NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM441177 Query DataSets for GSM441177
Status Public on Oct 05, 2010
Title testis fertile M. musculus rep 2
Sample type RNA
 
Source name testis, fertile
Organism Mus musculus
Characteristics cross: F1 PWK/PhJ X CZECHII/EiJ
tissue: testis
fertility: fertile
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
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
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.
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.
 
Hybridization protocol Arrays were hybridized, washed, and stained accoring to the array manufacturers instructions. Washing and stainig was performed on GeneChip fluidics station.
Scan protocol The arrays were scanned using a GeneChip 3000 scanner.
Description cross between two musculus strains
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.
 
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
 
Platform ID GPL6886
Series (1)
GSE17684 Widespread over-expression of the X chromosome in sterile F1 hybrid mice

Data table header descriptions
ID_REF
VALUE Quantile normalized log 2 gene level expression values calculated with PLIER.

Data table
ID_REF VALUE
ENSMUSG00000042210_at 9.654855158
ENSMUSG00000050304_at 10.20504119
ENSMUSG00000025420_at 8.998461806
ENSMUSG00000033658_at 6.982832204
ENSMUSG00000042607_at 6.228560937
ENSMUSG00000018372_at 8.38541583
ENSMUSG00000006527_at 7.701424264
ENSMUSG00000026018_at 9.506166651
ENSMUSG00000040013_at 9.524817933
ENSMUSG00000025519_at 7.454851521
ENSMUSG00000041571_at 10.32631074
ENSMUSG00000019986_at 8.929705901
ENSMUSG00000031583_at 7.517356363
ENSMUSG00000034706_at 6.778618593
ENSMUSG00000029402_at 8.491267668
ENSMUSG00000032595_at 9.112499363
ENSMUSG00000014503_at 8.329128164
ENSMUSG00000019178_at 9.93509264
ENSMUSG00000027001_at 6.88688112
ENSMUSG00000026163_at 7.739421105

Total number of rows: 7000

Table truncated, full table size 231 Kbytes.




Supplementary file Size Download File type/resource
GSM441177.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap