title: Triticum aestivum cv. Chinese spring SOLiD 3 sequencing
design: Library construction followed methods in the Applied Biosystems SOLiD 3 System Library Preparation Guide. For Emulsion PCR, templated beads were prepared from the mate-paired library using the ePCR kit v.3 and the Bead Enrichment Kit from Applied Biosystems for SOLiD3 and the SOLiD™ EZ Bead™ System. A Workflow Analysis was carried out after the first round of templated bead preparation using the Workflow Analysis kit from Applied Biosystems to check library quality and the amount of templated beads generated per ePCR. Templated beads were deposited on slides using the Bead Deposition kit from Applied Biosystems and sequencing was done according to the Applied Biosystems SOLiD 3 System Instrument Operation Guide using the reagents from Applied Biosystems
library_name: Triticum aestivum
library_construction_protocol: A 2x50bp Mate-paired library was constructed using the Applied Biosystems SOLiD™ 3 System Library Preparation Guide following the manufacturer’s recommendations. 50μg of gDNA were fragmented by HydroShear (Digilab Genomic Solutions Inc) to 1.5–3.5kb. The fragmented DNA was end-repaired and the LMP CAP adaptor was ligated to the ends. DNA Fragments between 2–3 kb were selected using a 1.0% agarose gel. Fragments were circularized with a biotinylated internal adaptor. Non-circularized DNA fragments were eliminated by Plasmid-Safe ATP-Dependent DNase (Applied Biosystem) and 2μg of circularized DNA were recovered after purification. Original DNA nicks at the LMP CAP oligo/genomic insert border were translated into the target genomic DNA to approximately 100bp by nick translation using E. coli DNA polymerase I.  Fragments containing the target genomic DNA and adaptors were cleaved from the circularized DNA by single-strand specific S1 nuclease. P1 and P2 adaptors were ligated to the fragments and the ligated mixture was amplified with 10 cycles of PCR. Finally, 250–300bp fragments were selected using E-Gel® system (Invitrogen) to ensure an average target length of around 100bp in the completed mate-paired library.