NGS Services Currently Provided:

All NGS-related sample preparation and sequencing runs are done on an Illumina MiSeq. This instrument is located in the Molecular Science Research Building of the University of Puerto Rico. But, we also generate libraries for a variety of applications and sequencing platforms (besides those that are Illumina-based).

We are also in collaboration with the University of Chicago Genomics Facility (Knapp Center for Biomedical Discovery), which houses several high throughput Illumina based sequencers. Researchers that prefer to sequence their libraries on Illumina HiSeq platforms bring their samples to SGF to generate the libraries and we send them to Chicago for the sequencing runs.



The following applications are currently being provided:
  • Targeted Resequencing
    • Metagenomic 16S rRNA Illumina Tags (iTags) SequencingThis type of library involves sequencing 16S variable regions to investigate prokaryotic diversity from environmental samples. These libraries are made using Nextera indexes (barcodes) after amplification of preferred region of interest.

    • Custom amplicon Sequencing
      This application involves rapid library preparation from an amplified product of interest from specific genes or gene regions. This type of application is  perfect for population genetics and evolution, higher level phylogenetics, DNA barcoding, as well as resequencing.


  • RNA-Sequencing
    There are two different RNA-Seq library types currently available:
    • Stranded Total RNA Sequencing
      This type of library is useful to capture expression changes and novel transcripts in coding and non-coding RNA. The client has the choice to deplete cytoplasmic rRNA, mitochondrial rRNA, or both.
      • Starting material: 0.1-1ug total RNA, quantified via qubit, RIN >8

    • Stranded mRNA Sequencing
      This type of library is useful to capture both poly-adenylated coding and non-coding RNA. rRNA depletion is performed by removing all non-poly-A rRNA.
      • Starting material: 0.1-4ug total RNA, quantified via qubit, RIN >8


  • Whole Genome Sequencing (WGS)

    WGS involves sequencing of the entire genome of a species for different purposes, including whole-genome phylogenetic inference & evolution, population genetic studies, therapeutic intervention studies, among other research fields. The sequences obtained with WGS will be that of chromosomal DNA, as well as organelle DNA (mtDNA and cpDNA for plants). 
    Library preparations methods include:
    • PCR-Free Library Preparation for GC rich genomes
      • Starting material: 500ng - 1ug gDNA
    • DNA Library Preparation using Illumina Nextera Chemistry, in which gDNA is fragmented enzymatically
    • DNA Library Preparation using Illumina TruSeq Chemistry, in which gDNA is fragmented mechanically, among other library preparation methods depending on the complexity of the genome.
    • Small Genome WGS for bacteria or viruses. In the case of RNA viruses, we perform First & Second Strand cDNA synthesis followed by small genome Library Preparation using Nextera XT Chemistry.
      • Starting material: 1ng gDNA


  • Single-Digest RAD Tag Library Prep & Sequencing (RAD Tags)
    RAD Tags are genetic markers used for genetic mapping, population genetics, evolution, population structure, genetic connectivity, phylogeography, invasion genetics, adaptive genomics, and other research fields. RAD Tags are useful for identifying and genotyping DNA sequence polymorphisms. The sequencing coverage obtained depends on the Genome Size, the Restriction Enzyme used, the GC content, and the sequencing equipment used. See our Protocols area to see our RAD Tag protocol.
    • Starting material: ~500ng - 1ug RNA-Free, gDNA


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SGF UPRRP,
Jan 22, 2015, 7:57 AM