modENCODE Embryonic RACE
Drosophila melanogaster RACE from pooled PCR products
Sequences of RNA Ligase Mediated Rapid Amplification of cDNA Ends (RLM-RACE) products representing 5' ends of selected transcripts. Total RNA isolated from mixed stage embryos of the "iso-1" isogenic  strain was provided by the laboratory of Peter Cherbas (University of Indiana, Bloomington). Gene-specific 5' RLM-RACE products were generated using the FirstChoice RLM-RACE procedure (Ambion). Normalized pools of RACE products were created and directly sequenced on a 454 Life Science sequencer. Vector sequences were removed and the RNA adapter sequence was used to determine the orientation of the PCR product and was removed from the sequence. Each sequence represents a potential transcription start site and is oriented along the direction of transcription. NOTE: PCR products are not preserved and are not available for distribution.
5' RACE of a pool of selected transcript targets known to be expressed in Drosophila was conducted to determine the transcription start site to high accuracy. For each experiment, a pooling of several thousand RACE products was sequenced on a 454 Life Science sequencer. Each sample read was trimmed of linker sequence and mapped to the Drosophila genome to determine the start site.