting and preparing eyes for RNA extraction

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  1. Place eyes for RNA extraction in RNA STAT-60 (Tel-Test Inc.) and process per manufacturer’s instructions (in brief form below).
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  2. Store RNA in 75% ethanol at –80 deg. C until use.
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Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:

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  1. homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue)
    2. +
  2. allowed the homogenate to stand for 5 min at room temperature
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  3. added 0.2 ml of chloroform per 1 ml RNA STAT-60
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  4. shook the sample vigorously for 15 sec and let the sample sit at room temperature for 3 min
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  5. centrifuged at 12,000 G for 15 min
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  6. transfered the aqueous phase to a fresh tube
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  7. added 0.5 ml of isopropanol per 1 ml RNA STAT-60
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  8. vortexed and allowed sample to stand at room temperature for 5-10 min
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  9. centrifuged at 12,000 G for 10-15 min
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  10. removed the supernatant and washed the RNA pellet with 75% ethanol
    11. +
  11. stored the pellet in 75% ethanol at -80 deg C until use
    12. +
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Sample Processing. All samples were processed in the VA Medical Center, Memphis, Rheumatology Disease Research Core Center led by Dr. Weikuan Gu. All arrays were processed by Dr. Yan Jiao. In brief, samples were purified using a standard sodium acetate in alcohol method (recommended by Affymetrix). The RNA quality was checked using a 1% agarose gel. The 18S and 28S bands had to be clear and the 28S band had to be more prominent. RNA concentation was measured using a spectrophotometer. The 260/280 ratios had to be greater than 1.7, and the majority were 1.8 or higher. We used a total of 8 micrograms of RNA as starting amount for cDNA synthesis using a standard Eberwine T7 polymerase method (Superscript II RT, Invitrogen Inc., Affy Part No 900431, GeneChip Expression 3' Amplification One-Cyle cDNA Synthesis Kit). The Affymetrix IVT labeling kit (Affy 900449) was used to generate labeled cRNA. At this point the cRNA was evaluated again using both the 260/280 ratio (values of 2.0 or above were acceptable) and 1% agarose gel inspection of the product (a size range from 200 to 7000 bp is considered suitable for use). We used 45 micrograms of labeled cRNA for fragmentation. Those samples that passed both QC steps (<10% usually fail) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No.900371). After fragmentation, samples were either stored at -80 deg. C until use (roughly one third) or were used immediately for hybridization.

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Dealing with ocular pigmentation: Variable ocular pigmentation is a potential confound in a study of the whole eye transcriptome. Even the most careful RNA preparations taken from brown and beige colored mice tend to have faint residual pigmentation that affects hybridization signal. To address this problem, Dr. Yan Jiao purified total RNA using the Qiagen RNeasy MinElute Cleanup Kit (Cat No. 74204) all four batches.

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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. Two strains are represented by a single male sample pool (BXD29 and A/J). Four lines are represented by two or three male sample pools (all of the five DeltaGen KO line). The SJL/J may be a single mixed sex sample. Users can study possible sex effects by comparing any results of expression data to that of a surrogate measurement that summarizes the overall sex balance of HEIMED. To do this just compare your data to those of probe sets 1427262_at (Xist, high in females) and probe set 1426438_at (Ddx3y, high in males). These two sex-specific probes are quantitative surrogates for the sex balance in this data set.

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Technical duplicates: One sample, highlighted in the tables below, is a technical duplicate. The pair of technical duplicates were both of high quality. For statistical analysis, they should be combined and treated as single biological sample.

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Batch structure: This data set consists of four batches (Table 2, far right column). The final September 2008 data set consists of a total of 221 arrays and 220 independent samples.

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  1. Batch 1: November 2005, n = 78 arrays original arrays of which 76 were accepted into this final data set.
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  2. Batch 2: January 2006, n = 62 arrays of which 62 were accepted.
    3. +
  3. Batch 3: August 2006, n = 39 arrays of which 36 were accepted. (These three batches, including some arrays that were eventually dropped from the final 2008 data set, were combined to form the September 2006 data set.)
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  4. Batch 4: Summer 2008, n = 53 arrays of which 47 were accepted.
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Table 1: HEIMED case IDs, including sample tube ID, strain, age, sex, and source of mice (see Table 2 for information on array quality control)

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+ + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
IndexTubeIDGroupStrainAgeSexSource
1R2595E.1GDP129S1/SvImJ59FUTHSC RW
2R2533E.1GDP129S1/SvImJ60MUTHSC RW
3R0754E.1GDPA/J60MJAX
4R4521EKOB6129P2F2N1-Clcn369MTChoi_Deltagen
5R4522EKOB6129P2F2N1-Clcn369MTChoi_Deltagen
6R4523EKOB6129P2F2N1-Clcn367MTChoi_Deltagen
7R4526EKOB6129P2F2N1-Gabbr116FTChoi_Deltagen
8R4509EKOB6129P2F2N1-Gabbr116MTChoi_Deltagen
9R4510EKOB6129P2F2N1-Gabbr119MTChoi_Deltagen
10R4511EKOB6129P2F2N1-Gabbr120MTChoi_Deltagen
11R4524EKOB6129P2F2N1-Gabbr119MTChoi_Deltagen
12R4525EKOB6129P2F2N1-Gabbr122MTChoi_Deltagen
13R4515EKOB6129P2F2N1-Gabra167MTChoi_Deltagen
14R4516EKOB6129P2F2N1-Gabra169MTChoi_Deltagen
15R4517EKOB6129P2F2N1-Gabra167MTChoi_Deltagen
16R4512EKOB6129P2F2N1-Gnb522FTChoi_Deltagen
17R4513EKOB6129P2F2N1-Gnb525MTChoi_Deltagen
18R4514EKOB6129P2F2N1-Gnb522MTChoi_Deltagen
19R4518EKOB6129P2F2N1-Gpr1970MTChoi_Deltagen
20R4519EKOB6129P2F2N1-Gpr1968MTChoi_Deltagen
21R2601E.1GDP BXDB6D2F173FUTHSC RW
22R2602E.1GDP BXDB6D2F173MUTHSC RW
23R1676E.1GDPBALB/cByJ83FJAX
24R1672E.1GDPBALB/cByJ83MJAX
25R4530EGDPBALB/cJ66FJAX
26R4529EGDPBALB/cJ66MJAX
27R2704E.2BXDBXD159FUTHSC RW
28R2707E.3BXDBXD159MBIDMC GR
29R1231E.2BXDBXD264FUTHSC RW
30R2598E.1BXDBXD261MUTHSC RW
31R2591E.1BXDBXD560FBIDMC GR
32R2714E.2BXDBXD558MUTHSC RW
33R2570E.1BXDBXD665FUTHSC RW
34R2694E.2BXDBXD658MUTHSC RW
35R2538E.1BXDBXD877FUTHSC RW
36R2709E.2BXDBXD861MUTHSC RW
37R2708E.2BXDBXD960FUTHSC RW
38R2569E.1BXDBXD967MUTHSC RW
39R2581E.1BXDBXD1165FUTHSC RW
40R2612E.2BXDBXD1170MUTHSC RW
41R2742E.2BXDBXD1271FUTHSC RW
42R2543E.1BXDBXD1263MUTHSC RW
43R2586E.1BXDBXD1360FBIDMC GR
44R877E.2BXDBXD1376MUTHSC RW
45R2557E.1BXDBXD1460FBIDMC GR
46R1128E.2BXDBXD1465MUTHSC RW
47R2701E.3BXDBXD1560FBIDMC GR
48R2716E.2BXDBXD1560MUTHSC RW
49R2711E.2BXDBXD1661FUTHSC RW
50R2567E.1BXDBXD1660MBIDMC GR
51R2720E.2BXDBXD1859FUTHSC RW
52R2559E.1BXDBXD1859MBIDMC GR
53R2560E.1BXDBXD1960FBIDMC GR
54R2713E.2BXDBXD1960MUTHSC RW
55R2584E.1BXDBXD2059FBIDMC GR
56R2731E.2BXDBXD2060MUTHSC RW
57R2702E.2BXDBXD2159FUTHSC RW
58R2541E2.1BXDBXD2161MUTHSC RW
59R2553E.1BXDBXD2258FBIDMC GR
60R2700E.2BXDBXD2259MUTHSC RW
61R2558E-2.1BXDBXD2360FBIDMC GR
62R1086E.2BXDBXD2355MUTHSC RW
63R2719E.2BXDBXD24123FUTHSC RW
64R2589E2.1BXDBXD2459MBIDMC GR
65R2573E-2.1BXDBXD2567FUAB
66R2683E.2BXDBXD2558MUTHSC RW
67R2703E.2BXDBXD2760FUTHSC RW
68R2729E.3BXDBXD2768MUTHSC RW
69R2562E.3BXDBXD2860FBIDMC GR
70R2721E.2BXDBXD2860MUTHSC RW
71R2561E.3BXDBXD2960MBIDMC GR
72R1258E.2BXDBXD3157FUTHSC RW
73R2597E.1BXDBXD3161MBIDMC GR
74R2563E.1BXDBXD3263FUTHSC RW
75R1216E.2BXDBXD3276MUTHSC RW
76R2542E.1BXDBXD3367FUTHSC RW
77R857E.2BXDBXD3377MUTHSC RW
78R1451E.2BXDBXD3461FUTHSC RW
79R2585E.1BXDBXD3460MBIDMC GR
80R2698E.3BXDBXD3658FBIDMC GR
81R2705E.3BXDBXD3657MBIDMC GR
82R2710E.2BXDBXD3855FUTHSC RW
83R2532E.1BXDBXD3862MUTHSC RW
84R2574E.1BXDBXD3970FUTHSC RW
85R2695E.2BXDBXD3959MUTHSC RW
86R2699E.2BXDBXD4059FUTHSC RW
87R2590E.1BXDBXD4060MBIDMC GR
88R2696E.2BXDBXD4258FUTHSC RW
89R2596E.1BXDBXD4259MBIDMC GR
90R994E.2BXDBXD4360FUTHSC RW
91R2607E.1BXDBXD4367MUTHSC RW
92R2594E.1BXDBXD4463FUTHSC RW
93R2610E.2BXDBXD4468MUTHSC RW
94R2732E.2BXDBXD4563FUTHSC RW
95R2592E.1BXDBXD4562MUTHSC RW
96R967E.2BXDBXD4864FUTHSC RW
97R2606E.1BXDBXD4878MUTHSC RW
98R2933E.3BXDBXD5061FUTHSC RW
99R2937E.3BXDBXD5061MUTHSC RW
100R2603E.1BXDBXD5166FUTHSC RW
101R1042E.2BXDBXD5162MUTHSC RW
102R2980E.3BXDBXD5576FUTHSC RW
103R2690E.2BXDBXD5565MUTHSC RW
104R4176EBXDBXD5667FUTHSC RW
105R4175EBXDBXD5653MUTHSC RW
106R1006E.3BXDBXD6060FUTHSC RW
107R2725E.2BXDBXD6061FUTHSC RW
108R1074E.3BXDBXD6059MUTHSC RW
109R2534E2.1BXDBXD6170FUTHSC RW
110R2684E.2BXDBXD6162MUTHSC RW
111R1107E.3BXDBXD6254FUTHSC RW
112R2681E.2BXDBXD6262MUTHSC RW
113R965E.3BXDBXD6254MUTHSC RW
114R1425E.2BXDBXD6361FUTHSC RW
115R2576E.3BXDBXD6370MUTHSC RW
116R943E-2.2BXDBXD6456FUTHSC RW
117R2611E.1BXDBXD6468MUTHSC RW
118R2689E.2BXDBXD6563FUTHSC RW
119R2583E.1BXDBXD6560MUTHSC RW
120R2728E.2BXDBXD6667FUTHSC RW
121R2536E2.1BXDBXD6664FUTHSC RW
122R1207E.2BXDBXD6683MUTHSC RW
123R1192E.2BXDBXD6764FUTHSC RW
124R2727E.3BXDBXD6765FUTHSC RW
125R2691E.3BXDBXD6765MUTHSC RW
126R2551E.1BXDBXD6867FUTHSC RW
127R2726E.2BXDBXD6864MUTHSC RW
128R2593E.1BXDBXD6959FUTHSC RW
129R975E.2BXDBXD7064FUTHSC RW
130R2537E2.1BXDBXD7059MUTHSC RW
131R4531EBXDBXD7187FUTHSC RW
132R4532EBXDBXD7186MUTHSC RW
133R2779E.2BXDBXD7364FUTHSC RW
134R3024E.3BXDBXD7354MUTHSC RW
135R2565E.1BXDBXD7561FUTHSC RW
136R1397E-re.2BXDBXD7558MUTHSC RW
137R2687E.3BXDBXD7760FUTHSC RW
138R2717E.2BXDBXD77107MUTHSC RW
139R1421E.3BXDBXD7762MUTHSC RW
140R2579E.1BXDBXD8065FUTHSC RW
141R2686E.2BXDBXD8061MUTHSC RW
142R2956E.3BXDBXD8358FUTHSC RW
143R2960E.3BXDBXD8358MUTHSC RW
144R2922E.3BXDBXD8461FUTHSC RW
145R2895E.3BXDBXD8467MUTHSC RW
146R2692E.2BXDBXD8563FUTHSC RW
147R2715E.2BXDBXD8591MUTHSC RW
148R1405E.2BXDBXD8658FUTHSC RW
149R1225E.3BXDBXD8658MUTHSC RW
150R2724E.2BXDBXD8763FUTHSC RW
151R2540E.1BXDBXD8763MUTHSC RW
152R1433E.2BXDBXD8963FUTHSC RW
153R2546E.1BXDBXD8966MUTHSC RW
154R2578E2.1BXDBXD9061FUTHSC RW
155R859E.2BXDBXD9072MUTHSC RW
156R2682E.2BXDBXD9266FUTHSC RW
157R1388E.3BXDBXD9262FUTHSC RW
158R1322E.3BXDBXD9255MUTHSC RW
159R2733E.2BXDBXD9667FUTHSC RW
160R2554E.1BXDBXD9667MUTHSC RW
161R2649E.2BXDBXD9774FUTHSC RW
162R2577E.1BXDBXD9755MUTHSC RW
163R2645E.3BXDBXD9866FUTHSC RW
164R2688E.2BXDBXD9867MUTHSC RW
165R4533EBXDBXD9980FUTHSC RW
166R4534EBXDBXD9991MUTHSC RW
167R2885E.3GDPBXSB/MpJ61FBIDMC GR
168R2883E.3GDPBXSB/MpJ61MBIDMC GR
169R1700E.1GDPC3H/HeJ83FUTHSC RW
170R1704E.1GDPC3H/HeJ83MUTHSC RW
171R2605E.1GDP BXDC57BL/6J79FUTHSC RW
172R0871EGDP BXDC57BL/6J65FUTHSC RW
173R0872E.1GDP BXDC57BL/6J66MUTHSC RW
174R0872EGDP BXDC57BL/6J66MUTHSC RW
175R4507EKOC57BL/6J-Nyx57MGeisert
176R4508EKOC57BL/6J-Nyx57MGeisert
177R4505EKOC57BL/6J-Rpe6557FGeisert
178R4506EKOC57BL/6J-Rpe6557FGeisert
179R4535EGDPC57BLKS/J66FJAX
180R4536EGDPC57BLKS/J66MJAX
181R2564E.1GDPCAST/EiJ64FJAX
182R2580E.1GDPCAST/EiJ64MJAX
183R4537EGDPCBA/CaJ66FJAX
184R4538EGDPCBA/CaJ66MJAX
185R4539EGDPCZECHII/EiJ66FJAX
186R4540EGDPCZECHII/EiJ66MJAX
187R2600E.1GDP BXDD2B6F172FUTHSC RW
188R2604E.1GDP BXDD2B6F169MUTHSC RW
189R1002E.3GDP BXDDBA/2J72FUTHSC RW
190R4541EGDP BXDDBA/2J65FJAX
191R959E.3GDP BXDDBA/2J60MUTHSC RW
192R2572E.1GDP BXDDBA/2J65MUTHSC RW
193R4542EGDP BXDDBA/2J59MJAX
194R2771E.3GDPFVB/NJ60FBIDMC GR
195R2772E.3GDPFVB/NJ60MBIDMC GR
196R2636E.1GDPKK/HlJ64FUTHSC RW
197R2637E.1GDPKK/HlJ64MUTHSC RW
198R0999E.1GDPLG/J57FUTHSC RW
199R1004E.1GDPLG/J65MUTHSC RW
200R4543EGDPLP/J65FJAX
201R4544EGDPLP/J65MJAX
202R2858E.3GDPMOLF/EiJ60FBIDMC GR
203R2919.3GDPMOLF/EiJ60MBIDMC GR
204R1688E.1GDPNOD/LtJ66FJAX
205R2566E-2.1GDPNOD/LtJ76MUTHSC RW
206R4545EGDPNZB/BlNJ61FBIDMC GR
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