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. --- .../Eye_AXBXA_1008_RankInv/acknowledgment.rtf | 11 + general/datasets/Eye_AXBXA_1008_RankInv/cases.rtf | 1 + .../datasets/Eye_AXBXA_1008_RankInv/platform.rtf | 7 + .../datasets/Eye_AXBXA_1008_RankInv/processing.rtf | 5 + .../datasets/Eye_AXBXA_1008_RankInv/specifics.rtf | 1 + .../datasets/Eye_AXBXA_1008_RankInv/summary.rtf | 769 +++++++++++++++++++++ 6 files changed, 794 insertions(+) create mode 100644 general/datasets/Eye_AXBXA_1008_RankInv/acknowledgment.rtf create mode 100644 general/datasets/Eye_AXBXA_1008_RankInv/cases.rtf create mode 100644 general/datasets/Eye_AXBXA_1008_RankInv/platform.rtf create mode 100644 general/datasets/Eye_AXBXA_1008_RankInv/processing.rtf create mode 100644 general/datasets/Eye_AXBXA_1008_RankInv/specifics.rtf create mode 100644 general/datasets/Eye_AXBXA_1008_RankInv/summary.rtf (limited to 'general/datasets/Eye_AXBXA_1008_RankInv') diff --git a/general/datasets/Eye_AXBXA_1008_RankInv/acknowledgment.rtf b/general/datasets/Eye_AXBXA_1008_RankInv/acknowledgment.rtf new file mode 100644 index 0000000..5cbb536 --- /dev/null +++ b/general/datasets/Eye_AXBXA_1008_RankInv/acknowledgment.rtf @@ -0,0 +1,11 @@ +
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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).

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    About this text file:

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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.

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diff --git a/general/datasets/Eye_AXBXA_1008_RankInv/cases.rtf b/general/datasets/Eye_AXBXA_1008_RankInv/cases.rtf new file mode 100644 index 0000000..864f3b6 --- /dev/null +++ b/general/datasets/Eye_AXBXA_1008_RankInv/cases.rtf @@ -0,0 +1 @@ +

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).

diff --git a/general/datasets/Eye_AXBXA_1008_RankInv/platform.rtf b/general/datasets/Eye_AXBXA_1008_RankInv/platform.rtf new file mode 100644 index 0000000..23268bc --- /dev/null +++ b/general/datasets/Eye_AXBXA_1008_RankInv/platform.rtf @@ -0,0 +1,7 @@ +
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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.

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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)".

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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.

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diff --git a/general/datasets/Eye_AXBXA_1008_RankInv/processing.rtf b/general/datasets/Eye_AXBXA_1008_RankInv/processing.rtf new file mode 100644 index 0000000..7d79970 --- /dev/null +++ b/general/datasets/Eye_AXBXA_1008_RankInv/processing.rtf @@ -0,0 +1,5 @@ +
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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.

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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.

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diff --git a/general/datasets/Eye_AXBXA_1008_RankInv/specifics.rtf b/general/datasets/Eye_AXBXA_1008_RankInv/specifics.rtf new file mode 100644 index 0000000..0cf2818 --- /dev/null +++ b/general/datasets/Eye_AXBXA_1008_RankInv/specifics.rtf @@ -0,0 +1 @@ +AXB/BXA \ No newline at end of file diff --git a/general/datasets/Eye_AXBXA_1008_RankInv/summary.rtf b/general/datasets/Eye_AXBXA_1008_RankInv/summary.rtf new file mode 100644 index 0000000..0bf1369 --- /dev/null +++ b/general/datasets/Eye_AXBXA_1008_RankInv/summary.rtf @@ -0,0 +1,769 @@ +
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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).

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

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

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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.

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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).

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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.

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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).

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

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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.

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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.

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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.

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    Data Table 1:

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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.

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IndexTube IDStrainAgeSexPool sizeSlide IdSlide PositionBatch IdSource
1R4893E1A/J59F04252491010A1JAX
2R4982E1A/J79M24252491006A1JAX
3R4894E1A/J59M04252491011A1JAX
4R3655E1A/J86M04252491031A2JAX
5R4897E1AXB190F04252491005C1JAX
6R5005E1AXB156M04252491008A1JAX
7R5001E1AXB1063F24252491008B1JAX
8R5002E1AXB1063M24252491021B1JAX
9R4891E1AXB1263F04252491009A1JAX
10R4999E1AXB1257M24252491005D1JAX
11R5000E1AXB1357M24252491008C1JAX
12R5003E1AXB1563F24252491005E1JAX
13R4963E1AXB1563M24252491031B1JAX
14R3661E1AXB1989F04252491008D1JAX
15R4962E1AXB1962M04252491005F1JAX
16R4975E1AXB279F24252491006C1JAX
17R4976E1AXB279M24252491021C1JAX
18R4973E1AXB2366F24252491009E1JAX
19R4972E1AXB2366M24252491006D1JAX
20R4959E1AXB24100F24252491006E1JAX
21R4960E1AXB24100M24252491019A1JAX
22R4994E1AXB454F24252491031C1JAX
23R5007E1AXB454M24252491006F1JAX
24R4995E1AXB561F24252491021F1JAX
25R4996E1AXB561M24252491009F1JAX
26R4997E1AXB660F24252491010C1JAX
27R4998E1AXB660M24252491021D1JAX
28R4958E1AXB852F24252491019D1JAX
29R4957E1AXB852M24252491010D1JAX
30R4991E1BXA154F24252491010E1JAX
31R4990E1BXA154M24252491009B1JAX
32R4980E1BXA1152F04252491020A1JAX
33R5006E1BXA1248F24252491011C2JAX
34R4993E1BXA1248M24252491031D1JAX
35R4968E1BXA1361F24252491011D1JAX
36R4969E1BXA1361M24252491008E1JAX
37R4966E1BXA1456F24252491031E1JAX
38R4967E1BXA1456M24252491011E1JAX
39R4970E1BXA1651F24252491011F1JAX
40R5004E1BXA1651M24252491031F1JAX
41R4981E1BXA250F24252491008F1JAX
42R4965E1BXA254M04252491020B1JAX
43R4984E1BXA2454F24252491021E1JAX
44R4974E1BXA2454M24252491019C1JAX
45R4988E1BXA2570M04252491020F1JAX
46R4964E1BXA2654F04252491019B1JAX
47R3636E1BXA2687M04252491009D1JAX
48R4977E1BXA465F04252491020C1JAX
49R3638E1BXA487M04252491019E1JAX
50R4978E1BXA765F24252491019F1JAX
51R4979E1BXA765M24252491021A1JAX
52R5008E1BXA852F24252491020E1JAX
53R4983E1BXA852M24252491020D1JAX
54R5012E1C57BL/6J87F24252491006B1UTHSC RW
55R5010E1C57BL/6J87F24252491011B1UTHSC RW
56R5011E1C57BL/6J79M24252491005B1UTHSC RW
57R5009E1C57BL/6J79M24252491010B1UTHSC RW
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    Downloading all data:

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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.

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    About data processing:

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

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