The GSAF is housed in approximately 2,000 square feet of controlled-access laboratory space and is an experienced NGS facility. Launched in 2008, the GSAF currently processes over 5,000 NGS samples per year.
Our equipment and capabilities include:
- Two Illumina HiSeq 2500 next-generation DNA sequencers and associated peripherals. The HiSeq can generate over 600 gigabases of sequence in an 11-day run or 120 gigabases in a ~1 day rapid run. The GSAF has experience generating small RNA, mRNA, genomic DNA fragment, RAD (including ddRAD), bacterial and fungal metagenomics, and genomic DNA large-insert mate-pair libraries for the Illumina platform.
- Two Illumina MiSeq next-generation DNA sequencers and associated peripherals. The MiSeq is intended for lower data output, faster turn-around time projects, or for projects requiring longer read lengths (up to 600 bp per template, as two 300 bp sequences).
- Informatic tools and hardware sufficient for analysis of next-generation DNA sequencing data, including:
- Multiple Dell PowerEdge R900 & R720 servers with 16-32 cores each, with BWA, Bowtie, Shrimp, SOAP, and mapreads aligners, NCBI BLAST, and R/Bioconductor, and several de novo assemblers, sequence editors, and genome browsers.
- The resources of Lonestar, a 22,656 core supercomputer, and Stampede, a 400,000 core supercomputer, both hosted by UT’s Texas Advanced Computing Center, with 15 petabyte of scratch disk storage.
- The GSAF has software stacks and experience appropriate to your project and both we and TACC staff can assist you in training your students to use this resource effectively.
Lab protocols we are experienced with:
- Creation of fragment (single-end or paired-end) sequencing libraries for all Illumina next-gen sequencers
- Creation of mate-pair or "jumping" sequencing libraries between 1.5kb and 4kb for Illumina next-gen sequencers
- Creation of RNA-seq libraries from total RNA, small RNA, and immuno-precipitated RNA for Illumina next-gen sequencers
- Creation of amplicon libraries (particularly 16s and ITS regions) for the Illumina next-gen sequencers
- Human exome and custom capture with the Agilent SureSelect, Illumina TruSeq, and Nimblegen SeqCap EZ kits
- Sample and library QC using the Agilent BioAnalyzer, Picogreen and Ribogreen fluorimetry, qPCR, and spectrophotometry
Bioinformatic protocols we are experienced with:
- RNA-seq for transcript abundance, alternative splicing analysis, and variant detection
- SNP/variant analysis
- small RNA abundance and alternative editing analysis
- de novo and reference-guided assembly from fragment, paired-end, and mate-pair data on both DNA and RNA (transcriptomes)
- Whole exome data analysis
Instruments in our lab:
- Illumina HiSeq 2500 sequencers (two)
- Illumina MiSeq sequencers (two)
- Illumina NextSeq 500 sequencer (one)
- Covaris S220 Adaptive Focused Acoustic shearing device
- DigiLab HydroShear shearing device
- Agilent BioAnalyzer 2100
- Agilent TapeStation
- Invitrogen Qubit fluorimeter
Computational and software resources:
- In addition, the GSAF uses and works with the TACC bioinformatics group, supporting tools and applications suitable to the TACC environment.
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