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. --- general/datasets/Ma_m2m_0706_r/acknowledgment.rtf | 24 + general/datasets/Ma_m2m_0706_r/cases.rtf | 44 + .../datasets/Ma_m2m_0706_r/experiment-design.rtf | 1864 ++++++++++++++++++++ general/datasets/Ma_m2m_0706_r/notes.rtf | 3 + general/datasets/Ma_m2m_0706_r/platform.rtf | 3 + general/datasets/Ma_m2m_0706_r/processing.rtf | 15 + general/datasets/Ma_m2m_0706_r/summary.rtf | 1 + general/datasets/Ma_m2m_0706_r/tissue.rtf | 3 + 8 files changed, 1957 insertions(+) create mode 100644 general/datasets/Ma_m2m_0706_r/acknowledgment.rtf create mode 100644 general/datasets/Ma_m2m_0706_r/cases.rtf create mode 100644 general/datasets/Ma_m2m_0706_r/experiment-design.rtf create mode 100644 general/datasets/Ma_m2m_0706_r/notes.rtf create mode 100644 general/datasets/Ma_m2m_0706_r/platform.rtf create mode 100644 general/datasets/Ma_m2m_0706_r/processing.rtf create mode 100644 general/datasets/Ma_m2m_0706_r/summary.rtf create mode 100644 general/datasets/Ma_m2m_0706_r/tissue.rtf (limited to 'general/datasets/Ma_m2m_0706_r') diff --git a/general/datasets/Ma_m2m_0706_r/acknowledgment.rtf b/general/datasets/Ma_m2m_0706_r/acknowledgment.rtf new file mode 100644 index 0000000..fea38e8 --- /dev/null +++ b/general/datasets/Ma_m2m_0706_r/acknowledgment.rtf @@ -0,0 +1,24 @@ +
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Data were generated with funds provided by a variety of public and private source to members of the Kidney Consortium. Members of the Kidney Consortium thank the following sources for financial support of this effort:

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diff --git a/general/datasets/Ma_m2m_0706_r/cases.rtf b/general/datasets/Ma_m2m_0706_r/cases.rtf new file mode 100644 index 0000000..465b87c --- /dev/null +++ b/general/datasets/Ma_m2m_0706_r/cases.rtf @@ -0,0 +1,44 @@ +
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The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 30 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. We have also included 24 BXD lines generated by Lu and Peirce. All of these strains have been genotyped at 13,377 SNPs.

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Mouse Diversity Panel (MDP). We have profiled a MDP consisting 15 inbred strains and a pair of F1 hybrids; D2B6F1. These strains were selected for the following reasons: This panel will be a powerful tool in systems genetic analysis of a wide variety of traits, and will provide additional power in fine mapping modulators through an association analysis of sequence variants.

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  1. BTBR T+tf/J
    +     Multiple recessive stock; Homozygotes show repeated waves of hair loss and regrowth, which begin in the nose and pass posteriorly along the body.
    2. +
  2. C3H/HeJ
    +     Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
    3. +
  3. C57BL/6J
    +     Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
    4. +
  4. C57BL/6ByJ
    +     Paternal substrain of B6 used to generate the CXB panel
    5. +
  5. CAST/Ei
    +     Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
    6. +
  6. DBA/2J
    +     Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
    7. +
  7. KK/HlJ
    +     Sequenced by Perlegen/NIEHS
    8. +
  8. NOD/LtJ
    +     Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
    9. +
  9. PWD/PhJ
    +     Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
    10. +
  10. PWK/PhJ
    +     Collaborative Cross strain; Phenome Project D list
    11. +
  11. WSB/EiJ
    +     Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
    12. +
  12. D2B6F1
    + F1 hybrid generated by crossing C57BL/6J with DBA/2J
    13. +
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These inbred strains can be ordered from The Jackson Laboratory. BXD43 through BXD100 are available from Lu Lu and colleagues at UTHSC.P>

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diff --git a/general/datasets/Ma_m2m_0706_r/experiment-design.rtf b/general/datasets/Ma_m2m_0706_r/experiment-design.rtf new file mode 100644 index 0000000..464e50d --- /dev/null +++ b/general/datasets/Ma_m2m_0706_r/experiment-design.rtf @@ -0,0 +1,1864 @@ +
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Sample Processing: : Samples were processed at the Mount Sinai School of Medicine in the laboratory of Dr. Erwin Bottinger. All processing steps were performed Kremena Star. Total RNA was extracted with TRIZOL, followed by Rneasy Mini Kit purification (QUAGEN) by Kremena Star at MSSM. RNA purity was evaluated using the 260/280 nm (protein contamination) and the 260/230 nm (TRIZOL contamination) absorbance ratios, and values had to be greater than 1.9 and 0.8 respectively. Most of the samples 260/280 nm values fell between 1.9 and 2.1 and the majority of the 260/230 nm measurements were in the range 1.8 to 2.3. RNA integrity was assessed with the Agilent Bioanalyzer 2100. We set a quality threshold at 28s/18s rRNA greater than 0.9 or RNA integrity number (RIN) of greater than 6.9. When the two metrics were in disagreement we gave priority on the RIN value as recommended by the Agilent Bioanalyzer 2100 technical support representative. Synthesis of cDNA template from total RNA was performed using the one-cyclecDNA synthesis kit from Affymetrix (Affymetrix, P/N 900431). The Affymetrix IVT-labeling kit ((Affymetrix, P/N 900449)) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 1.9 to 2.1). The cRNA is then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup (Affymetrix, P/N 900371). Fragmented cRNA samples were accessed with Agilent Bioanalyzer 2100 (cRNA frgments between 25 and 200 nucleotides are required for optimal hybridization and immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.

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Replication and Sample Balance: We obtained a male sample pool and female sample pool from each isogenic group. Initially all strains were represented by male and female samples, however, not all data sets passed the quality control steps. Forty-two (thirty-one BXD, D2B6F1 and ten inbred strains) are represented by male and female samples.

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Experimental Design and Batch Structure: The data set consists of arrays processed in twenty-three groups over a six month period (March 2006 to July 2006). Each group consists of 4 to 12 arrays. All arrays were processed using the Affymetrix Eukaryotic Sample and Array Processing protocol (701024 Rev. 3), by a single operator, Kremena Star. All samples in a group were labeled on the same. The hybridization station accommodates up to 4 samples, and since most of the groups had 12 samples, processed in 3 batches on the same day. Samples were washed in groups of four and kept at 4° C until all 12 (or 4-12) arrays were ready to scan. Samples were scanned in sets of four.

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This table lists all arrays ordered by strain and includes Microarray ID, number of mice per pool, Microarray date, GAPDH 3`/5`Signal Ratio, Percent of transcripts present on the microarray chip, Strain, Generation, Sex, Age and Source of mice.
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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Microarray_ID# miceMicroarray DateGAPDH (3`/5`)% presentstrainsgenerationsexageMice Source
GKHI-KS-050603.07-051706305/14/020.7337.6C57BL/6J M56UTM RW
GKHI-KS-070803.01-051706305/14/020.7541.6C57BL/6J F69UTM RW
GKHI-KS-DBA-Male-070706207/06/020.7137.3DBA/2J M56JAX
GKHI_KS_121404.75-042106404/18/02  DBA/2J F59UTM RW
GKHI_KS_121404.75-033006403/19/020.7348.5DBA/2J F59UTM RW
GKHI_KS_121404.78-042006404/17/020.8340.6DBA/2J F59UTM RW
GKHI_KS_070804.39-042006404/17/020.8239.0D2B6F1 M59UTM RW
GKHI_KS_030904.01-042006404/17/020.8235.9D2B6F1 M57UTM RW
GKHI-KS-121404.73-070706207/06/020.7636.3D2B6F1 F69UTM RW
GKHI-KS-010705.38-051206505/09/020.8139.9BXD1 M59Harvard/BIDMC
GKHI-KS-060905.19506/05/020.7542.3BXD1 M68UTM RW
GKHI-KS-051206.13-070706307/06/020.7136.3BXD1 F57UTM RW
GKHI-KS-021304.10-051206405/09/020.8139.1BXD2 M61Harvard/BIDMC
GKHI-KS-040303-04-050406305/01/020.8037.6BXD5 F56UMemphis
GKHI-KS-010705-53-050306505/01/020.7637.1BXD5 F58Harvard/BIDMC
GKHI-KS-031103.01-062206306/21/020.7537.1BXD5 M71UMemphis
GKHI-KS-040505-51-050306505/01/020.7135.5BXD6 M58UTM RW
GKHI-KS-092705-29--050406505/02/020.7536.1BXD6160F64UTM RW
GKHI_KS_092404.01-042106404/18/020.7136.3BXD8 M59Harvard/BIDMC
GKHI-KS-051205-25-042706504/23/020.9237.9BXD8 F77UTM RW
KS-021605-17-042606504/22/020.8540.8BXD9 F67UTM RW
KS-032905-32-042606504/22/020.9136.8BXD9 F60UTM RW
GKHI-KS-062006.08-070706307/06/020.7436.3BXD9 M78UTM RW
GKHI-KS-031505.22-051206505/09/020.7439.5BXD11 F65UTM RW
GKHI-KS-031605.01506/05/020.7443.4BXD11 F69UTM RW
GKHI_KS_102104.40-042106404/18/020.7238.5BXD12 M60Harvard/BIDMC
GKHI-KS-112002.07-051106205/08/020.7742.0BXD12 F64UMemphis
GKHI-KS-120904.33-051206405/09/020.7138.4BXD13 F60Harvard/BIDMC
GKHI-KS-042304.01406/05/020.7144.1BXD13 F58Harvard/BIDMC
GKHI-KS-020905.34-051106505/08/020.7540.7BXD14 F68UTM RW
GKHI-KS-022405.46-051106505/08/020.7140.2BXD14 F60Harvard/BIDMC
GKHI-KS-091704.09-062206406/21/020.7339.0BXD14 M59Harvard/BIDMC
GKHI-KS-013004.45-062206406/21/020.7638.5BXD15 M61Harvard/BIDMC
GKHI-KS-022405.43-051106505/08/020.7340.5BXD15 F60Harvard/BIDMC
GKHI-KS-041604.10-051106405/08/020.7342.6BXD15 F60Harvard/BIDMC
GKHI-KS-031805.01-051106505/08/020.7942.4BXD16 F59Harvard/BIDMC
GKHI-KS-031805.04-051106505/08/020.7739.9BXD16 M60Harvard/BIDMC
GKHI-KS-040805.10-051006505/05/020.9338.7BXD18 F59Harvard/BIDMC
GKHI-KS-052804.09-051106405/05/020.6737.6BXD19 F60Harvard/BIDMC
GKHI-KS-010705.47-051106505/05/020.7342.3BXD19 F60Harvard/BIDMC
GKHI-KS-010705.44-070706307/06/020.7336.1BXD19 M60Harvard/BIDMC
GKHI-KS-062905.07-051106505/05/020.7237.9BXD20 M60Harvard/BIDMC
GKHI-KS-072104.58-051106405/05/020.7337.0BXD20 F59Harvard/BIDMC
GKHI-KS-050405.21-051206405/09/020.8135.1BXD21 F60Harvard/BIDMC
GKHI-KS-040705.24506/05/020.8040.2BXD21 F99UAB
GKHI-KS-110405.01-051006505/05/020.7142.1BXD22 F60Harvard/BIDMC
GKHI-KS-110405.04-051006505/05/020.7640.6BXD22 M60Harvard/BIDMC
GKHI-KS-040805.01-051206505/09/020.7436.4BXD23 F60Harvard/BIDMC
GKHI-KS-040805.04-051006505/05/020.7339.3BXD23 M60Harvard/BIDMC
GKHI_KS_091704.13-042106404/18/020.7337.7BXD24 M59Harvard/BIDMC
GKHI-KS-040303-20-050206304/30/020.7736.3BXD24 F71UMemphis
GKHI-KS-021805.20-051006505/05/020.8340.5BXD25 F67UAB
GKHI-KS-090705.05-062206506/21/020.7638.4BXD25 M58UTM RW
GKHI-KS-090705.03-051006505/05/020.8140.1BXD25 F58UTM RW
GKHI-KS-022105.42-051006505/05/020.8141.8BXD27 M70UAB
GKHI-KS-032205.31-051006505/05/020.7439.0BXD27 M60UTM RW
GKHI-KS-060706.10-070706307/06/020.6937.8BXD27 F85UTM RW
GKHI-KS-012805-41-050506505/04/020.8134.2BXD28 F60Harvard/BIDMC
GKHI-KS-012805-44-050506505/04/020.8135.8BXD28 M60Harvard/BIDMC
GKHI-KS-012805-38-050506505/04/020.7742.7BXD29 F60Harvard/BIDMC
GKHI-KS-012805-35-050506505/04/020.8435.8BXD29 F60Harvard/BIDMC
GKHI-KS-012805-32-050506505/04/020.7439.9BXD31 F60Harvard/BIDMC
GKHI-KS-100604-07-050506405/04/020.7940.2BXD31 M60Harvard/BIDMC
GKHI-KS-021605.26-051706505/14/021.1139.0BXD32 F63UTM RW
GKHI-KS-112002.01-051206205/09/020.7638.1BXD32 F60UMemphis
GKHI-KS-072605-01-050506505/04/020.7941.3BXD3350F63UTM RW
GKHI-KS-091405-23-050506505/04/020.8438.4BXD3350M76UTM RW
GKHI-KS-111104-18-050506405/04/020.7942.2BXD36 F61Harvard/BIDMC
GKHI-KS-031804-07-050506405/04/020.8542.5BXD36 F58Harvard/BIDMC
GKHI-KS-092005.16-051206505/09/020.7237.2BXD3846F65UTM RW
GKHI-KS-031403.01-060806106/07/020.6939.6BXD38 M69UMemphis
GKHI-KS-090104.21-051106405/08/020.7236.3BXD39 F60Harvard/BIDMC
GKHI-KS-040204.30406/05/020.7743.9BXD39 F59Harvard/BIDMC
GKHI-KS-051805-16-050506505/04/022.1643.8BXD40 F61UTM RW
GKHI-KS-111902-04-050506205/04/020.8441.0BXD40 F56UMemphis
GKHI-KS-050604-01-050406405/01/020.8535.6BXD4323F61UTM RW
GKHI-KS-080905-43-050406505/01/020.7833.7BXD4328F62UTM RW
GKHI-KS-031004-01-050406405/01/020.7536.2BXD4421F57UTM RW
GKHI-KS-020504-01-050406405/01/020.7530.8BXD4420M66UTM RW
GKHI-KS-071504-01-050406405/01/020.7437.7BXD4520F58UTM RW
GKHI-KS-081104-05-050406405/01/020.7834.2BXD4520M93UTM RW
GKHI-KS-031204-01-050406405/01/020.7535.6BXD4822M60UTM RW
GKHI-KS-021104.06-051706405/14/020.7541.1BXD4821F58UTM RW
GKHI-KS-033005-21-050306505/01/020.7834.9BXD5127M64UTM RW
GKHI-KS-090204-01-050306405/01/020.7238.3BXD5124F63UTM RW
GKHI_KS-010704.01-040606404/03/020.7537.5BXD6021M64UTM RW
GKHI_KS_013004.38-042006404/17/020.7840.1BXD6021F60UTM RW
GKHI-KS-030905-28-050206504/30/020.7336.6BXD6120F63UTM RW
GKHI-KS-050305-18-050206504/30/020.8335.8BXD6121F70UTM RW
GKHI_KS-121803.01-040706304/03/020.8040.0BXD6220M54UTM RW
GKHI_KS_021204.01-042006404/17/020.8539.8BXD6221F59UTM RW
GKHI-KS-020905-25-050206504/30/020.8435.2BXD6321M70UTM RW
GKHI-KS-040705.49-060806206/07/020.8539.4BXD6520F55UTM RW
GKHI-KS-040406.12-060806206/07/020.7340.4BXD6523F60UTM RW
GKHI-KS-052405-36-050406505/02/020.8436.8BXD6720F65UTM RW
GKHI-KS-041205-01-050206504/30/020.7739.7BXD6720F54UTM RW
GKHI-KS-062305-01-050206504/30/020.7636.0BXD6820F59UTM RW
GKHI-KS-062305-09-050206504/30/020.9337.4BXD6820F64UTM RW
GKHI_KS_110105.30-042006504/17/020.8039.0BXD6926F66UTM RW
GKHI-KS-061504.64-062206406/21/020.7239.3BXD6920M55UTM RW
GKHI_KS-050404.04-040606404/03/020.7738.3BXD6920F63UTM RW
GKHI-KS-042705-01-042706504/23/020.8338.6BXD7021F64UTM RW
GKHI-KS-051705-59-042706504/23/020.8938.5BXD7022F61UTM RW
GKHI-KS-030805-40-042706504/23/020.8638.5BXD7323F61UTM RW
GKHI-KS-041905.172-062206506/21/020.7937.6BXD7324M64UTM RW
GKHI-KS-072605-03-042706504/23/020.8738.2BXD7325F72UTM RW
GKHI-KS-041205-04-050406505/02/020.8341.4BXD7522F60UTM RW
GKHI-KS-041205.07506/05/020.7945.8BXD7522F60UTM RW
GKHI-KS-101805-35-050406505/02/020.7938.4BXD7724F60UTM RW
GKHI-KS-070605.43506/05/020.7742.8BXD7723F62UTM RW
GKHI-KS-071205-31-042706504/23/020.9137.7BXD8020F65UTM RW
GKHI-KS-071205-2-042706504/23/020.9038.1BXD8020F65UTM RW
KS-011305-11-042606504/22/020.8239.0BXD8522M91UTM RW
KS-110805-27-042606504/22/020.9135.2BXD8525F63UTM RW
KS-080404-28-042606404/22/020.8436.8BXD8621F58UTM RW
KS-080504-04-042606404/22/020.8133.4BXD8620M77UTM RW
KS-051705-57-042606504/22/021.1135.6BXD8720M63UTM RW
KS-032905-46-042606504/22/020.8536.1BXD8720M57UTM RW
GKHI-KS-080905-49-042706504/23/020.8937.6BXD9023F71UTM RW
GKHI-KS-101105.26506/05/020.8443.6BXD9025F70UTM RW
GKHI_KS-062304.02-040606404/03/020.8540.9BXD9221M55UTM RW
GKHI_KS_071404.01-042006404/17/020.7739.5BXD9221F62UTM RW
GKHI_KS_031005.17-042006504/17/020.7738.1BXD9620M65UTM RW
GKHI-KS-111505.12506/05/020.7744.1BXD9623M66UTM RW
GKHI-KS-012406.21-060806306/07/020.7336.6BTBR T+tf/J F60Harvard/BIDMC
GKHI-KS-012406.24-060806306/07/021.2839.2BTBR T+tf/J F60Harvard/BIDMC
GKHI-KS-030206.13-060806306/07/020.7141.2BXSB/MpJ F61Harvard/BIDMC
GKHI-KS-030206.16-060806306/07/020.6637.2BXSB/MpJ F61Harvard/BIDMC
GKHI-KS-011906.31-060806306/07/020.8037.2C3H/HeJ M60Harvard/BIDMC
GKHI-KS-011906.34-060806306/07/020.7638.5C3H/HeJ M60Harvard/BIDMC
GKHI-KS-060806.04-070706307/06/020.6837.3C3H/HeJ F76Harvard/BIDMC
GKHI-KS-071505.08-060806306/07/020.7137.4C57BL/6ByJ F51JAX
GKHI-KS-071505.11-060806206/07/020.7339.2C57BL/6ByJ F51JAX
GKHI-KS-030305.15-060806306/07/020.7137.4CAST/Ei F64JAX
GKHI-KS-031005.35-060906306/08/020.7035.7CAST/Ei M64JAX
GKHI-KS-022206.16-060906306/08/020.7137.9KK/HlJ F61Harvard/BIDMC
GKHI-KS-022206.07-060906306/08/020.7235.5KK/HlJ M61Harvard/BIDMC
GKHI-KS-031606.01-060906306/08/020.8635.9MOLF/Ei M60Harvard/BIDMC
GKHI-KS-022206.16-060906306/08/020.8737.4MOLF/Ei F60Harvard/BIDMC
GKHI-KS-012006.25-060906306/08/020.7538.3NOD/LtJ F58Harvard/BIDMC
GKHI-KS-012006.28-061306306/11/020.8237.1NOD/LtJ F58Harvard/BIDMC
GKHI-KS-032306.04.060906306/08/020.7340.2NZB/BlNJ F61Harvard/BIDMC
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GKHI-KS-020706.04-060906306/08/020.7141.6NZW/LacJ F65Harvard/BIDMC
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GKHI-KS-020206.01-062206306/21/021.0235.9PWK/PhJ F60Harvard/BIDMC
GKHI-KS-020206.04-062206306/21/020.9638.7PWK/PhJ F60Harvard/BIDMC
GKHI-KS-020206.07-062206306/21/020.9836.6PWK/PhJ M60Harvard/BIDMC
GKHI-KS-020206.10-062206306/21/020.8735.2PWK/PhJ M60Harvard/BIDMC
GKHI-KS-052705.01-061306206/11/020.7238.3WSB/EiJ F52UTM RW
GKHI-KS-051005.07-061306306/11/020.7738.0WSB/EiJ M58JAX
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diff --git a/general/datasets/Ma_m2m_0706_r/notes.rtf b/general/datasets/Ma_m2m_0706_r/notes.rtf new file mode 100644 index 0000000..d41fda1 --- /dev/null +++ b/general/datasets/Ma_m2m_0706_r/notes.rtf @@ -0,0 +1,3 @@ +
+

This text file originally generated by Kremena Star on July 22 ,2006. Updated by KS on July 25, 2006.

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diff --git a/general/datasets/Ma_m2m_0706_r/platform.rtf b/general/datasets/Ma_m2m_0706_r/platform.rtf new file mode 100644 index 0000000..cb0e8d5 --- /dev/null +++ b/general/datasets/Ma_m2m_0706_r/platform.rtf @@ -0,0 +1,3 @@ +
+

Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.

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diff --git a/general/datasets/Ma_m2m_0706_r/processing.rtf b/general/datasets/Ma_m2m_0706_r/processing.rtf new file mode 100644 index 0000000..b313d60 --- /dev/null +++ b/general/datasets/Ma_m2m_0706_r/processing.rtf @@ -0,0 +1,15 @@ +
+

Probe set data from the CHP file: The expression values were generated using RMA. The same simple steps described above were also applied to these values.

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+ +
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Probe level QC: Log2 probe data of all arrays were inspected in DataDesk. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients.

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Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.

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Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.

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All data links (right-most column above) will be made active as sooon as the global analysis of these data by the Consoritum 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 the PDNN probe set data. Contact RW Williams regarding data access probelms.

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diff --git a/general/datasets/Ma_m2m_0706_r/summary.rtf b/general/datasets/Ma_m2m_0706_r/summary.rtf new file mode 100644 index 0000000..9055ba0 --- /dev/null +++ b/general/datasets/Ma_m2m_0706_r/summary.rtf @@ -0,0 +1 @@ +
The July 2006 Kidney QTL Consortium data set provides estimates of mRNA expression in the adult kidney of 70 genetically diverse strains of mice including 54 BXD recombinant inbred strains, a set of 15 inbred strains, and 1 F1 hybrid; D2B6F1. Kidney samples were processed using a total of 153 Affymetrix Mouse Expression 430 2.0 microarrays (M430v2.0). This particular data set was processed using the RMA protocol. CAUTION: This dataset is not sex-balanced.
diff --git a/general/datasets/Ma_m2m_0706_r/tissue.rtf b/general/datasets/Ma_m2m_0706_r/tissue.rtf new file mode 100644 index 0000000..5bc52e9 --- /dev/null +++ b/general/datasets/Ma_m2m_0706_r/tissue.rtf @@ -0,0 +1,3 @@ +
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BXD animals were obtained from UTHSC, and the Jackson Laboratory (Table 1). Animals were housed at UTHSC, at Harvard/BIDMC (Glenn Rosen), at the University of Memphis (Douglas Matthews), or the Jackson Laboratory before sacrifice (see Table 1). Mice were killed by cervical dislocation and kidneys were removed and placed in RNAlater prior to dissection. Kidneys were dissected whole and cleaned from the adrenal glands by Hong Tao Zhang in Dr. Lu’s lab. Kidneys from two to six animals per strain were pooled and shipped to Kremena Star at Mount Sinai School of Medicine (MSSM). Animals used in this study were between 50 and 99 days of age (average of 62 days; see Table 1).

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