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. --- .../Hqfneoc_1210_rankinv/acknowledgment.rtf | 6 + general/datasets/Hqfneoc_1210_rankinv/cases.rtf | 54 ++ .../Hqfneoc_1210_rankinv/experiment-design.rtf | 937 +++++++++++++++++++++ .../Hqfneoc_1210_rankinv/experiment-type.rtf | 1 + general/datasets/Hqfneoc_1210_rankinv/platform.rtf | 7 + .../datasets/Hqfneoc_1210_rankinv/processing.rtf | 3 + general/datasets/Hqfneoc_1210_rankinv/summary.rtf | 16 + general/datasets/Hqfneoc_1210_rankinv/tissue.rtf | 9 + 8 files changed, 1033 insertions(+) create mode 100644 general/datasets/Hqfneoc_1210_rankinv/acknowledgment.rtf create mode 100644 general/datasets/Hqfneoc_1210_rankinv/cases.rtf create mode 100644 general/datasets/Hqfneoc_1210_rankinv/experiment-design.rtf create mode 100644 general/datasets/Hqfneoc_1210_rankinv/experiment-type.rtf create mode 100644 general/datasets/Hqfneoc_1210_rankinv/platform.rtf create mode 100644 general/datasets/Hqfneoc_1210_rankinv/processing.rtf create mode 100644 general/datasets/Hqfneoc_1210_rankinv/summary.rtf create mode 100644 general/datasets/Hqfneoc_1210_rankinv/tissue.rtf (limited to 'general/datasets/Hqfneoc_1210_rankinv') diff --git a/general/datasets/Hqfneoc_1210_rankinv/acknowledgment.rtf b/general/datasets/Hqfneoc_1210_rankinv/acknowledgment.rtf new file mode 100644 index 0000000..3135d79 --- /dev/null +++ b/general/datasets/Hqfneoc_1210_rankinv/acknowledgment.rtf @@ -0,0 +1,6 @@ +

Data were generated with funds to RW Williams, Glenn D. Rosen, Weikuan Gu, and Lu Lu from the High Q Foundation. Informatics support also provided by NIH NIAAA INIA grants to RWW and LL.

+ + diff --git a/general/datasets/Hqfneoc_1210_rankinv/cases.rtf b/general/datasets/Hqfneoc_1210_rankinv/cases.rtf new file mode 100644 index 0000000..a98a7ff --- /dev/null +++ b/general/datasets/Hqfneoc_1210_rankinv/cases.rtf @@ -0,0 +1,54 @@ +

The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 27 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 25 new inbred strains BXD (F21+) generated by Lu and Peirce. All of these strains were been genotyped at 13,377 SNPs in 2005 (Shifman et al., 2006).

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Mouse Diversity Panel (MDP). We have profiled a MDP consisting 20 inbred strains and an F1 hybrid (B6D2F1). These strains were selected for several reasons:

+ + + +

All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.

+ +
    +
  1. 129S1/SvImJ
    +     Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
    2. +
  2. A/J
    +     Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
    3. +
  3. AKR/J
    +     Sequenced by NIEHS; Phenome Project B list
    4. +
  4. BALB/cByJ
    +     Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
    5. +
  5. BALB/cJ
    +     Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
    6. +
  6. C3H/HeJ
    +     Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
    7. +
  7. C57BL/6J
    +     Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
    8. +
  8. C57BL/6ByJ
    +     Paternal substrain of B6 used to generate the CXB panel
    9. +
  9. CAST/EiJ
    +     Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
    10. +
  10. DBA/2J
    +     Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
    11. +
  11. KK/HlJ
    +     Sequenced by Perlegen/NIEHS
    12. +
  12. LG/J
    +     Paternal parent of the LGXSM panel
    13. +
  13. NOD/LtJ
    +     Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
    14. +
  14. NZO/HlLtJ
    +     Collaborative Cross strain
    15. +
  15. PWD/PhJ
    +     Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
    16. +
  16. PWK/PhJ
    +     Collaborative Cross strain; Phenome Project D list
    17. +
  17. WSB/EiJ
    +     Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
    18. +
  18. B6D2F1
    + This F1 hybrid was generated by crossing C57BL/6J with DBA/2J.
    19. +
+ +

These strains are available from The Jackson Laboratory. BXD43 through BXD100 strains are available from Lu Lu and colleagues at UTHSC.

diff --git a/general/datasets/Hqfneoc_1210_rankinv/experiment-design.rtf b/general/datasets/Hqfneoc_1210_rankinv/experiment-design.rtf new file mode 100644 index 0000000..322268a --- /dev/null +++ b/general/datasets/Hqfneoc_1210_rankinv/experiment-design.rtf @@ -0,0 +1,937 @@ +

This data set consists arrays processed in XX groups over a XX month period (from Month Year to Month Year). Most groups consisted of XX samples. All arrays in this data set were processed using a single protocol by a single operator, NAME HERE. Processing was supervised directly by Dr. Lu Lu. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between Month Day and Month Day, Year. Details on sample assignment to slides and batches is provide in the table below.

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Error checking

+ + + +

Data Table 1:

+ +

This table lists all arrays by order of strain (index) and includes data on strain, sex, slide ID and slide position (A through F).

+ + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
IndexStrainSexSlide IDSlide
+ Position
1B6D2F1F1848071018D
2B6D2F1M1957998076B
3C57BL/6JF1957998083A
4C57BL/6JM1833451021A
5DBA/2JF1957998083C
6DBA/2JM1833451021C
7BXD1M4051964030B
8BXD5F1736925307A
9BXD5M4051964028C
10BXD6F4051964028F
11BXD6M1736925307D
12BXD8F4060001025A
13BXD8M1957998111E
14BXD9F4060001025D
15BXD9M1736925359B
16BXD11F4051964030D
17BXD11M1848071017B
18BXD12F4051964030E
19BXD12M1848071017C
20BXD13F4051964030F
21BXD13M1848071017D
22BXD14F4051964065A
23BXD14M1848071017E
24BXD15F4051964065B
25BXD15M1848071017F
26BXD16F1848071024A
27BXD16M4051964065C
28BXD18F4051964065D
29BXD18M1848071024B
30BXD19F4051964065E
31BXD19M1848071024C
32BXD21F1848071024D
33BXD21M4051964065F
34BXD23F1848071024E
35BXD23M4051964022A
36BXD27F1848071024F
37BXD27M4051964022B
38BXD28F1848071025A
39BXD28M4051964022C
40BXD31F4051964022D
41BXD31M1848071025B
42BXD32F4051964022E
43BXD32M1848071025C
44BXD33F4051964022F
45BXD33M1848071025D
46BXD34F4051964023A
47BXD34M1848071025E
48BXD36F1848071025F
49BXD36M4051964023B
50BXD38F4051964023C
51BXD38M1957998101A
52BXD39F4051964023D
53BXD39M1957998101B
54BXD40F4051964023E
55BXD40M1957998101C
56BXD42F4060001026B
57BXD43F1957998101D
58BXD43F4051964023F
59BXD44F1957998101E
60BXD44M4051964028A
61BXD45F4051964028B
62BXD45M1957998101F
63BXD51F4051964028D
64BXD51M1736925307B
65BXD55F1736925307C
66BXD55M4051964028E
67BXD60F4060001014A
68BXD60M1736925307E
69BXD61F4060001014B
70BXD61M1736925307F
71BXD62F4060001014C
72BXD62M1957998111A
73BXD65F1957998111B
74BXD65M4060001014D
75BXD66M4060001026C
76BXD68F4060001026D
77BXD69M1957998111C
78BXD69M4060001014E
79BXD70M4060001026E
80BXD73F1957998111D
81BXD73M4060001014F
82BXD75M4060001026F
83BXD77F4060001027A
84BXD80M4060001027B
85BXD84F1957998111F
86BXD84M4060001025B
87BXD86M4060001027C
88BXD87F4060001027F
89BXD87M4060001025C
90BXD89M4060001027D
91BXD90F1736925359C
92BXD90M4060001025E
93BXD96F4060001025F
94BXD96M1736925359D
95BXD97M4060001027E
96BXD100F1848071017A
97BXD100M4051964030C
98129S1/SvImJF1736925359E
99129S1/SvImJM1848071018A
100A/JF1848071018B
101A/JM1736925359F
102AKR/JF1848071018C
103AKR/JM1957998076A
104BALB/cByJF1957998076C
105BALB/cByJM1953348019A
106C3H/HeJF1953348019D
107C3H/HeJM1957998076F
108CAST/EiJF1833451021B
109CAST/EiJM1957998083B
110KK/HlJF1957998083E
111KK/HlJM1848071023F
112BXSB/MpJF1957998076E
113BXSB/MpJM1953348019C
114FVB/NJF1833451021D
115FVB/NJM1957998083D
116MOLF/EiJF1957998083F
117MOLF/EiJM1848071001B
118NOD/LtJF1848071001C
119NOD/LtJM4060001004A
120NZB/BlNJF4060001004B
121NZB/BlNJM1848071001D
122NZO/HlLtJF4060001004C
123NZW/LacJF4060001004D
124PWD/PhJF4060001004E
125PWK/PhJM4060001004F
126WSB/EiJF4051964030A
127BTBRT<+>tf/JF1957998076D
128BTBRT<+>tf/JM1953348019B
+
diff --git a/general/datasets/Hqfneoc_1210_rankinv/experiment-type.rtf b/general/datasets/Hqfneoc_1210_rankinv/experiment-type.rtf new file mode 100644 index 0000000..4af1832 --- /dev/null +++ b/general/datasets/Hqfneoc_1210_rankinv/experiment-type.rtf @@ -0,0 +1 @@ +None \ No newline at end of file diff --git a/general/datasets/Hqfneoc_1210_rankinv/platform.rtf b/general/datasets/Hqfneoc_1210_rankinv/platform.rtf new file mode 100644 index 0000000..f0c5210 --- /dev/null +++ b/general/datasets/Hqfneoc_1210_rankinv/platform.rtf @@ -0,0 +1,7 @@ +

Illumina Sentrix Mouse-6.1 BeadArray Platform (ILM6v1.1): The Mouse6.1 array consists of 46,643 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).

+ +

ANNOTATION: In summer of 2008, Xusheng Wang and Robert W. Williams reannotated the Illumina Mouse-6.1 array content. This new annotation is now incorporated into GeneNetwork. For 46643 probes on the Mouse 6.1 array platform (including control probes) we have identified XXXXX NCBI Entrez Gene IDs; XXXXX matched human Gene IDs; XXXXX matched rat Gene IDs; XXXXX NCBI HomoloGene IDs; and XXXXX 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).

diff --git a/general/datasets/Hqfneoc_1210_rankinv/processing.rtf b/general/datasets/Hqfneoc_1210_rankinv/processing.rtf new file mode 100644 index 0000000..895fa91 --- /dev/null +++ b/general/datasets/Hqfneoc_1210_rankinv/processing.rtf @@ -0,0 +1,3 @@ +

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 ILM104280446.

diff --git a/general/datasets/Hqfneoc_1210_rankinv/summary.rtf b/general/datasets/Hqfneoc_1210_rankinv/summary.rtf new file mode 100644 index 0000000..ca42527 --- /dev/null +++ b/general/datasets/Hqfneoc_1210_rankinv/summary.rtf @@ -0,0 +1,16 @@ +

The February 2008 High Q Foundation Neocortex data set provides estimates of mRNA expression in the cerebral cortex of 73 lines of mice, including 52 BXD strains, 20 standard inbred strains, and B6D2F1 isogenic hybrids. All samples are from normal adult control animals raised in a standard laboratory environment. All data were generated with funds provided by the High Q Foundation using the Illumina Mouse 6.1 bead array (the second version of the Illumina Mouse-6 platform).

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While this February data release is still a provisional, we are not aware of any specific errors.

+ +

 

+ +

A total of 129 pooled neocortex samples were processed using approximately XX Illumina Sentrix Mouse-6.1 oligomer microarray BeadArray slides. XX Mouse-6.1 slides and a total of 128 samples passed stringent quality control and error checking. This data set is a companion to the High Q Foundation Striatum data set and was processed using very closely matched methods and most of the same samples. This is our third large data set generated using the Illumina platform. This particular data set was processed using the Illumina "Rank Invariant" protocol. Values were log2 transformed and the current data range from XXX (very low or no expression) to XXXX (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 Neocortex Illumina (Feb 08) RankInv data set, 1564 probes have LRS values >46 (LOD >10).

+ +

Users of these mouse neocortex data may also find the following complementary resources and papers useful:

+ +
    +
  1. Rossner and colleagues, 2006: a paper on the transcriptome of identified subtypes of neurons in the mouse neocortex.
    2. +
  2. A movie of the dissection of the brain by Dr. Glenn Rosen.
    3. +
diff --git a/general/datasets/Hqfneoc_1210_rankinv/tissue.rtf b/general/datasets/Hqfneoc_1210_rankinv/tissue.rtf new file mode 100644 index 0000000..48d0a2c --- /dev/null +++ b/general/datasets/Hqfneoc_1210_rankinv/tissue.rtf @@ -0,0 +1,9 @@ +

All animals were raised at the Jackson Laboratory or at UTHSC in SPF facilities. All mice were killed by cervical dislocation. Whole brain dissections were performed at either Beth Israel Deaconess Medical Center by Glenn Rosen or at UTHSC by Lu Lu and colleagues. Neocortex samples were close to complete but are likely to include variable amounts of underlying white matter. Samples may also include parts of the pyriform cortex and subiculum.

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A pool of dissected neocortical tissue from two to three 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 (CHECK LAST STATEMENT WITH LU).

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All animals used in this study were between XX and XX days of age (average of XX days; see Table 1 below). All animals were sacrifice between 9 AM and 5 PM during the light phase.

+ +

Sample Processing: Samples were processed by Lu Lu and colleagues in the Illumina Core at UTHSC between December 2007 and January 2008. 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 Mouse-6 v 1.1 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 as many strains as possible. However, a number of strains are represented by samples from a single sex (see figure at bottom of page).

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