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/Uthsc_spl_rma_1010/cases.rtf | 3 + .../Uthsc_spl_rma_1010/experiment-design.rtf | 3 + general/datasets/Uthsc_spl_rma_1010/notes.rtf | 4 + general/datasets/Uthsc_spl_rma_1010/processing.rtf | 1932 ++++++++++++++++++++ general/datasets/Uthsc_spl_rma_1010/summary.rtf | 3 + 5 files changed, 1945 insertions(+) create mode 100644 general/datasets/Uthsc_spl_rma_1010/cases.rtf create mode 100644 general/datasets/Uthsc_spl_rma_1010/experiment-design.rtf create mode 100644 general/datasets/Uthsc_spl_rma_1010/notes.rtf create mode 100644 general/datasets/Uthsc_spl_rma_1010/processing.rtf create mode 100644 general/datasets/Uthsc_spl_rma_1010/summary.rtf (limited to 'general/datasets/Uthsc_spl_rma_1010') diff --git a/general/datasets/Uthsc_spl_rma_1010/cases.rtf b/general/datasets/Uthsc_spl_rma_1010/cases.rtf new file mode 100644 index 0000000..7fa108f --- /dev/null +++ b/general/datasets/Uthsc_spl_rma_1010/cases.rtf @@ -0,0 +1,3 @@ +

Cases. A total of 111 strains, including 81 BXD strains, both parental strains (C57BL/6J and DBA/2J) and both reciprocal F1 hybrids (B6D2F1 and D2B6F1), and 26 other common inbred strains were quantified. In most cases, two arrays were processed per strain--one for males and one for females. All tissue and RNA was extracted by Lu Lu and colleagues. Samples were pooled by sex and usually include at least two cases per sex and strain.

+ +

Sex Balance. XX strains have matched male and female samples. XX strains have male only samples (BXDX, XX, XX, XXX and XXX). XX strains have only female samples (BXDXX, XX, and XX.) Please review the expression data for Xist probe set 10606178. This non-coding RNA is expressed highly only in females and can be used to check the sex of a sample or pool of tissue. Ddx3y probe set 10608138 can also be used. This is a Y chromosome gene that is expressed abundantly in male samples and at background levels in female samples.

diff --git a/general/datasets/Uthsc_spl_rma_1010/experiment-design.rtf b/general/datasets/Uthsc_spl_rma_1010/experiment-design.rtf new file mode 100644 index 0000000..a0aeba6 --- /dev/null +++ b/general/datasets/Uthsc_spl_rma_1010/experiment-design.rtf @@ -0,0 +1,3 @@ +

RNA Processing. Total RNA was purified using the RNAeasy micro kit on the QIAcube system (www.qiagen.com). RNA purity and concentration was checked using 260/280 nm absorbance ratio and RNA integrity was analyzed using the Agilent Bioanalyzer 2100 (Agilent Technologies).

+ +

Array Processing: All arrays were processed by Lorne Rose in the UTHSC Molecular Resources Center (MRC), Memphis TN. The table below provides a summary of cases, sex, and age. The spleen was dissected by both Dr. Lu Lu and colleagues and Dr. Abdeltawab and colleagues. All arrays were run together (interleaved) as a single large batch.

diff --git a/general/datasets/Uthsc_spl_rma_1010/notes.rtf b/general/datasets/Uthsc_spl_rma_1010/notes.rtf new file mode 100644 index 0000000..c7bb873 --- /dev/null +++ b/general/datasets/Uthsc_spl_rma_1010/notes.rtf @@ -0,0 +1,4 @@ +

Data Status and Use. This is a provisional release that will soon be replaced by a final corrected data set. In the interim this data set is open for exploration and use for focused analysis of single genes. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data regarding the best citation.
+This data set is not yet freely available for global analysis. This data set has not yet been used or described in any publication. Please see the GeneNetwork data sharing policy for more background on data use.

+ +

Contact. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data.

diff --git a/general/datasets/Uthsc_spl_rma_1010/processing.rtf b/general/datasets/Uthsc_spl_rma_1010/processing.rtf new file mode 100644 index 0000000..deaf264 --- /dev/null +++ b/general/datasets/Uthsc_spl_rma_1010/processing.rtf @@ -0,0 +1,1932 @@ +

Data Processing. Array data sets were generated by the vendors GCOS system. Expression values were logged and then were further normalized and rescaled so that the mean value for each array data set is 8 units with a standard deviation of 2 units. Data were processed by Arthur Centeno.

+ +

Batch Effects. This data set required some correction for batch effects and the data in this initial release incorporate any additional corrections. There are several additional confounder-like factors that should be considered:

+ +
    +
  1. Sex imbalance in the sample: use probe sets for Xist as correction in partial correlation
    2. +
  2. Background noise factors: examine and use probe sets with very low expression using the search "mean=(3.900 4.135)". This will extract the probe sets with the lowest expression. (Note that the number 54 is less than the total number of cases in this data set; important in computing principal components.) Add these probe sets to your collection window and then compute the correlation matrix. Use the first few principal components as surrogates for nuisance factors in partial correlation analysis. The first principal component of the lowest probe sets in this spleen data set accounts of XX% of the the variance. Mapping of this noise trait can be used to evaluate the effects of shared noise on QTL results. The first principal component in the spleen data set can be mapped as a trait.
    3. +
+ +

Data Release. This data set was first uploaded into GeneNetwork by Arthur Centeno, October 11, 2010 and made accessible without a password to all users on November 1, 2010. The initial data release had numerous strain identification errors that have now largely been fixed. Based on an analysis of the top 20 Mendelian loci, the following 21 strains were likely to have been incorrectly identified or assigned in the current release:

+ +
    +
  1. BXD8, e.g., Probe set 10450161, 1036098. 10338684
    2. +
  2. BXD13, e.g., Probe set 10450161, 1036098, 10402390, 10592493, 10342568,
    3. +
  3. BXD21 (may be ok, only one probe set 10338684 is problematic)
    4. +
  4. BXD23 (may be ok, only two probe sets 10421128, 10419465 is problematic)
    5. +
  5. BXD36 (may be ok, only one probe set 10421128 is problematic)
    6. +
  6. BXD40, e.g., Probe set 10341070
    7. +
  7. BXD43, e.g., Probe set 10450161, 1036098, 10338684
    8. +
  8. BXD48, e.g., Probe set 1036098, 10402390, 10514896, 10592493, 10357381, 10342568, 10571444, 10419465
    9. +
  9. BXD62, e.g., Probe set 1036098, 1036098, 10402390, 10514896, 10592493, 10421128, 10571444
    10. +
  10. BXD68 (may be ok, only one probe set 10338684 is problematic)
    11. +
  11. BXD69, e.g., Probe set 10450161
    12. +
  12. BXD73, e.g., Probe set 10341070, 1036098, 10402390, 10514896, 10587633, 10342568, 10421128
    13. +
  13. BXD74, e.g., Probe set 10402390
    14. +
  14. BXD80, e.g., Probe set 10341070, 1036098, 10592493, 10400109, 10338684, 10342568, 10421128, 10419465
    15. +
  15. BXD83, e.g., Probe set 10450161, 10338684
    16. +
  16. BXD87 (may be ok, only one probe set 10421128 is problematic)
    17. +
  17. BXD89, e.g., Probe set 10450161, 1036098, 10402390, 10592493, 10357381, 10419465
    18. +
  18. BXD93, e.g., Probe set 10402390, 10357381
    19. +
  19. BALB/cByJ, e.g., Probe set 10388042, 1036098, 10587633, 10357381, 10342568, 10421128
    20. +
  20. LP/J, e.g., Probe set 10592493
    21. +
  21. DBA/2J, e.g., Probe set 10592493
    22. +
+ +

Data Evaluation Summary

+ +
    +
  1. Before correction: eQLTs with LOD >10 (LRS>46.1): n = 638
    2. +
  2. After strain assignment correction: eQLTs with LOD >10 (LRS>46.1): n = 820
    3. +
  3. Before correction: eQTL with high LOD and LRS: Trait ID 10450161 (H2-Ea-ps) LOD = 51.6, LRS = 237.9
    4. +
  4. After correction: eQTL with high LOD and LRS: Trait ID 10450161 (H2-Ea-ps) LOD = 51.6, LRS = 278.1
    5. +
  5. Lowest mean value: Trait ID 10344361, mean = 3.998
    6. +
  6. Highest mean value: Trait ID 10598025, mean = 14.475 (MT-ND1)
    7. +
  7. Greatest sex difference: Trait ID: 10606178 (Xist)
    8. +
  8. Great variation within and among strains: Trait ID 10454192 (Ttr +

    Table 1 (please confirm that these assignments are after correction)

    + +
    + + + + + + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    IndexArray IDPhaseStrainAgeSex
    1R5583S1129P3/J65F
    2R5584S1129P3/J66M
    3R5585S1129S1/SvImJ66F
    4R5586S1129S1/SvImJ66M
    5R5587S1129X1/SvJ65F
    6R5588S1129X1/SvJ66M
    7R6348S3B6D2F167F
    8R6347S3B6D2F162F
    9R5590S1B6D2F179M
    10R5662S1BALB/cByJ59F
    11R5664S1BALB/cByJ59M
    12R5591S1BALB/cJ51F
    13R5592S1BALB/cJ51M
    14R6154S2BTBR T+ tf/J60F
    15R6516S3BXD182F
    16R6584S3BXD195M
    17R5759S1BXD2N/AF
    18R5837S1BXD2106M
    19R5874S2BXD586F
    20R6554S3BXD560M
    21R6359S3BXD672F
    22R5777S1BXD6149M
    23R6364S3BXD876F
    24R5637S1BXD871F
    25R6365S3BXD876M
    26R5746S1BXD970F
    27R5981S2BXD967M
    28R5980S2BXD967M
    29R6182S2BXD1184F
    30R6486S3BXD1158M
    31R6711S24BXD1271F
    32R6608S3BXD1248F
    33R5885S2BXD1244M
    34R5755S1BXD13160F
    35R5887S2BXD1353M
    36R6180S2BXD1470F
    37R5669S1BXD1491M
    38R6456S3BXD1560F
    39R6622S3BXD1560F
    40R6626S3BXD1560M
    41R6181S2BXD1674F
    42R6515S3BXD1664M
    43R5673S1BXD1880F
    44R5674S1BXD1865M
    45R6553S3BXD19158F
    46R6551S3BXD1960M
    47R6643S44BXD2059F
    48R6595S3BXD2060M
    49R5735S1BXD2164F
    50R5892S2BXD2199M
    51R5896S2BXD2260F
    52R6414S3BXD2273M
    53R6550S3BXD2374F
    54R6586S3BXD23102F
    55R5630S1BXD2471F
    56R6356S3BXD2457M
    57R6162S2BXD2567F
    58R6625S3BXD2567F
    59R6642S44BXD2558M
    60R5761S1BXD27N/AF
    61R5763S1BXD2790M
    62R6621S3BXD28113F
    63R6548S3BXD2860M
    64R6547S3BXD2960F
    65R6453S3BXD3148F
    66R6452S3BXD3148M
    67R6583S3BXD3260F
    68R5765S1BXD3271M
    69R5689S1BXD3365F
    70R6450S3BXD3355M
    71R5767S1BXD3472F
    72R5900S2BXD3470M
    73R6588S3BXD3661F
    74R6490S3BXD3663M
    75R6417S3BXD3864F
    76R6439S3BXD3872M
    77R5769S1BXD39N/AF
    78R5771S1BXD3974M
    79R5773S1BXD40N/AF
    80R5775S1BXD40N/AM
    81R6494S3BXD4172F
    82R5910S2BXD4279F
    83R6493S3BXD4269M
    84R6341S3BXD4359F
    85R6401S3BXD4399M
    86R5916S2BXD4379M
    87R5839S1BXD44141F
    88R5779S1BXD44124M
    89R6405S3BXD4558F
    90R6610S3BXD4555M
    91R5922S2BXD4864F
    92R5925S2BXD4860M
    93R6719S14BXD4958F
    94R6485S3BXD4979M
    95R5781S1BXD5061F
    96R6464S3BXD5165F
    97R6585S3BXD5163M
    98R6500S3BXD5558F
    99R5938S2BXD5593M
    100R6504S3BXD5658F
    101R6503S3BXD5658M
    102R5783S1BXD60111F
    103R5784S1BXD6085M
    104R5786S1BXD6186F
    105R6449S3BXD6165M
    106R6716S14BXD6254F
    107R5790S1BXD62115M
    108R6519S3BXD6354F
    109R6717S14BXD6370M
    110R5792S1BXD64167F
    111R6641S44BXD6468M
    112R6630S3BXD6468M
    113R6477S3BXD6558F
    114R6628S3BXD6570M
    115R6511S3BXD6670F
    116R6448S3BXD6661M
    117R5794S1BXD66144M
    118R6502S3BXD6766F
    119R6545S3BXD6761M
    120R6337S3BXD6856F
    121R6594S3BXD6864M
    122R5796S1BXD6985F
    123R5798S1BXD6998M
    124R6402S3BXD7093F
    125R5841S1BXD70121F
    126R6592S3BXD7059M
    127R6328S3BXD7187F
    128R5967S2BXD7164M
    129R5969S2BXD7364F
    130R5800S1BXD73120M
    131R6646S3BXD7440F
    132R6524S3BXD7472M
    133R6445S3BXD7585F
    134R5843S1BXD75103F
    135R5845S1BXD75103M
    136R6604S3BXD7764F
    137R6513S3BXD7772M
    138R6582S3BXD78144F
    139R6563S3BXD7895M
    140R6645S44BXD7966F
    141R5806S1BXD7978M
    142R5847S1BXD8089F
    143R5852S1BXD8079M
    144R6562S3BXD8199F
    145R6468S3BXD8165M
    146R6560S3BXD8285F
    147R6512S3BXD8368F
    148R5810S1BXD83139M
    149R6510S3BXD8487F
    150R5970S2BXD84107F
    151R6603S3BXD8499M
    152R6517S3BXD8558F
    153R6718S14BXD8586M
    154R5812S1BXD8661F
    155R5814S1BXD8659M
    156R5816S1BXD87112F
    157R6488S3BXD87137M
    158R6580S3BXD88125F
    159R5977S2BXD8968F
    160R5979S2BXD8979M
    161R5978S2BXD8979M
    162R5818S1BXD90106F
    163R5820S1BXD90131M
    164R6343S3BXD9262F
    165R5984S2BXD9255M
    166R6581S3BXD93173M
    167R6557S3BXD93126M
    168R6509S3BXD9559F
    169R5822S1BXD9589M
    170R6640S44BXD9670F
    171R6514S3BXD9664M
    172R6506S3BXD9778F
    173R5849S1BXD97130F
    174R6591S3BXD97122M
    175R5990S2BXD9865F
    176R6596S3BXD9867M
    177R5993S2BXD9974F
    178R5995S2BXD9950M
    179R6607S3BXD10075F
    180R6411S3BXD100104M
    181R6508S3BXD10159F
    182R5593S1BXD10159M
    183R6523S3BXD10260F
    184R6466S3BXD10250M
    185R6404S3BXD10372F
    186R6609S3BXD10357M
    187R6555S3C57BL/10J73M
    188R5596S1C57BL/10J73M
    189R5597S1C57BL/6ByJ51F
    190R5598S1C57BL/6ByJ69M
    191R5600S1C57BL/6J79F
    192R5599S1C57BL/6J60F
    193R6451S3C57BL/6J77M
    194R6410S3C57BL/6J85M
    195R5603S1C57BLKS/J66F
    196R5604S1C57BLKS/J66M
    197R5996S2CBA/CaJ66F
    198R6349S3CBA/CaJ66M
    199R6458S3D2B6F164F
    200R6353S3D2B6F160M
    201R5605S1DBA/2J79F
    202R6446S3DBA/2J83M
    203R6597S3FVB/NJ60F
    204R5643S1FVB/NJ60F
    205R6598S3FVB/NJ60M
    206R5606S1ILS74F
    207R5607S1ILS74M
    208R5610S1ISS97M
    209R6627S3KK/HlJ64F
    210R6444S3KK/HlJ65M
    211R5702S1KK/HlJ61M
    212R5613S1LG/J63F
    213R5704S1LG/J65M
    214R5614S1LP/J65F
    215R5615S1LP/J65M
    216R6599S3MOLF/EiJ60F
    217R6606S3MOLF/EiJ60M
    218R6544S3NOD/LtJ77F
    219R5709S1NOD/LtJ58M
    220R6601S3NZB/BlNJ61F
    221R5711S1NZB/BlNJ61F
    222R6427S3NZB/BlNJ58M
    223R6150S2NZO/HlLtJ71F
    224R6155S2NZW/LacJ65F
    225R5654S1NZW/LacJ60M
    226R5721S1PL/J59M
    227R5616S1PWD/PhJ60M
    228R5725S1PWK/PhJ121M
    229R6174S2SJL/J63F
    230R6350S3SJL/J65M
    231R6419S3WSB/EiJ60F
    232R5620S1WSB/EiJ60M
    +
    +
    + +
      +
    +
    9. +
diff --git a/general/datasets/Uthsc_spl_rma_1010/summary.rtf b/general/datasets/Uthsc_spl_rma_1010/summary.rtf new file mode 100644 index 0000000..d9478f8 --- /dev/null +++ b/general/datasets/Uthsc_spl_rma_1010/summary.rtf @@ -0,0 +1,3 @@ +

This is a near final release of a spleen gene expression data set generated by a DOD-funded consortium (Byrne, Kotb, Williams, and Lu). Please contact Lu Lu or Robert Williams regarding status of this data set. The initial data enterted in 2010 had many errors described below. The data set is much improved and has no known errors of strain assignment.

+ +

Animals were generated at UTHSC by Lu Lu and colleagues. The spleen of untreated young adult mice was profiled using the Affymetrix GeneChip Mouse Gene 1.0 ST array that contains approximately 34,728 probe sets that target approximately 29,000 well defined transcripts (RefSeq mRNA isoforms) and essentially all known protein coding genes in mouse. This array is an "exon style" array with multiple probes in all known exons of each gene (an average of about 27 per gene) and is an abridged version of the Affymetrix Exon 1.0 ST array. However, it also does contain some probes that target non-coding RNAs and even miRNA precursors (search "ncrna").

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