User guide

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Fragment Library Preparation Using the AB Library Builder
™
System: 5500 Series SOLiD
™
Systems User Guide
Glossary
barcode
A short, unique sequence that is incorporated into a library that enables identification
of the library during multiplex sequencing.
Barcoded Adaptor
During fragment library preparation, the double-stranded oligonucleotide that is
ligated to the genomic DNA fragment such that the internal adaptor, barcode
sequence, and the P2 Adaptor are at the 3' end of the sequencing template.
barcoded library
A library that has a unique barcode sequence incorporated that enables identification
of the library during multiplex sequencing.
fragment library
A library that has a single insert prepared from genomic DNA for sequencing on the
SOLiD™ System. Fragment libraries compatible with the 5500 Series SOLiD
™
Sequencers can be sequenced with a forward-only run or with a paired-end run.
internal adaptor (IA)
The internal adaptor sequence is incorporated into the template during library
construction and provides a common hybridization target for SOLiD™ sequencing
primers. The IA sequence is different in DNA-source libraries and RNA-source
libraries, therefore sequencing primers specific for RNA and DNA libraries must be
used for reverse reads (F5 tag). The IA-containing adaptors used during mate-paired
library preparation are different from the adaptors used for fragment library
preparation, but the sequencing primers used for forward reads originating in the IA
sequence (R3 and BC tags) are the same. See the 5500 Series SOLiD
™
Systems Sequencing
Products Ordering Guide for a schematic of sequencing primers compatible with each
type of SOLiD™ library.
library
A set of DNA or cDNA molecules prepared from the same biological specimen and
prepared for sequencing on the SOLiD™ System.
Library PCR
Primer 1
Single-stranded oligonucleotide used in library amplification and corresponding to the
P1-T Adaptor sequence.
Library PCR
Primer 2
Single-stranded oligonucleotide used in library amplification and corresponding to the
P2 Adaptor sequence.
mate-paired library
Library consisting of two DNA segments that reside a known distance apart in the
genome, linked by an internal adaptor, and with P1 and P2 Adaptors ligated to the 5'
and 3' ends of the template strand, respectively.
multiplex
sequencing
Sequencing runs in which multiple barcoded libraries are simultaneously sequenced
in a single flowchip lane. Each bead is assigned to the correct library after the
sequencing run according to the sequence of its barcode.