Methylation analysis (SOLiD System, Ion Torrent PGM)

ChIP seq (SOLiD System, Ion Torrent PGM)


SOLiD 5500 Wildfire (W) System is based sequencing by ligation and gives out short reads (up to 75 bp forward and 50 bp reverse), which are latter mapped on reference sequence or connected via de novoalgorithms. Instead of beads the 5500 W system uses direct amplification and that reduces the template preparation time. The advantage in comparison to polymerase-based sequencing is the higher accuracy (up to 99,9999 %), while the colour space method is applied and every nucleotide is sequenced twice. The high throughput SOLiD platform is optimal for larger projects, but smaller projects could also be considered as we offer pay-per-lane sequencing. 5500 W is robust and powerful platform delivering 320 Gbase high quality sequencing data per run. With our SOLID 5500 W configuration we can sequence up to 72 exomes or transcriptomes or up to 288 small RNA samples per run or even more in certain cases.


Ion Torrent PGM(Personal Genome Machine) is a next generation sequencer, which detects changes in pH for sequencing and no camera or imaging is needed. Thus, the platform is perfect for fast and easy sequencing. There are three different-sized chips – up to 400 bp reads could be sequenced and up to 2 Gbase of data could be reached with one run. Within two days sequencing starting from library preparation and data analysis could be performed. Additionally, Ion Torrent PGM System has several ready to use panels suitable for both RNA and DNA sequencing (Ion AmpliSeq Target Selection Technology).


OpenArray AccuFill System could be applied for genotyping, qRT-PCR technology and it allows simultaneous detecting of 16 to 256 SNPs in one OpenArray plate. OpenArray technology uses special microscope slide-sized plates filled with 3072 through-holes, each acting as a 33nL reactor. Genomic DNA input amount per subarray is 125 ng. Plates are available in several formats, from 144 samples against 16 TaqMan genotyping assays to 12 samples against 256 TaqMan genotyping assays. Laboratory capacity allows to load, amplify and scan 6 TaqMan OpenArray Genotyping plates in an 8-hour workday. Each genotyping plate is preloaded with 16 to 256 TaqMan assays. Minimum number of OpenArray plates for one project is 10.


Fast Real-Time PCR Systemsuitable for smaller projects and is applicable for both genotyping and gene expression studies. TaqMan SNP genotyping assays provide a detection of polymorphisms within any genome. Workflow is based on 5’ nuclease assay chemistry with TaqMan MGB probes. Assays are ideal for genotyping applications including screening, association, candidate region, candidate gene, and fine-mapping studies. You need to provide the SNP information number for us (specific Applied Biosystems SNP assay). We are using 384-well plate mode, which is suitable for tens of SNPs and about 1000s of samples. For higher throughput projects customers should consider OpenArray System. For gene expression studies we are using TaqMan Gene expression assays. Customer should provide for us with the gene of interest and RNA or CDNA.  


Input material requirements for the applications

Applications with SOLiD System:

whole genome sequencing - mate-pair library input 1-5 mg gDNA and fragment library input 10 ng -5 mg gDNA

whole exome sequencing (human) – input 3 mg gDNA

whole transcriptome sequencing – input 50 ng -10 mg total RNA

small RNA sequencing – input £ 1 mg total RNA or enriched small RNA


Applications with Ion PGM:

Ion AmpliSeq Target Selections Technology:

Custom and ready-to-use panels for DNA – input 10-40 ng gDNA, FFPE DNA

Custom and ready-to-use panels for RNA – input 500 pg total RNA, 5 ng FFPE RNA

DNA sequencing – fragment library input 100 ng – 1 mg gDNA

whole transcriptome sequencing – input 50 ng -10 mg total RNA

small RNA sequencing – input £ 1 mg total RNA or enriched small RNA


Applications with OpenArray AccuFill System

custom SNP genotyping – TaqMan genotyping gDNA input amount per subarray is 125 ng (Recommended starting concentration for human DNA samples is 50ng/ml)


7900HT Fast Real-Time PCR System

custom SNP genotyping – input 40ng gDNA

custom CNV analysis – input 20ng gDNA

Single or multiple gene expression analysis (absolute and relatative quantitation)