SOLiD 5500xl System of Life Technologies
Technical background
The Life Technologies SOLiD 5500xl System provides parallel sequencing of clonally amplified DNA fragments linked to magnetic beads. The sequencing methodology is based on sequential ligation with dye-labeled oligonucleotides. All fluorescently labeled oligonucleotide probes are present simultaneously, competing for incorporation. After each ligation, fluorescence is measured before another round of ligation takes place. More about technology
The use of a two-base encoding mechanism, which interrogates each base twice for errors during sequencing, discriminates between true polymorphisms and system noise. More about two-base encoding
The SOLiD system supports a wide range of applications:
Experiment design and pricing.
Each experiment is unique and the cost varies widely. The cost depends on the source of DNA to be sequenced, the application, the desired coverage, the read length, the level of analysis required, etc.
Please contact us and we will work with you on planning your experiment.
SOLiD analyzer specifications:
Slides and Samlpes
Number of FlowChips per run -1 or 2.
Each FlowChip is divided to 6 independent lanes.
Up to 96 samples can be sequenced together using different barcodes (multiplexing).
Read length
Fragment libraries - 75 bases.
Paired-end libraries - 75 x 35 bases.
System Accuracy
Greater than 99.99% accuracy with Exact Call Chemistry Module.
Sample submission:
Recommended Amount of Starting Material
Required input of starting material varies by application
Fragment library: DNA - 10 ng to 5 μg
Mate-paired library: DNA - 5 µg to 20 μg
Gene expression profiling: total RNA - 2 µg to 10 μg
Small RNA profiling: total RNA enriched for small RNA - 1 µg to 10 μg
or purified small RNA - 100 ng
Please contact for further guidelines for samples’ preparations and concentration.
Quantification of RNA
Integrity of total RNA samples will be evaluated by Agilent 2100 Bioanalyzer.
RIN (RNA Integrity Number)>7 is acceptable.
Spectrophotometric absorbance parameters of the sample should be:
Ratio 260/280=1.8-2.0
Ratio 260/230 close to 2.0
Recommended kits for RNA Isolation.
For eukaryote samples:
PureLink™ RNA Mini Kit (Invitrogen - Cat. No. 12183018A or 12183020)
TRIzolR Reagent (Invitrogen - Cat. No. 15596- 026)
For plant samples:
Plant RNA Reagent (Invitrogen - Cat. No. 12322-012),
PureLink™ RNA Mini Kit (Invitrogen - Cat. No. 12183018A or 12183020),
TRIzolR Reagent (Invitrogen - Cat. No. 15596-026)
For Small RNA libraries:
Isolation of total RNA that contains fraction of small RNA 10–40 nt:
mirVana™ miRNA Isolation Kit (Ambion - Cat. No. AM1560)
mirVana™ PARIS™ Kit (Ambion - Cat. No. AM1556)
Isolation of small RNA from tissues or cells:
PureLink™ miRNA Isolation Kit (Invitrogen - Cat. No. K1570-01)
Whole Genome Resequencing
Comparative sequencing for organisms with known reference sequence that enable variant’s detection.
Using mate paired libraries enables to detect structural variation such as insertion, deletions, inversions, and translocations in addition to SNPs.
Sequence of large candidate regions against reference sequence.
It requires preliminary enrichment protocol.
The initial generation of the primary genetic sequence of a particular organism is called de novo sequencing. A detailed genetic analysis of any organism is possible only after de novo sequencing has been performed.
SOLiD™ System enable the de novo assembly of small organisms.
Whole Transcriptome Analysis
Detection of all known and novel RNAs in a transcriptome
Expression of all coding and non-coding RNAs
Conserve strandedness of cDNA, allowing you to know exactly which strand a particular transcript originated from.
Identification of alternative splicing events
Expressed SNPs (single nucleotide polymorphisms) or mutations
Translocations and fusion transcripts
Identify allele specific expression patterns
SAGE - Gene Expression Profiling
SAGE™ – Serial Analysis of Gene Expression System.
Quantification of gene expression levels on a genome-wide scale.
Sequencing unique 27 bp sequence tags isolated from the 3’ ends of mRNAs.
Detection of known and novel mRNAs with transcript’s expression from < 1 copy per cell to over 100,000 copies per cell.
Quantification of both traditional poly(A) and non-poly(A) transcripts.
Analysis of small RNA expression patterns and discover of novel small RNA. Detection of low small RNA expression levels.
Conserve strandedness of cDNA, allowing to know exactly which strand a particular transcript originated from.
Chromatin Immunoprecipitation Sequencing (ChIP-Seq)
Characterization of protein-DNA interactions and the identification of DNA binding sites for a particular protein of interest on the entire genome.
Analyzing genome-wide DNA methylation with a much higher level of resolution than traditional methods.
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DNA Sequencing