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Status |
Public on Oct 05, 2010 |
Title |
testis fertile M. musculus rep 2 |
Sample type |
RNA |
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Source name |
testis, fertile
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Organism |
Mus musculus |
Characteristics |
cross: F1 PWK/PhJ X CZECHII/EiJ tissue: testis fertility: fertile
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Treatment protocol |
Testis were immediately dissected after being euthanized. One testis was cross-sectioned, stored immediately in RNAlater (Ambion, Inc., Austin, TX), and archived at -80C
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Growth protocol |
All breeding colonies were established using individuals purchased from the Jackson Laboratory (Bar Harbor, ME). To represent M. domesticus, we used M. domesticus LEWES/EiJ and M. domesticus WSB/EiJ. Both were derived from natural populations in eastern North America. We used M. musculus CZECHII/EiJ and M. musculus PWK/PhJ to represent M. musculus, which were isolated from different localities within the Czech Republic. The mice were maintained at the University of Arizona Central Animal Facility following IACUC regulations. Breeding pairs were housed two per cage and pregnant females were isolated prior to giving birth. Male offspring were weaned at approximately 20 days postpartum, housed in sibling groups of up to four until 40 days postpartum, and then caged singly until being sacrificed at 60 days old
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Extracted molecule |
total RNA |
Extraction protocol |
We extracted total RNA from whole testis using an RNeasy Midi kit (QIAGEN Inc., Valencia, CA) with mortar and pestle disruption and syringe homogenization. RNA sample quality and quantification was determined with an RNA Nano LabChip on an Agilent Bioanalyzer 2100 (Santa Clara, CA). Only samples with an RNA integrity number of 10 were used.
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Label |
biotin
|
Label protocol |
Biotinylated complementary RNA was generated from 5 μg of total RNA through reverse trasncription, second strand synthesis, and invitro transcription according to the array manufacturers instructions.
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Hybridization protocol |
Arrays were hybridized, washed, and stained accoring to the array manufacturers instructions. Washing and stainig was performed on GeneChip fluidics station.
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Scan protocol |
The arrays were scanned using a GeneChip 3000 scanner.
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Description |
cross between two musculus strains
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Data processing |
Updated transcript definition were downloaded (www.brainarray.org) and used instead of the chip description file provided by affymetrix. All data processing and analysis was done in R. Data analysis was performed using probe logarithmic intensity error estimation (PLIER) on the signal intensity measurements as implemented with the justPlier function in BioConductor. We only considered for analysis those genes with detectable expression in all individuals based on Wilcoxon signed rank tests (P < 0.01) between perfect versus mismatch signals. Expression values were quantile normalized. We considered genes to have significantly different expression between groups based on gene-by-gene students t-tests (P < 0.05), excluding genes with no variation between individuals.
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Submission date |
Aug 17, 2009 |
Last update date |
Oct 05, 2010 |
Contact name |
Thomas Giger |
E-mail(s) |
giger@eva.mpg.de
|
Organization name |
Max-Planck-Institute of Evolutionary Anthropology
|
Department |
Evolutionary Genetics
|
Street address |
Deutscher Platz 6
|
City |
Leipzig |
ZIP/Postal code |
04106 |
Country |
Germany |
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Platform ID |
GPL6886 |
Series (1) |
GSE17684 |
Widespread over-expression of the X chromosome in sterile F1 hybrid mice |
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