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| Status |
Public on Jun 30, 2017 |
| Title |
Array-Set I_single animal / chip_Ctrl line_Testis_12w_biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Ctrl line: FBN proprietary Outbred Mouse Line, 172nd generation, 12w/13w, testis
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Ctrl line, FBN outbred long-term selection mouse line, unselected Control Line (also known as FzTDU), 172nd generation
selection criteria: randomly selected
background: two-factorial breeding experiment, 4th replicate
age: 12w/13w
gender: male
tissue: testis
|
| Treatment protocol |
12/13 weeks old murine bucks were euthanized with carbon dioxide gas prior to removal and preparation of testis. Gained samples were preserved by submerging in RNAlater® RNA Stabilization Solution (Ambion®/Thermo Fisher Scientific) according to the manufacturers protocol.
|
| Growth protocol |
The animals were maintained in a specific pathogen-free (SPF) environment with defined hygienic conditions at a temperature of 22.5°C, at least 40% humidity and a controlled light regime with a 12:12-h light-dark cycle. Mice were fed with water and pellet concentrate ad libitum. Bucks involved in 2nd or 4th replicate of two-factorial breeding experiment (both array sets) were allowed to mate at age of 10w with simultaneously caged females of 3 different lines each (FL1, FL2, Ctrl). The mating period was granted for 2 weeks, following preparation of these males at age of 12/13 w for array experiment. Advantageously, all our two-factorial breeding experiment samples could be provided simultaneously regardless any line-affiliation in contrast to routinely generated standard breeding animals that require line-specific breeding periods. Thus, a more suitable comparability could be ensured.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from mouse testis was extracted using the RNeasy Plus Mini Kit (Qiagen®) including removal of genomic DNA. Isolated RNA was checked for integrity and quantity by an electrophoretic assay performed on a 2100 Bioanalyzer nanochip (Agilent).
|
| Label |
Biotin
|
| Label protocol |
100ng total RNA was converted to fragmented biotinylated cDNA using the standard WT Plus protocol (Affymetrix Inc.)
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| |
|
| Hybridization protocol |
Labeled samples were hybridized to GeneChip® Mouse Transcriptome Arrays 1.0 (GPL 20258, Affymetrix Inc.) for 16h at 45°C inside GeneChip® Hybridization Oven 645 (Affymetrix Inc.). Hybridization and following washing and staining steps were performed in GeneChip® Fluidics Station 450 according to standard protocols.
|
| Scan protocol |
Scanning of the microarray was conducted at 1.56 micron resolution with GeneChip® Scanner 3000 7G (Affymetrix Inc.). Image processing was accomplished with help of software Affymetrix GeneChip® Command Console 4.0 (AGCC 4.0).
|
| Description |
first transcriptome profiling: hypothesis generation for differential expression
|
| Data processing |
Data analysis was performed with Expression Console (Version V1.4.1.46, Affymetrix Inc.) using the SST-RMA algorithm for normalization. Further comparative analysis was done with Transcriptome Analysis Console (Version V3.0.0.466, Affymetrix Inc.).
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| |
|
| Submission date |
Aug 25, 2016 |
| Last update date |
Jun 30, 2017 |
| Contact name |
Alexander - Sobczak |
| E-mail(s) |
[email protected]
|
| Phone |
03820868765
|
| Organization name |
Leibniz Institute for Farm Animal Biology Dummerstorf (FBN)
|
| Department |
Institute for Reproductive Biology
|
| Lab |
Reproductive Biochemistry
|
| Street address |
Wilhelm-Stahl-Allee 2
|
| City |
Dummerstorf |
| State/province |
Mecklenburg Western-Pomerania |
| ZIP/Postal code |
18196 |
| Country |
Germany |
| |
|
| Platform ID |
GPL20258 |
| Series (1) |
| GSE86063 |
Testis transcriptional profiling of males deriving from two high fertility mouse lines (FL1, FL2) which have been long-term selected for the characteristics large and heavy litters in comparison to randomly selected control line (Ctrl) |
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