Methods and kits for preparing nucleic acid samples

A method for analyzing a plurality of transcripts comprising:

• a) hybridizing a primer mixture with the plurality of RNA transcripts or nucleic acids derived from the RNA transcripts and synthesizing first strand cDNAs complementary to the RNA transcripts and second strand cDNAs complementary to the first strand cDNAs to produce first cDNAs, wherein the primer mixture comprises oligonucleotides with a promoter region and a random sequence primer region;
• b) transcribing RNA initiated from the promoter region to produce cRNAs;
• c) hybridizing a random primer mixture with the cRNAs;
• d) synthesizing second cDNAs from the random primers in the presence of one modified DNA precursor nucleotide substrate for a DNA glycosylase.
• e) fragmenting the second cDNAs to produce fragmented cDNAs;
• f) hybridizing fragmented cDNAs with a plurality of nucleic acid probes to detect the nucleic acids representing target transcripts.