strain: FVB gender: male tissue: whole organism age: newborn
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted with Trizol ® following manufacturer´s protocol
Label
dUTP-Cy5
Label protocol
12 µg of total RNA were primed with 1 µg of random hexamers plus 1 µg of oligo-dT at 75°C for 10 min, then reversed transcribed at 42°C for 2.5 h with 500 U SuperScript II (Invitrogen), and 0.5 mM each dATP, dCTP, dGTP, 0.2 mM dTTP, and 0.1 mM dUTP-Cy3 (or Cy5, when corresponded).
strain: BalbC gender: female tissue: ovary age: 8 weeks old
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted with Trizol ® following manufacturer´s protocol
Label
dUTP-Cy3
Label protocol
12 µg of total RNA were primed with 1 µg of random hexamers plus 1 µg of oligo-dT at 75°C for 10 min, then reversed transcribed at 42°C for 2.5 h with 500 U SuperScript II (Invitrogen), and 0.5 mM each dATP, dCTP, dGTP, 0.2 mM dTTP, and 0.1 mM dUTP-Cy3 (or Cy5, when corresponded).
Hybridization protocol
Labeled test and reference cDNAs were mixed with 35 µg of mouse Cot1 DNA, 35 µg of poli-dA in a solution containing 0.1% SDS and 3.5X SSC. Slides were place in closed hybridization chambers and incubated for 16-20 hrs in a water bath at 65°C. Washes in 2X SSC-0.1% SDS, 1X SSC, 0.2X SSC, and 0.05X SSC were performed sequentially, 1-min each.
Scan protocol
Microarrays were quickly dried and scanned at 10-µm resolution in a ScanArray-Lite scanner (Perkin Elmer, MA). PMT was adjusted to obtain maximal signal intensities with minimal saturation
Description
n/a
Data processing
Microarray images were saved in TIFF format and extracted as GenePix result (gpr) files using GenePix Pro III software (Molecular Devices, CA). Data was subjected to print-tip (local) Loess normalization and scale adjustment with the DNMAD tool (http://dnmad.bioinfo.cnio.es) and then filtered/imputed for missing values with the preP tool (http://prep.bioinfo.cnio.es/).
Ovarian transcriptional profiles of four mouse strains
Data table header descriptions
ID_REF
VALUE
lowess normalized log2 ratio representing test/reference (Cy5/Cy3 in direct, and Cy3/Cy5 in reverse experiments). The suffixes d and r in Sample names and matrix headers stand for direct and reverse experiments, respectively. Data from reverse experiments has been multiplied by (-1.0) in the matrix data spreadsheet.
