|Applied Biological Materials, Inc. is an Illumina Certified Service Provider, dedicated to ensuring the delivery of the highest-quality data available for genetic analysis applications. Click here for more details about the Illumina CSpro program.|
Key Features of abm’s Sequencing Panel Services:
• enable identification of:
- rare and common single-nucleotide variants (SNV's)
- small insertion/deletion variants
- de novo mutations
• guaranteed, high-quality data read-out of sample(s)
• library construction and target capture are performed using Illumina’s comprehensive TruSight Sequencing Panels
TruSight One Sequencing Panel Service - Cat# ID50120
Targeting > 4,800 genes associated with known clinical phenotypes; enabling labs to expand and streamline their assay portfolio and sequencing portfolio. For more information about gene lists and probe manifests, please refer to Illumina’s product files: http://www.illumina.com/products/trusight-one-sequencing-panel.html
With just 50ng of high quality input DNA, the TruSight One panel targets 12Mb of genomic content for Paired-End sequencing on the MiSeq V3 (2x150nt reads) at 200X mean sequencing coverage, which gives up to 8M reads per sample.
TruSight Cancer Sequencing Panel Service - Cat# ID50150
Targeting 94 genes and 284 SNPs previously linked to a predisposition towards both common (e.g. breast, colorectal) and rare cancers. For more information about gene lists and probe manifests, please refer to Illumina’s product files: http://www.illumina.com/products/trusight_cancer.html
With just 50ng of high quality input DNA, the TruSight Cancer panel targets 255Kb of genomic content for Paired-End sequencing on the MiSeq V2 kit (2x150nt reads) at 200X mean sequencing coverage, which gives up to 200,000 reads per sample.
TruSight Inherited Disease Sequencing Panel Service - Cat# ID50400
Focusing on severe, recessive pediatric onset diseases; targeting 552 genes, including coding exons, intron-exon boundaries, and regions known to harbor pathogenic mutations. For more information about gene lists and probe manifests, please refer to Illumina’s product files: http://www.illumina.com/products/trusight_inherited_disease.html
With just 50ng of high quality input DNA, the TruSight Inherited Disease panel targets 2.25Mb of genomic content for Paired-End sequencing on the MiSeq V2 kit (2x150nt reads) at 100X mean sequencing coverage, which gives up to 1 M reads per sample.
For each service, the results are provided in industry standard FASTQ format (default), while the Sequencing Panel Analysis package also delivers the alignment .bam file, as well as the list of detected variants in .vcf format. The kits used for the above target enrichments during library prep are part of the Illumina's TruSight product line. Alternative enrichment kits and panels can be requested at an additional cost.
The library QC will also be performed using the Agilent Bioanalyzer to determine library size and purity. Also, prior to loading the libraries on the sequencer, we perform qPCR quantification. The cost for this is included in the sequencing service.
For the QC of the final data from our sequencing service, the integrated software will generally do the job and provide adequate QC information, however, we can also provide additional QC data such as FASTQC upon request.
The data we output will pass our Q30 filter, which means that the error rate in base calls is less than 1 in 1000, or 0.1%. We will get a percentage at the end of the run which states the percentage of bases that have a Q score > 30, and this percentage is usually ≥85%.
mirVana™ PARIS™ Kit or PureLink® miRNA Isolation kit to enable adequate enrichment of your sample. If preferred, it should be okay to use Qiagen's kit, as long as the RNA Integrity Number (RIN) of the sample is above 8.0 to make sure there is no significant degradation. (Samples with a RIN lower than 8.0 may contain smaller degraded RNA fragments that can be sequenced in addition to the miRNAs). We prefer receiving Total RNA sample however so we can perform the bioanalyzer QC to check the RNA quality before beginning library construction. There will be no extra-charges if you submit Total RNA instead of isolated miRNA.
For miRNA sequencing we require 200ng-2ug of total RNA in 10ul of nuclease free water, as quantified with a fluorometric method. Lower amounts might result in inefficient ligation and low yield. If you are supplying purified miRNA, please submit a minimum of 50-100 ng of purified small RNA in 10ul is required. Purified small RNAs must be in nuclease free water or 10 mM Tris-HCI, pH 8.5.
For other services, there are generally no preferred DNA/RNA isolation kits as long as minimum requirements for QC are met.
The RNASeq_sample_cufflinks_output.tar.gz will also need to be unzipped to see the text files by vim, nano, gedit, or Notepad plus plus. The unzipped data an also be imported as text into the data tab of Excel 2007. Other versions may differ.
To analyze further, Excel can sort, filter, find, match, etc and has many functions for conditional coloring, graphing, etc.