Hippocampus Illumina NON (Oct08) RankInv beta**

From d0911a04958a04042da02a334ccc528dae79cc17 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 27 Mar 2015 20:28:51 +0000 Subject: Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files' --- web/dbdoc/Illum_LXS_Hipp_NON_1008.html | 480 --------------------------------- 1 file changed, 480 deletions(-) delete mode 100755 web/dbdoc/Illum_LXS_Hipp_NON_1008.html (limited to 'web/dbdoc/Illum_LXS_Hipp_NON_1008.html') diff --git a/web/dbdoc/Illum_LXS_Hipp_NON_1008.html b/web/dbdoc/Illum_LXS_Hipp_NON_1008.html deleted file mode 100755 index 1b341fe9..00000000 --- a/web/dbdoc/Illum_LXS_Hipp_NON_1008.html +++ /dev/null @@ -1,480 +0,0 @@ - -Hippocampus Illumina NON (Oct08) RankInv beta** - - - - - - - - - - - - - - - - - - - - - - - -

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Hippocampus Illumina NON (Oct08) RankInv beta** -

Accession number: GN219

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This is control expression data (No restraint and No injections, NON) for the four companion experimental data sets: No restraint and saline injection (NOS), No restraint and ethanol injection (NOE), Restraint stress and saline injection (RSS), and Restrain stress and ethanol injection (RSE). - -

This data set is a subset of the much larger Hippocampus Illumina (May07) RankInv data set. The subset was selected by Lu Lu to match the set of strains in the NOS, NOE, RSS, and RSE data sets. The NON subset uses the original Mouse 6.0 array and some probe sequences differ from the Mouse 6.1 array used for the experimental treatments. - -

WRONG ARRAY platform ID: This data set uses the ORGINAL Illumina Mouse 6.0 array. - - - -

Summary:

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-May 07 ILLUMINA Mouse-6 DATA SET Rank Invariant 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, ILS/Ibg and ISS/Ibg (Inbred Long Sleep and Inbred Short Sleep strains from the Institute of Behavioral Genetics), and the two reciprocal F1 strains (ILSXISSF1, ISSXILSF1). 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 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). - -
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 Hippocampus Illumina (May 07) RankInv data set, 1183 probes have LRS values >46. - -
In comparison, here are the yields of QTLs with LOD>10 for other closely related data sets: - -
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NO DATA for Hippocampus Illumina (Aug07) RSN -
NO DATA for Hippocampus Illumina (Aug07) RSN_NB -
1050 for Hippocampus Illumina (Aug07) LOESS -
1162 for Hippocampus Illumina (Aug07) LOESS_NB -
1129 for Hippocampus Illumina (Aug07) QUANT -
1176 for Hippocampus Illumina (Aug07) QUANT_NB -
1183 for Hippocampus Illumina (May 07) RankInv (THIS DATA SET) -
1167 for Hippocampus Illumina (Oct06) Rank -
1170 for Hippocampus Illumina (Oct06) RankInv -
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The LRS achieved in the different version of the LXS Hippocampus data for probe ILM103520706 (Disabled 1; Dab1) are as follows: - -
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374.8 for Hippocampus Illumina (Aug07) RSN -
363.0 for Hippocampus Illumina (Aug07) RSN_NB -
338.4 for Hippocampus Illumina (Aug07) LOESS -
339.8 for Hippocampus Illumina (Aug07) LOESS_NB -
370.2 for Hippocampus Illumina (Aug07) QUANT -
363.5 for Hippocampus Illumina (Aug07) QUANT_NB -
360.3 for Hippocampus Illumina (May 07) RankInv -
358.1 for Hippocampus Illumina (Oct06) Rank -
358.8 for Hippocampus Illumina (Oct06) RankInv -
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Legend: UPDATE FIGURE: 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 an LRS 360.3 in this May07 RankInv data set vs 358.8 for the previous Oct06 data set.
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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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- -About the strains used to generate this set of data:

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

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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). - -
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. - -
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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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. - -
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). - - -
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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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, 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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index	tube ID	strain	age	sex	gener- ation	pool size	slide ID	slide position	batch by slide	scan batch
1	R2851H2	ILS	77	F	>100	4	1523516003	B	1	1
2	R0595H2	ILS	71	F	>100	2	1523516030	B	4	2
3	R2874H2	ILS	78	M	>100	4	1523516011	B	2	1
4	R0585H2	ILS	65	M	>100	2	1523516028	A	3	2
5	R3281H1	ILSXISSF1	90	F	NA	3	1562224029	A	28	13
6	R2857H2	ISS	75	F	>100	4	1523516011	A	2	1
7	R0589H2	ISS	73	F	>100	2	1523516028	B	3	2
8	R2955H2	ISS	53	M	>100	3	1523516003	A	1	1
9	R0578H2	ISS	67	M	>100	2	1523516030	A	4	2
10	R3282H1	ISSXILSF1	97	M	NA	3	1562224029	B	28	13
11	R2013H2	LXS10	84	F	27	2	1562224049	E	18	9
12	R1993H2	LXS10	78	M	27	2	1562224036	E	17	9
13	R1997H2	LXS100	70	F	25	2	1562224049	A	18	9
14	R1983H2	LXS100	77	M	25	2	1562224047	F	16	8
15	R2083H2	LXS101	85	F	28	2	1562224050	B	19	9
16	R2084H2	LXS101	85	M	28	2	1562224050	C	19	9
17	R2186H2	LXS102	73	F	29	2	1523516001	C	9	5
18	R2187H2	LXS102	73	M	29	2	1562224053	C	20	10
19	R2809H2	LXS103	72	F	26	2	1562224034	C	23	11
20	R2854H1	LXS103	69	M	26	2	1523516006	D	6	3
21	R2735H2	LXS107	78	F	26	2	1523516028	D	3	2
22	R2738H2	LXS107	78	M	26	2	1562224054	C	21	10
23	R2840H2	LXS110	67	F	25	2	1562224037	D	24	11
24	R2157H2	LXS110	75	M	27	2	1523516033	E	8	4
25	R2172H2	LXS112	72	F	27	2	1523516001	B	9	5
26	R2841H2	LXS112	84	M	27	2	1562224042	D	27	12
27	R2188H2	LXS114	72	F	28	2	1562224053	D	20	10
28	R2204H2	LXS114	72	M	28	2	1523516001	D	9	5
29	R2168H2	LXS115	80	F	27	2	1523516001	A	9	5
30	R2085H2	LXS115	71	M	27	2	1562224050	D	19	9
31	R2811H2	LXS117	72	F	28	2	1562224034	D	23	11
32	R2212H2	LXS117	74	M	27	2	1523516001	E	9	5
33	R1992H2	LXS122	86	F	26	2	1562224036	D	17	9
34	R2219H2	LXS122	72	M	26	2	1562224054	A	21	10
35	R2876H2	LXS123	87	F	28	2	1562224038	C	25	11
36	R2832H1	LXS123	77	M	27	2	1523516011	E	2	1
37	R2872H1	LXS124	83	F	28	2	1523516006	E	6	3
38	R2871H2	LXS124	85	M	28	2	1562224042	F	27	12
39	R1909H2	LXS13	79	F	25	2	1523516024	D	13	7
40	R1901H2	LXS13	81	M	26	2	1562224041	D	26	12
41	R2023H2	LXS14	86	F	25	2	1562224050	A	19	9
42	R1612H2	LXS14	85	M	26	2	1523516015	A	10	5
43	R1936H2	LXS16	81	F	25	2	1523516024	E	13	7
44	R1912H2	LXS16	81	M	25	2	1523516033	B	8	4
45	R1961H2	LXS19	66	F	26	2	1523516029	F	14	7
46	R1904H2	LXS19	66	M	26	2	1523516024	B	13	7
47	R1883H2	LXS2	71	F	27	2	1523516009	F	12	6
48	R2753H2	LXS2	74	M	28	2	1523516030	E	4	2
49	R1729H2	LXS22	72	F	27	2	1523516032	E	7	4
50	R2743H2	LXS22	79	M	27	2	1562224054	D	21	10
51	R1966H2	LXS23	73	F	26	2	1562224032	D	15	8
52	R1971H2	LXS23	73	M	26	2	1562224047	A	16	8
53	R2795H2	LXS24	74	F	26	2	1523516003	C	1	1
54	R1755H2	LXS24	56	M	25	2	1523516007	A	11	6
55	R1986H2	LXS25	75	F	27	2	1562224036	A	17	9
56	R2006H2	LXS25	75	M	27	2	1562224049	C	18	9
57	R2014H2	LXS26	82	F	25	2	1562224049	F	18	9
58	R2009H2	LXS26	82	M	26	2	1562224049	D	18	9
59	R2824H1	LXS28	67	F	28	2	1562224042	A	27	12
60	R1753H1	LXS28	72	M	27	2	1562224041	F	26	12
61	R2765H2	LXS3	63	F	27	2	1523516005	B	5	3
62	R1898H2	LXS3	81	M	26	2	1562224041	C	26	12
63	R2764H2	LXS31	73	F	29	2	1562224060	C	22	10
64	R1908H2	LXS31	80	M	28	2	1523516024	C	13	7
65	R2758H2	LXS32	70	F	26	2	1523516030	F	4	2
66	R1743H1	LXS32	67	M	25	2	1562224041	E	26	12
67	R2794H2	LXS34	75	F	27	2	1562224034	B	23	11
68	R2870H2	LXS34	78	F	27	2	1562224029	C	28	13
69	R2746H2	LXS35	80	F	22	2	1523516030	C	4	2
70	R2747H2	LXS35	81	M	22	2	1562224060	A	22	10
71	R1968H2	LXS36	76	F	25	2	1562224032	E	15	8
72	R1640H2	LXS36	76	M	25	2	1523516032	C	7	4
73	R2835H1	LXS38	67	F	27	2	1523516011	F	2	1
74	R2842H2	LXS38	67	M	27	2	1562224042	E	27	12
75	R2210H2	LXS39	81	F	28	2	1562224053	E	20	10
76	R2736H2	LXS39	75	M	27	2	1523516028	E	3	2
77	R1978H2	LXS41	78	F	26	2	1562224047	C	16	8
78	R1783H2	LXS41	56	M	26	2	1523516007	D	11	6
79	R2822H2	LXS42	66	F	27	2	1562224034	F	23	11
80	R2769H2	LXS42	70	M	27	2	1562224042	B	27	12
81	R1974H2	LXS43	84	F	26	2	1562224047	B	16	8
82	R1733H2	LXS43	72	M	26	2	1523516015	C	10	5
83	R1756H2	LXS46	56	F	25	2	1523516007	B	11	6
84	R1727H2	LXS46	70	M	25	2	1523516032	D	7	4
85	R1970H2	LXS48	72	F	27	2	1562224032	F	15	8
86	R1981H2	LXS48	72	M	27	2	1562224042	C	27	12
87	R1957H2	LXS49	72	F	25	2	1523516029	C	14	7
88	R2259H2	LXS49	72	M	25	2	1523516028	C	3	2
89	R2836H1	LXS5	68	F	28	2	1523516006	A	6	3
90	R2213H2	LXS5	80	M	27	2	1562224053	F	20	10
91	R2791H2	LXS50	68	F	27	2	1562224034	A	23	11
92	R1789H2	LXS50	57	M	26	2	1523516033	A	8	4
93	R1740H2	LXS51	68	F	27	2	1523516032	F	7	4
94	R1734H2	LXS51	68	M	26	2	1523516015	D	10	5
95	R2786H2	LXS52	61	F	27	2	1562224060	D	22	10
96	R2768H2	LXS52	61	M	27	2	1523516005	C	5	3
97	R2154H2	LXS54	70	F	27	2	1523516033	D	8	4
98	R2155H2	LXS54	70	M	27	2	1562224053	A	20	10
99	R1821H2	LXS55	77	F	25	2	1523516009	C	12	6
100	R1951H2	LXS55	74	M	26	2	1523516024	F	13	7
101	R2789H2	LXS56	71	F	25	2	1523516005	F	5	3
102	R2788H2	LXS56	71	M	25	2	1562224060	F	22	10
103	R2787H2	LXS59	66	F	29	2	1562224060	E	22	10
104	R2785H2	LXS59	62	M	29	2	1523516005	E	5	3
105	R1791H2	LXS60	58	F	27	2	1562224038	D	25	11
106	R1792H2	LXS60	64	M	27	2	1523516007	E	11	6
107	R1796H2	LXS62	58	F	27	2	1523516007	F	11	6
108	R1797H2	LXS62	58	M	27	2	1562224038	E	25	11
109	R2220H2	LXS64	71	F	28	2	1523516001	F	9	5
110	R2221H2	LXS64	71	M	28	2	1562224054	B	21	10
111	R1989H2	LXS66	73	F	26	2	1562224036	B	17	9
112	R1843H2	LXS66	78	M	27	2	1523516009	E	12	6
113	R2820H2	LXS68	67	F	29	2	1523516003	E	1	1
114	R2819H2	LXS68	67	M	29	2	1562224034	E	23	11
115	R1963H2	LXS7	78	F	28	2	1562224032	B	15	8
116	R1964H2	LXS7	78	M	28	2	1562224032	C	15	8
117	R2166H2	LXS70	72	F	27	2	1523516033	F	8	4
118	R2745H2	LXS70	71	M	28	2	1562224054	F	21	10
119	R2848H2	LXS72	72	F	27	2	1562224038	A	25	11
120	R1902H2	LXS72	66	M	27	2	1523516024	A	13	7
121	R2750H2	LXS73	81	F	25	2	1523516030	D	4	2
122	R1835H2	LXS73	90	M	24	2	1523516009	D	12	6
123	R1979H2	LXS75	59	F	27	2	1562224047	D	16	8
124	R2826H2	LXS75	72	M	27	2	1523516003	F	1	1
125	R2142H2	LXS76	77	F	26	2	1562224050	E	19	9
126	R1884H2	LXS76	85	M	26	2	1562224041	A	26	12
127	R1959H2	LXS78	69	F	26	2	1523516029	E	14	7
128	R1958H2	LXS78	69	M	26	2	1523516029	D	14	7
129	R2845H1	LXS8	70	F	28	2	1523516006	C	6	3
130	R2156H2	LXS8	76	M	27	2	1562224053	B	20	10
131	R1955H2	LXS80	71	F	25	2	1523516029	A	14	7
132	R1956H2	LXS80	71	M	25	2	1523516029	B	14	7
133	R2830H1	LXS84	66	F	26	2	1523516011	D	2	1
134	R2829H2	LXS84	66	M	26	2	1562224037	A	24	11
135	R2839H2	LXS86	68	F	27	2	1562224037	C	24	11
136	R2838H1	LXS86	68	M	27	2	1523516006	B	6	3
137	R2882H1	LXS87	66	F	27	2	1523516006	F	6	3
138	R2744H2	LXS87	71	M	26	2	1562224054	E	21	10
139	R2831H2	LXS88	69	F	27	2	1562224037	B	24	11
140	R2762H2	LXS88	71	M	27	2	1523516005	A	5	3
141	R2828H1	LXS89	75	F	26	2	1523516011	C	2	1
142	R1962H2	LXS89	73	M	25	2	1562224032	A	15	8
143	R1746H2	LXS9	66	F	26	2	1523516015	F	10	5
144	R2801H2	LXS9	68	M	27	2	1523516003	D	1	1
145	R1812H2	LXS90	61	F	25	2	1562224038	F	25	11
146	R1813H2	LXS90	61	M	25	2	1523516009	A	12	6
147	R1736H2	LXS92	66	F	23	2	1523516015	E	10	5
148	R1609H2	LXS92	87	M	23	2	1523516032	A	7	4
149	R1624H2	LXS93	74	F	26	2	1523516032	B	7	4
150	R1815H2	LXS93	61	M	26	2	1523516009	B	12	6
151	R1991H2	LXS94	70	F	25	2	1562224036	C	17	9
152	R2002H2	LXS94	70	M	25	2	1562224049	B	18	9
153	R1996H2	LXS96	75	F	23	2	1562224036	F	17	9
154	R1772H2	LXS96	63	M	23	2	1523516007	C	11	6
155	R2759H2	LXS97	73	F	26	2	1562224060	B	22	10
156	R2739H2	LXS97	79	M	26	2	1523516028	F	3	2
157	R2149H2	LXS98	78	F	26	2	1523516033	C	8	4
158	R1888H2	LXS98	76	M	26	2	1562224041	B	26	12
159	R1644H2	LXS99	79	F	26	2	1523516015	B	10	5
160	R2145H2	LXS99	77	M	27	2	1562224050	F	19	9

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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 Dr. Lu Lu if you have any questions on the use of these open data.
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About the array platform:

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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. - -
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). - -
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. - -
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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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. - -
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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Data source acknowledgment:

Data were generated with funds to Lu Lu, Beth Bennett, Mike Miles, Melloni Cook from INIA. - -
Lu Lu, M.D. -
Grant Support: NIH U01AA13499, U24AA13513 (Lu Lu, PI) - - - - -

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About this text file:

-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. Updated with data on LOD scores, Oct 24, 2007 by RWW> - - -
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