MCIC Computational Biology Laboratory: Open house is on November 16, 2012. By Tea meulia
The MCIC is very pleased to announce that we are expanding our bioinformatics core services by launching the Computational Biology Laboratory (MCBL). The creation of the MCBL has been part of a joint MCIC and CAPS effort aimed to strengthen bioinformatics collaborations and computational support available to biologists at OSU. We aspire for the MCBL to become an engaging environment for learning and performing bioinformatics research at the OARDC...
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To learn more come to the Open House on Friday, November 16, 2012 from 10:30 AM to 3:30 PM
Download detailed information about MCBL infrastructure and membership.
On line MCBL membership registration.
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MCBL upcoming tutorials, training sessions and user group. BY Asela Wijeratne and Stephen Opiyo
In spring and summer 2012 we offer two tutorials that were very well received. Saranaga Wijeratne taught a basic hands-on bioinformatics session that included (1) Introduction to Galaxy tools; (2) How to manage history in Galaxy; (3) Running basic Text manipulation tools; (4) How to upload and download data from and to the UCSC genome browser. Asela Wijeratne taught a tutorial on RNA-Seq data analysis that covered an (1) Introduction to RNA-seq and experimental planning, (2) Short read mapping and data visualization, (3) Differential gene expression analyses, (4) De novo and reference guided transcriptome assembly and (5) Transcript annotation of assembled transcripts. ........
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Upcoming tutorials
December, 2012: RNA-Seq and transcritome assemblies. Asela Wijeratne.
January, 2013: Introduction to R. Stephen Opiyo.
If you want to be part of the MCIC bioinformatics and genomics discussion group: ‘Genomics_MCIC’. Subscribe byt sending an e-mail to aselaw90@gmail.com
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Sequencing on the Illumina GAII is becoming cheaper and is ideal for smaller pilot projects. By Tea Meulia
Sequencing on the Illumina GAII genome analyzer is as expensive as sequencing on the HiSeq, however the throughput is about 3-4 times lower. We were finally able to negotiate a discount for the Illumina GAII sequencing reagents, and these are our new prices:
Single read, up to 36 cycles (or 29 bases, plus 7 index bases): $600.00 per lane
Paired-end, up to 76 bases: $1,400.00,
Paired-end, up to 100 bases: $1,700.00
Paired-end, up to 150 bases: $2,000.00
We also offer and additional 15% per lane discounts for the submission of 7-8 samples (or multiples).
These new prices.....
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MCIC rates are found at
http://www.oardc.ohio-state.edu/mcic/rates/rates.html
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Mass SNP Genotyping by Sequencing on the Illumina GAII Genome Analyzer. By Tea Meulia
We are exploring possibilities to expand the use of the Illumina GAII Genome Analyzer for new applications. One such application could be the Mass SNP Genotyping by Sequencing that is being developed by Eureka Genomics. The assay enables to screen hundreds of SNPs and thousands of samples in parallel using a single lane of the Illumina GAII Genome Analyzer. This same assay is also compatible with copy number variation (CNV), methylation and gene expression applications. .....
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If you are interested in this technology, please contact Tea Meulia
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Automation of RNA-seq library preparation using the Eppendorf liquid handling robot. BY ASELA WIJERATNE and maria elena hernandez-gonzalez
We have evaluated the use of the Eppendorf EpMotion liquid handler for Illumina TruSeq RNA-Seq library preparation. Four RNA samples were divided into two aliquots and RNA-Seq libraries were prepared manually or using the liquid handler. Initial quality controls suggested that manual sample preparation yielded higher quantity compared the automated sample preparation, however .........
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