From e34e7da50fc0ff5ed41e8bdaf2b1d41c9e9cf534 Mon Sep 17 00:00:00 2001 From: Bonface Date: Thu, 15 Feb 2024 06:09:54 -0600 Subject: Update dataset RTF Files. --- .../Hipp_Illumina_Rank_1006/acknowledgment.rtf | 8 - general/datasets/Hipp_Illumina_Rank_1006/cases.rtf | 5 - .../Hipp_Illumina_Rank_1006/experiment-design.rtf | 2123 -------------------- general/datasets/Hipp_Illumina_Rank_1006/notes.rtf | 1 - .../datasets/Hipp_Illumina_Rank_1006/platform.rtf | 9 - .../Hipp_Illumina_Rank_1006/processing.rtf | 13 - .../datasets/Hipp_Illumina_Rank_1006/summary.rtf | 14 - .../datasets/Hipp_Illumina_Rank_1006/tissue.rtf | 7 - 8 files changed, 2180 deletions(-) delete mode 100644 general/datasets/Hipp_Illumina_Rank_1006/acknowledgment.rtf delete mode 100644 general/datasets/Hipp_Illumina_Rank_1006/cases.rtf delete mode 100644 general/datasets/Hipp_Illumina_Rank_1006/experiment-design.rtf delete mode 100644 general/datasets/Hipp_Illumina_Rank_1006/notes.rtf delete mode 100644 general/datasets/Hipp_Illumina_Rank_1006/platform.rtf delete mode 100644 general/datasets/Hipp_Illumina_Rank_1006/processing.rtf delete mode 100644 general/datasets/Hipp_Illumina_Rank_1006/summary.rtf delete mode 100644 general/datasets/Hipp_Illumina_Rank_1006/tissue.rtf (limited to 'general/datasets/Hipp_Illumina_Rank_1006') diff --git a/general/datasets/Hipp_Illumina_Rank_1006/acknowledgment.rtf b/general/datasets/Hipp_Illumina_Rank_1006/acknowledgment.rtf deleted file mode 100644 index 959532f..0000000 --- a/general/datasets/Hipp_Illumina_Rank_1006/acknowledgment.rtf +++ /dev/null @@ -1,8 +0,0 @@ -
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Data were generated with funds to Lu Lu, Beth Bennett, Mike Miles, Melloni Cook from INIA.

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The LXS genetic reference panel of recombinant inbred strains consists of just over 77 strains. All of these strains have been inbred for more than 23 generations (F23). All strains have been genotyped at 13,377 SNPs. Thanks to the efforts of Dr. Timothy Wiltshire at the Genome Institute of the Novartis Research Foundation, the two parental strains have been genotyped at 156,551 SNPs. These genotypes are incorporated in the GeneNetwork SNP Browser.

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Strains are currently available from Drs. Beth Bennett and Tom Johnson at the Institute of Behavioral Genetics (IBG) in Boulder Colorado.

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diff --git a/general/datasets/Hipp_Illumina_Rank_1006/experiment-design.rtf b/general/datasets/Hipp_Illumina_Rank_1006/experiment-design.rtf deleted file mode 100644 index da9d781..0000000 --- a/general/datasets/Hipp_Illumina_Rank_1006/experiment-design.rtf +++ /dev/null @@ -1,2123 +0,0 @@ -
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Sample Processing: Samples were processed by Lu Lu and colleagues in the Illumina Core at UTHSC between July 25 and Dec 20, 2006. All processing steps were performed by Feng Jiao. 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 (1-3% failed and new RNA samples had to be acquired and processed) were immediately used on the original Mouse-6 v 1.0 slide. 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 each strain. While all strains were orginally represented by matched male and female samples, one strain LXS34 consists of two female samples. Given the expression of Xist, we suspect that strain LXS114 is represented by two male pools (see figure at bottom of page).

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Experimental Design and Batch Structure: This data set consists arrays processed in 13 groups over a five month period (July 2006 to Dec 2006). Most groups consisted of 12 samples. All arrays in this data set were processed using a single protocol by a single operator, Feng Yiao. Processing was supervised directly by Dr. Lu Lu. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between July 28 and Dec 21, 2006. Details on sample assignment to slides and batches is provide in the table below.

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This table lists all arrays by order of strain (index) and includes data on tube ID, strain, age, sex, F generation number, number of animals in each sample pool (pool size), slide ID, slide position (A through F), scan date, and scan batch.
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indextube IDstrainagesexgener-
- ation		pool
- size		slide
- ID		slide
- position		batch
- by slide		scan
- batch
1R2851H2ILS77F>10041523516003B11
2R0595H2ILS71F>10021523516030B42
3R2874H2ILS78M>10041523516011B21
4R0585H2ILS65M>10021523516028A32
5R3281H1ILSXISSF190FNA31562224029A2813
6R2857H2ISS75F>10041523516011A21
7R0589H2ISS73F>10021523516028B32
8R2955H2ISS53M>10031523516003A11
9R0578H2ISS67M>10021523516030A42
10R3282H1ISSXILSF197MNA31562224029B2813
11R2013H2LXS1084F2721562224049E189
12R1993H2LXS1078M2721562224036E179
13R1997H2LXS10070F2521562224049A189
14R1983H2LXS10077M2521562224047F168
15R2083H2LXS10185F2821562224050B199
16R2084H2LXS10185M2821562224050C199
17R2186H2LXS10273F2921523516001C95
18R2187H2LXS10273M2921562224053C2010
19R2809H2LXS10372F2621562224034C2311
20R2854H1LXS10369M2621523516006D63
21R2735H2LXS10778F2621523516028D32
22R2738H2LXS10778M2621562224054C2110
23R2840H2LXS11067F2521562224037D2411
24R2157H2LXS11075M2721523516033E84
25R2172H2LXS11272F2721523516001B95
26R2841H2LXS11284M2721562224042D2712
27R2188H2LXS11472F2821562224053D2010
28R2204H2LXS11472M2821523516001D95
29R2168H2LXS11580F2721523516001A95
30R2085H2LXS11571M2721562224050D199
31R2811H2LXS11772F2821562224034D2311
32R2212H2LXS11774M2721523516001E95
33R1992H2LXS12286F2621562224036D179
34R2219H2LXS12272M2621562224054A2110
35R2876H2LXS12387F2821562224038C2511
36R2832H1LXS12377M2721523516011E21
37R2872H1LXS12483F2821523516006E63
38R2871H2LXS12485M2821562224042F2712
39R1909H2LXS1379F2521523516024D137
40R1901H2LXS1381M2621562224041D2612
41R2023H2LXS1486F2521562224050A199
42R1612H2LXS1485M2621523516015A105
43R1936H2LXS1681F2521523516024E137
44R1912H2LXS1681M2521523516033B84
45R1961H2LXS1966F2621523516029F147
46R1904H2LXS1966M2621523516024B137
47R1883H2LXS271F2721523516009F126
48R2753H2LXS274M2821523516030E42
49R1729H2LXS2272F2721523516032E74
50R2743H2LXS2279M2721562224054D2110
51R1966H2LXS2373F2621562224032D158
52R1971H2LXS2373M2621562224047A168
53R2795H2LXS2474F2621523516003C11
54R1755H2LXS2456M2521523516007A116
55R1986H2LXS2575F2721562224036A179
56R2006H2LXS2575M2721562224049C189
57R2014H2LXS2682F2521562224049F189
58R2009H2LXS2682M2621562224049D189
59R2824H1LXS2867F2821562224042A2712
60R1753H1LXS2872M2721562224041F2612
61R2765H2LXS363F2721523516005B53
62R1898H2LXS381M2621562224041C2612
63R2764H2LXS3173F2921562224060C2210
64R1908H2LXS3180M2821523516024C137
65R2758H2LXS3270F2621523516030F42
66R1743H1LXS3267M2521562224041E2612
67R2794H2LXS3475F2721562224034B2311
68R2870H2LXS3478F2721562224029C2813
69R2746H2LXS3580F2221523516030C42
70R2747H2LXS3581M2221562224060A2210
71R1968H2LXS3676F2521562224032E158
72R1640H2LXS3676M2521523516032C74
73R2835H1LXS3867F2721523516011F21
74R2842H2LXS3867M2721562224042E2712
75R2210H2LXS3981F2821562224053E2010
76R2736H2LXS3975M2721523516028E32
77R1978H2LXS4178F2621562224047C168
78R1783H2LXS4156M2621523516007D116
79R2822H2LXS4266F2721562224034F2311
80R2769H2LXS4270M2721562224042B2712
81R1974H2LXS4384F2621562224047B168
82R1733H2LXS4372M2621523516015C105
83R1756H2LXS4656F2521523516007B116
84R1727H2LXS4670M2521523516032D74
85R1970H2LXS4872F2721562224032F158
86R1981H2LXS4872M2721562224042C2712
87R1957H2LXS4972F2521523516029C147
88R2259H2LXS4972M2521523516028C32
89R2836H1LXS568F2821523516006A63
90R2213H2LXS580M2721562224053F2010
91R2791H2LXS5068F2721562224034A2311
92R1789H2LXS5057M2621523516033A84
93R1740H2LXS5168F2721523516032F74
94R1734H2LXS5168M2621523516015D105
95R2786H2LXS5261F2721562224060D2210
96R2768H2LXS5261M2721523516005C53
97R2154H2LXS5470F2721523516033D84
98R2155H2LXS5470M2721562224053A2010
99R1821H2LXS5577F2521523516009C126
100R1951H2LXS5574M2621523516024F137
101R2789H2LXS5671F2521523516005F53
102R2788H2LXS5671M2521562224060F2210
103R2787H2LXS5966F2921562224060E2210
104R2785H2LXS5962M2921523516005E53
105R1791H2LXS6058F2721562224038D2511
106R1792H2LXS6064M2721523516007E116
107R1796H2LXS6258F2721523516007F116
108R1797H2LXS6258M2721562224038E2511
109R2220H2LXS6471F2821523516001F95
110R2221H2LXS6471M2821562224054B2110
111R1989H2LXS6673F2621562224036B179
112R1843H2LXS6678M2721523516009E126
113R2820H2LXS6867F2921523516003E11
114R2819H2LXS6867M2921562224034E2311
115R1963H2LXS778F2821562224032B158
116R1964H2LXS778M2821562224032C158
117R2166H2LXS7072F2721523516033F84
118R2745H2LXS7071M2821562224054F2110
119R2848H2LXS7272F2721562224038A2511
120R1902H2LXS7266M2721523516024A137
121R2750H2LXS7381F2521523516030D42
122R1835H2LXS7390M2421523516009D126
123R1979H2LXS7559F2721562224047D168
124R2826H2LXS7572M2721523516003F11
125R2142H2LXS7677F2621562224050E199
126R1884H2LXS7685M2621562224041A2612
127R1959H2LXS7869F2621523516029E147
128R1958H2LXS7869M2621523516029D147
129R2845H1LXS870F2821523516006C63
130R2156H2LXS876M2721562224053B2010
131R1955H2LXS8071F2521523516029A147
132R1956H2LXS8071M2521523516029B147
133R2830H1LXS8466F2621523516011D21
134R2829H2LXS8466M2621562224037A2411
135R2839H2LXS8668F2721562224037C2411
136R2838H1LXS8668M2721523516006B63
137R2882H1LXS8766F2721523516006F63
138R2744H2LXS8771M2621562224054E2110
139R2831H2LXS8869F2721562224037B2411
140R2762H2LXS8871M2721523516005A53
141R2828H1LXS8975F2621523516011C21
142R1962H2LXS8973M2521562224032A158
143R1746H2LXS966F2621523516015F105
144R2801H2LXS968M2721523516003D11
145R1812H2LXS9061F2521562224038F2511
146R1813H2LXS9061M2521523516009A126
147R1736H2LXS9266F2321523516015E105
148R1609H2LXS9287M2321523516032A74
149R1624H2LXS9374F2621523516032B74
150R1815H2LXS9361M2621523516009B126
151R1991H2LXS9470F2521562224036C179
152R2002H2LXS9470M2521562224049B189
153R1996H2LXS9675F2321562224036F179
154R1772H2LXS9663M2321523516007C116
155R2759H2LXS9773F2621562224060B2210
156R2739H2LXS9779M2621523516028F32
157R2149H2LXS9878F2621523516033C84
158R1888H2LXS9876M2621562224041B2612
159R1644H2LXS9979F2621523516015B105
160R2145H2LXS9977M2721562224050F199
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diff --git a/general/datasets/Hipp_Illumina_Rank_1006/notes.rtf b/general/datasets/Hipp_Illumina_Rank_1006/notes.rtf deleted file mode 100644 index 4ae3a03..0000000 --- a/general/datasets/Hipp_Illumina_Rank_1006/notes.rtf +++ /dev/null @@ -1 +0,0 @@ -

Data uploaded by Hongqiang Li, Oct 30, 2006. This text file originally generated by LL and RWW on November 29, 2006. Updated by LL, Dec 1, 2006. Updated March 25, April 25 by RWW.

diff --git a/general/datasets/Hipp_Illumina_Rank_1006/platform.rtf b/general/datasets/Hipp_Illumina_Rank_1006/platform.rtf deleted file mode 100644 index cb0e31f..0000000 --- a/general/datasets/Hipp_Illumina_Rank_1006/platform.rtf +++ /dev/null @@ -1,9 +0,0 @@ -
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Illumina Sentrix Mouse-6 BeadArray Platform: The Mouse6 array consists of 46,116 unique probe sequences, each 50 nucleotides in length, that have been arrayed on glass slides using a novel bead technology.

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Dunning M, Smith M, Thorne N, Tavare S (2006) beadarray: An R package to analyse Illumina BeadArrays. R News (the Newsletter of the P Project) 6:17-23. (see pages 17-23 of http://CRAN.R-project.org/doc/Rnews/Rnews_2006-5.pdf).

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ANNOTATION: In spring of 2007, Robert W. Williams and Hongqiang Li reannotated the Illumina Mouse-6 array content. This new annotation is now incorporated into GeneNetwork. For 46166 probes on the Mouse 6 array platform (including control probes) we have identified 35975 NCBI Entrez Gene IDs; 26481 matched human Gene IDs; 23899 matched rat Gene IDs; 26883 NCBI HomoloGene IDs; and 12791 OMIM IDs.

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Position data for the 50-mer Illumina Mouse-6 array were initially downloaded from Sanger at http://www.sanger.ac.uk/Users/avc/Illumina/Mouse-6_V1.gff.gz but we then updated all positions by BLAT analysis from mm6 positions to mm8 positions (Hongqiang Li).

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diff --git a/general/datasets/Hipp_Illumina_Rank_1006/processing.rtf b/general/datasets/Hipp_Illumina_Rank_1006/processing.rtf deleted file mode 100644 index 678856e..0000000 --- a/general/datasets/Hipp_Illumina_Rank_1006/processing.rtf +++ /dev/null @@ -1,13 +0,0 @@ -
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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 Dr. Lu Lu if you have any questions on the use of these open data.

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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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Sex of the samples was validated using sex-specific probe set: Xist (probe ILM106520068, also known as scl00213742.1_141-S).

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Legend: Checking that the sex of samples was labeled correctly in mouse array data sets using Xist expression measured by probe ILM106520068. In this bar chart the expression of Xist is very low in LXS114 and has a low error term. This is because both arrays are male samples rather than 1 male and 1 female sample. In contrast LXS34 has very high expression and no error bar because the sample is from a single female pool.

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diff --git a/general/datasets/Hipp_Illumina_Rank_1006/summary.rtf b/general/datasets/Hipp_Illumina_Rank_1006/summary.rtf deleted file mode 100644 index 357e642..0000000 --- a/general/datasets/Hipp_Illumina_Rank_1006/summary.rtf +++ /dev/null @@ -1,14 +0,0 @@ -
ILLUMINA Mouse-6 DATA SET: The LXS Hippocampus Illumina Rank Invariant data set provides estimates of mRNA expression in the hippocampus of 75 LXS recombinant inbred strains, the two parental strains and ILS/Ibg and ISS/Ibg (Inbred Long Sleep and Inbred Short Sleep strains from the Institute of Behavioral Genetics).All samples are from normal adult control animals raised in a standard laboratory environment. Subsequent data sets will provide estimates of mRNA expression following restraint stress, ethanol treatment, and stress followed by ethanol using many of the same strains (Lu Lu and colleagues). - -

A total of 240 pooled hippocampal samples were processed using 40 Illumina Sentrix Mouse-6 v 1.0 oligomer microarray (GEO GPL6099) BeadArray slides. Twenty-seven Mouse-6 slides and a total of 160 samples passed stringent quality control and error checking. We should note that this is our first experience using the Illumina platform and the initial set of 13 slides were are not included. This particular data set was processed using the Illumina "Rank Invariant" protocol. Values were log2 transformed and the current data range from 6.141 average (very low or no expression) to 19.987 (extremely high).

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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 (LRS > 46). In this initial data set, 1170 probes have LRS values >46. The maximum LRS achieved in this data set is 358.8 for probe ILM103520706 (Disabled 1; Dab1).

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Legend: Bar chart of the expression of Dab1 probe ILM103520706 in the LXS data set. This probe has a Mendelian segregation pattern and is associated with a LOD score of 77.7 (LRS 358.8). The two parental strains are shown to the far left, followed by all of the LXS strains for which we have acquired mRNA expression estimates in the hippocampus.

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ABOUT THE HIPPOCAMPUS. The hippocampus is an important and intriguing part of the forebrain that is crucial in memory formation and retrieval. This region of the brain is particularly vulnerable to the effects of environmental stressors and is a key upstream modulator of the hypothalamic-pituitary-adrenal axis (the HPA). The hippocampus is also often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3) is a joint effort of 14 investigators supported by numerous agencies described in the Acknowledgments section.

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diff --git a/general/datasets/Hipp_Illumina_Rank_1006/tissue.rtf b/general/datasets/Hipp_Illumina_Rank_1006/tissue.rtf deleted file mode 100644 index 04565fc..0000000 --- a/general/datasets/Hipp_Illumina_Rank_1006/tissue.rtf +++ /dev/null @@ -1,7 +0,0 @@ -
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All animals were raised at the IBG by Bennett and colleagues in an SPF facility. No cases were MHV positive. Mice were killed by cervical dislocation. Whole brain dissections were performed at the IBG by Bennett and colleagues and shipped in RNAlater to Lu Lu and colleagues at UTHSC. Most hippocampal dissections (all were bilateral) were performed by Zhiping Jia. Cerebella, olfactory bulbs, and brain stems were also dissected and stored at -80 deg C using further use. Hippocampal samples are very close to complete (see Lu et al., 2001 but probably include variable amounts of fimbria and choroid plexus (see expression of transthyretin, Ttr, as a marker of choroid plexus).

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A pool of dissected tissue from four hippocampi taken from two naive adults of the same strain, sex, and age was collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at UTHSC by Zhiping Jia.

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All animals used in this study were between 53 and 90 days of age (average of 72 days; see Table 1 below).

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