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. --- general/datasets/HZI_0408_M/cases.rtf | 784 ++++++++++++++++++++++++++++++++ general/datasets/HZI_0408_M/summary.rtf | 37 ++ 2 files changed, 821 insertions(+) create mode 100644 general/datasets/HZI_0408_M/cases.rtf create mode 100644 general/datasets/HZI_0408_M/summary.rtf (limited to 'general/datasets/HZI_0408_M') diff --git a/general/datasets/HZI_0408_M/cases.rtf b/general/datasets/HZI_0408_M/cases.rtf new file mode 100644 index 0000000..83b146d --- /dev/null +++ b/general/datasets/HZI_0408_M/cases.rtf @@ -0,0 +1,784 @@ +
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IndexArraySampleStrainSexAgeColorPool SizeSource
1R4435LU.CELR4435LUBXD100F64black2UTM RW
2R4436LU.CELR4436LUBXD14F85black2UTM RW
3R4437LU.CELR4437LUBXD34F58black5UTM RW
4R4438LU.CELR4438LUBXD39F63gray3UTM RW
5R4439LU.CELR4439LUBXD40F54gray3ORNL
6R4440LU.CELR4440LUBXD45F60dilute brown DBA4UTM RW
7R4441LU.CELR4441LUBXD50F64dilute brown DBA4ORNL
8R4442LU.CELR4442LUBXD1F88dilute brown DBA3UTM RW
9R4443LU.CELR4443LUBXD16F79gray3ORNL
10R4444LU.CELR4444LUBXD12F61gray5UTM RW
11R4445LU.CELR4445LUBXD21F50dilute brown DBA3ORNL
12R4446LU.CELR4446LUBXD19F49gray3ORNL
13R4447LU.CELR4447LUBXD27F85brown3UTM RW
14R4448LU.CELR4448LUBXD31F81black3UTM RW
15R4449LU.CELR4449LUBXD32F68black5ORNL
16R4450LU.CELR4450LUBXD33F61gray2ORNL
17R4451LU.CELR4451LUBXD42F65black2UTM RW
18R4452LU.CELR4452LUBXD43F79black2UTM RW
19R4453LU.CELR4453LUBXD45F60dilute brown DBA4UTM RW
20R4454LU.CELR4454LUBXD55M80brown3UTM RW
21R4455LU.CELR4455LUBXD56M91black3UTM RW
22R4456LU.CELR4456LUBXD66F80brown3UTM RW
23R4457LU.CELR4457LUBXD68F65brown4UTM RW
24R4459LU-re.CELR4459LUBXD89F79dilute brown DBA2UTM RW
25R4460LU.CELR4460LUBXD51M81black2UTM RW
26R4461LU.CELR4461LUBXD97FN/AN/AN/AN/A
27R4462LU.CELR4462LUBXD48F61black3ORNL
28R4463LU.CELR4463LUBXD60M93brown2UTM RW
29R4464LU.CELR4464LUBXD62M80brown2UTM RW
30R4465LU.CELR4465LUBXD69M63dilute brown DBA5UTM RW
31R4466LU.CELR4466LUBXD70M75dilute brown DBA3UTM RW
32R4467LU.CELR4467LUBXD71M64dilute brown DBA4UTM RW
33R4468LU.CELR4468LUBXD73M59dilute brown DBA3UTM RW
34R4469L.CELR4469LUBXD75M51dilute brown DBA4UTM RW
35R4470L.CELR4470LUBXD2M84black3UTM RW
36R4471H-re.CELR4471LUBXD83M75dilute brown DBA2UTM RW
37R4472L.CELR4472LUBXD84M78dilute brown DBA2UTM RW
38R4473LU.CELR4473LUBXD86M77black3UTM RW
39R4474LU.CELR4474LUBXD87M67black3UTM RW
40R4475LU.CELR4475LUBXD9M78dilute brown DBA3UTM RW
41R4476LU.CELR4476LUBXD90M63dilute brown DBA3UTM RW
42R4477LU.CELR4477LUBXD65M59brown3ORNL
43R4478LU.CELR4478LUBXD6M92gray3UTM RW
44R4479LU.CELR4479LUBXD96M71black3UTM RW
45R4480LU.CELR4480LUBXD97M80brown3UTM RW
46R4481LU.CELR4481LUBXD98M80dilute brown DBA2UTM RW
47R4482LU.CELR4482LUBXD99M72dilute brown DBA2UTM RW
48R4483LU.CELR4483LUBXD22M66gray2UTM RW
49R4484LU.CELR4484LUBXD25M54brown3UTM RW
50R4485LU.CELR4485LUB6D2F1M62black5UTM RW
51R4486LU.CELR4486LUB6D2F1F70black2UTM RW
52R4487LU.CELR4487LUBALB/cByJF91white3UTM RW
53R4488LU.CELR4488LUBALB/cByJM91white2UTM RW
54R4489LU.CELR4489LUD2B6F1F61black2UTM RW
55R4490LU.CELR4490LUD2B6F1M61black3UTM RW
56R4491LU.CELR4491LUFVB/NJF62white5UTM RW
57R4492LU.CELR4492LUFVB/NJM73white3UTM RW
58R4493LU.CELR4493LUWSB/EiJF76agouti3UTM RW
59R4494LU.CELR4494LUWSB/EiJM76agouti3UTM RW
60R4495LU.CELR4495LUC57BL/6JF65black3UTM RW
61R4496LU.CELR4496LUC57BL/6JM65black2UTM RW
62R4497LU.CELR4497LU129X1/SvJF65white4JAX
63R4498LU.CELR4498LU129X1/SvJM66white4JAX
64R4499LU.CELR4499LUDBA/2JF65dilute brown DBA3ORNL
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66R4501LU.CELR4501LULP/JF65agouti4JAX
67R4502LU.CELR4502LULP/JM65agouti4JAX
68R4503LU.CELR4503LUSJL/JF63white4JAX
69R4504LU.CELR4504LUSJL/JM65white4JAX
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diff --git a/general/datasets/HZI_0408_M/summary.rtf b/general/datasets/HZI_0408_M/summary.rtf new file mode 100644 index 0000000..5d3c1a7 --- /dev/null +++ b/general/datasets/HZI_0408_M/summary.rtf @@ -0,0 +1,37 @@ +

Phase I of BXD lung transcriptome mapping project. Project organized by Drs. Robert Williams, Klaus Schughart, Lu Lu. Started November 29, 2008. There are total 70 samples in phase I including 50 BXD strains and 10 paired inbred strains.

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 2011 May 2;12:61. doi: 10.1186/1465-9921-12-61.

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Genome-wide analysis of the mouse lung transcriptome reveals novel molecular gene interaction networks and cell-specific expression signatures.

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Alberts R1, Lu L, Williams RW, Schughart K.

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Erratum in

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Abstract

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BACKGROUND: 

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The lung is critical in surveillance and initial defense against pathogens. In humans, as in mice, individual genetic differences strongly modulate pulmonary responses to infectious agents, severity of lung disease, and potential allergic reactions. In a first step towards understanding genetic predisposition and pulmonary molecular networks that underlie individual differences in disease vulnerability, we performed a global analysis of normative lung gene expression levels in inbred mouse strains and a large family of BXD strains that are widely used for systems genetics. Our goal is to provide a key community resource on the genetics of the normative lungtranscriptome that can serve as a foundation for experimental analysis and allow predicting genetic predisposition and response to pathogens, allergens, and xenobiotics.

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METHODS: 

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Steady-state polyA+ mRNA levels were assayed across a diverse and fully genotyped panel of 57 isogenic strains using the Affymetrix M430 2.0 array. Correlations of expression levels between genes were determined. Global expression QTL (eQTL) analysis and network covariance analysis was performed using tools and resources in GeneNetwork http://www.genenetwork.org.

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RESULTS: 

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Expression values were highly variable across strains and in many cases exhibited a high heritability factor. Several genes which showed a restricted expression to lung tissue were identified. Using correlations between gene expression values across all strains, we defined and extended memberships of several important molecular networks in the lung. Furthermore, we were able to extract signatures of immune cell subpopulations and characterize co-variation and shared genetic modulation. Known QTL regions for respiratory infection susceptibility were investigated and several cis-eQTL genes were identified. Numerous cis- and trans-regulated transcripts and chromosomal intervals with strong regulatory activity were mapped. The Cyp1a1 P450 transcript had a strong trans-acting eQTL (LOD 11.8) on Chr 12 at 36 ± 1 Mb. This interval contains the transcription factor Ahr that has a critical mis-sense allele in the DBA/2J haplotype and evidently modulates transcriptional activation by AhR.

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CONCLUSIONS: 

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Large-scale gene expression analyses in genetic reference populations revealed lung-specific and immune-cell gene expression profiles and suggested specific gene regulatory interactions.

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PMID:21535883 PMCID:PMC3105947 DOI:10.1186/1465-9921-12-61
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