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Two different adaptor-ligated tester cDNAs were separately denatured at 98 °C for 90 s and then hybridized at 68 °C for 8 h with an excess of relative driver cDNA in a ratio of tester: driver = 1: 30.
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The successive rounds of subtraction and amplification were performed using hybridization tester-driver ratios of 1 10 and 1 100.
When subtractive amplification is performed, only Tester-Tester homodimers are exponentially amplified while Tester-Driver heterodimers follow a linear amplification and progressively become underrepresented.
The Tester-Driver co-precipitate was dissolved in 5 μl of EEB buffer (Sigma EPPS buffer 30 mM, pH 8 with 3 mM EDTA).
The following stages were used in tester-driver subtractions: - for rabbit embryonic activation: early morulae (16 32 cell stage) – one cell stage (rab1 library) and early morulae – 4 cell stage (rab3 library).
The procedure involves two successive tester-driver hybridisation steps, the first of which induces a normalisation of tester-specific molecules, thus allowing the subsequent cloning of rare, tester-specific transcripts.
Because we were interested in the more systematic establishment of SSH libraries dedicated to the analysis of early mammalian embryo development, we designed a procedure involving exogenous reporter transcripts that mimic either tester-specific or tester-driver common transcripts to enable the large scale assessment of the quality of such libraries.
Two of them (3P11 and 3I20) were tester-specific, but the others (3L22 and 3C24) were expressed in both tester and driver, with double their relative abundance in tester than in driver (3L22 and 3C24 representing respectively about 1.2 and 1.5% of morula driver cDNAs).
The tester to driver hybridisation steps in the SSH procedure require one hundred nanograms of tester and driver cDNA, whereas a preimplantation embryo only contains a few picograms of mRNAs.
Tester and driver cDNAs were separately digested with Rsa I.
All Asplenium and Garovaglia tester and driver digestion products were phenol chloroform extracted, isopropanol precipitated and resuspended in deionized water.
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