The GARP Core offers some bioinformatics support for data analysis. Our basic data services currently include:
- The Illumina NextSeq 500 and NovaSeq 6000 pipeline software for the customer’s specific experiment, including image analysis, base calling and sequence alignment steps.
- A detailed report including sequence reads, exon location, exon-intron junction region, gene location and SNP calls.
- Experiment quality parameters such as base quality scores, quality control metrics, and sequencing run statistics.
- .BAM files generation available for fee upon request
GARP has access to both free ware and commercial data analysis software such as MAC, MAQ, BWA, Partek and GeneSpring. If you have specific requirements for your data analysis please contact us. GARP offers Next Generation Sequencing Services on the Illumina NextSeq 500 and NovaSeq 6000 Systems. The services include DNA Sequencing, Gene Regulation Analysis, Sequencing-Based Transcriptome Analysis, SNP Discovery and Structural Variation Analysis, Cytogenetic Analysis, DNA-Protein Interaction Analysis (ChIP-seq), Sequencing-Based Methylation Analysis, Small RNA Discovery, and Analysis for our users. We currently accept DNA and RNA samples from all species. However, for samples other than human and mouse, customers should provide their species' Reference Genome Sequence. In most cases the volumes of the data output will exceed two TB. If customers want to keep all these data, they can provide a large external hard drive or they can download their data from our secure website. Once users receive their data, these data are no longer kept in our computer system.
DNA-Protein Interaction Analysis (ChIP-seq)
The NextSeq 500 and NovaSeq 6000 also offer powerful DNA-Protein interaction analysis. By combining chromatin immunoprecipitation with Illumina's sequencing technology (ChIP-seq) on a genome-wide scale, biologists can accurately identify a broad range of interactions, accurately survey interactions between protein, DNA and RNA to interpret regulation events central to many biological processes and disease states.
Gene Regulation Analysis
Whether you are interested in CpG methylation, histone modifications, chromatin structure, or DNA-protein interactions, Illumina's unique sequencing chemistry gives you unbiased coverage of every base in the genome.
Use Illumina's ChIP-seq protocol to generate accurate and precise DNA-protein interaction maps from a single chromatin immunoprecipitated sample. Map genome-wide methylation patterns by sequencing bisulfite-converted DNA, methylation-sensitive restriction digest-enriched fragments, anti-methyl-C precipitated fragments, or chromatin immunoprecipitates of methyltransferases trapped to aza-labeled DNA.
The NextSeq 500 and NovaSeq 6000 make it possible for biologists to characterize all transcriptional activity, coding and non-coding, in any organism without a priori assumptions and achieve an unprecedented view of the transcriptome. By combining long and short reads, strand specificity, and millions of counts, Illumina allows you to annotate coding SNPs, discover transcript isoforms, identify regulatory RNAs, characterize splice junctions, and determine the relative abundance of transcripts.
SNP Discovery and Structural Variation Analysis
Illumina's NextSeq 500 and NovaSeq 6000 generate the highest quality data available to analyze any genome for any species, and every genetic variant. A flexible, convenient workflow allows you to combine both short-insert paired-end and long-insert mate pair libraries to create an optimal level of detail and accuracy for any study. Go rapidly from DNA to data with minimal hands-on effort to produce meaningful results, reliably and efficiently.
Gene Regulation and Epigenetic Analysis/Sequence-Based Methylation Analysis
Identify and track methylation patterns by directly sequencing bisulfite-converted DNA, methylation-sensitive restriction digest-enriched fragments, anti-methyl C-precipitated fragments, or chromatin immunoprecipitates of methyltransferases trapped to aza-labeled DNA on the NextSeq 500 and NovaSeq 6000. Correctly map more reads to the methylated genome using accurate 100+ base paired-end reads. Easily prepare highly diverse libraries needed for comprehensive characterization of methylation status. Using Illumina sequencing technology, you can evenly sequence a repetitive bisulfite-converted genome and detect variations in methylation signatures at single-base resolution to pinpoint rare binding events to within 50 bases of the actual binding site.