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- See this web page for sample input guidelines.
- For Metagenomics and GBS projects, note that DNA concentrations should be normalized before submission.
- Have a lot of samples? Download this sample submission template (required for jobs with more than 30 samples; optional otherwise
Announcements:
Join us for the GSAF Spring Lunch and Learn Series
Single-cell RNA Sequencing (Illumina)
- Wednesday April 12, 11am - 12:30pm
- MBB 1.210
- Next-Generation Sequencing Tools for Single-Cell Gene Expression and Transcriptome Analysis
- Mehdi Keddache, PhD, Sequencing and Data Analysis Specialist, Illumina Inc.
- More information at Illumina's Event Registration Page
Long-read Sequencing Technology and Applications (Oxford Nanopore Technologies)
- Tuesday April 25, 12 noon - 1:30pm
- NHB 1.720
Real time DNA sequencing using Oxford Nanopore Technologies 'Nanopore Sensing' Platform
James Brayer, Associate Director, Market Development
Expand title Talk abstract Oxford Nanopore Technologies has developed a disruptive platform for the direct, electronic analysis of single molecules. Our instruments the MinIONTM, the PromethIONTM and the GridION X5 ™ are adaptable for the detection and analysis of a range of analytes that include DNA, RNA, proteins and small molecules. At the heart of our platform is a biological protein called a 'nanopore'. A single nanopore create a hole in a membrane made from a proprietary synthetic polymer. An electric potential is applied across the membrane resulting in a current flowing only through the aperture of the nanopore. Single molecules that enter the nanopore cause characteristic disruptions in the current, by measuring these disruptions single molecules from a sample are identified. The MinION is a small device that is designed for portability and simplicity of its workflow. The MinION plugs into a standard PC or laptop using the USB port. GridION X5 is a compact benchtop system designed to run and analyse up to five MinION Flow Cells. The PromethION is a standalone high throughput benchtop instrument that provides the flexibility to run up to 192 libraries in an asynchronous manner. This allows for large projects that requires the flexibility and throughput to interrogate complex eukaryotic genomes. Oxford Nanopore is integrating the data produced by the MinION, the GridION X5 and the PromethION into a cloud-based analytics company, Metrichor. Metrichor is powered by its EPI2ME platform. Metrichor is providing tools to automate data analysis workflows to help people track, trend and predict biological data resulting in real time actionable interpretation of their data. Users of the technology have access to our 'Nanopore Community’. The Nanopore Community helps new users get started with technical documentation as well as user driven forums and encourages discussion and collaborative experimentation using our technology. There is a growing list of publications on the many uses for our nanopore sensing platform that include field based applications, real time pathogen detection and surveillance, metagenomics analysis, anti-microbial resistance detection, education and many more including sequencing on the International Space Station. I look forward to sharing with you the unique opportunities enabled by our nanopore sensing approach. Reserve your lunch at https://utexas.qualtrics.com/jfe/form/SV_0O1FrR6CsHkL941
Long-read Sequencing Technology and Applications (Pacific Biosciences)
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Data analysis tools and demonstration (starting at noon with lunch)
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4April18: GSAF introduces a new library prep service, TagSeq based on the published methods below. TagSeq is a 3' RNA library prep method, please visit our pricing page for more details.
Evaluation of TagSeq, a reliable low‐cost alternative for RNAseq
Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA‐Seq procedure
19April17
PacBio® is the world leader in long-read sequencing. PacBio SMRT Sequencing delivers an average ~10-15 kb read length, high consensus accuracy, and uniform coverage, with simultaneous epigenetic characterization and single-molecule resolution. SMRT Sequencing is preferred for a variety of applications to achieve a comprehensive view of genomes and is available via the Sequel System. Join us to hear the latest updates on application and platform development at PacBio.
Dr. Harold Lee attended the University of Texas at Austin, where he studied the incorporation kinetics of the Mitochondrial DNA polymerase in the lab of Dr. Kenneth Johnson. After earning his PhD in 2005, he went to Bill Konigsberg’s lab at Yale where he studied the RB69 DNA polymerase. He joined the enzymology group within the R&D department at Pacific Biosciences in 2008, where he was part of a team developing and characterizing the polymerases used in the SMRT sequencing technology. Harold joined the field team in 2011 and is currently a senior field applications scientist.
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Index Switching Preprint Concerns Sequencing Community *Update-19Apr17 See Below for Notes from Illumina
What is Index Switching?
A preprint released April 9, 2017 by Sinha, et. al., describes a "spreading-of-signal" phenomenon that is attributed with causing 5-10% of sequencing reads to be incorrectly assigned in situations where multiplexed libraries are run on Illumina's HiSeq 3000/4000 systems. The observed errors are restricted to the HiSeq 3000/4000 and X Ten systems that use the exclusion amplification method for generating clusters in the nanowells of patterned flow cells. According to the pre-print titled: "Index switching causes 'spreading-of-signal' among multiplexed samples in Illumina HiSeq 4000 DNA sequencing," low levels of free index primers in the pool get extended by DNA polymerase to create a new library molecules in the Cbot during the initial stage of cluster generation but prior to binding to the patterned flow cell.
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Review this self-paced training presentation. Read this page further to learn what instruments we have and what we're experienced with. Sign-up on our mailing list by joining "gsafusers" at UT's list server - just select "subscribe" and enter "gsafusers". If you want to submit samples for the first time, first get a UT EID if you don't have one, then go to our sample submission section for more info, to check our queues, etc.. |
Protocols, instruments, computers, and software of the UT GSAF
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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:
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: The GSAF hosts a Dell R720 32-core, 196 GB server with a total of 74 TB local disk dedicated to NGS analysis. Access is available free of charge to all GSAF customers. We maintain a wide range of tools for NGS analysis and assembly on this server. Here are instructions to Getting an account on our server. In addition, the GSAF uses and works with the TACC bioinformatics group, supporting tools and applications suitable to the TACC environment. Want to get started? Contact us if we can help, or here's some documentation describing how to submit samples to the GSAF. Need to start analyzing your data? Get an account on our computational server. New to Unix? Check out some Unix and Perl resources for beginners. Need Accounts? Here's how you can get an account on the GSAF server |
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