Frequently Asked Questions

General
Who can perform projects with FGC?
FGC is a facility open to everybody, researchers at IRB, in Barcelona, Spain, Europe and the rest of the world. We work with academia as well as with industry.

How is payment of services organized at FGC?
In general, we have two prices, one for IRB researchers and one for everybody else (IRB gives us a lot of money to run the facility).
       Our pricing policy is very transparent: Download our orderforms, plug in the number of samples you want to be processed on a certain platform and the price is automatically shown.
       For Spanish researchers: The government still does not give research institutions a tax-exempt status. Therefore, you have to add IVA to our prices.
.
Tools for Genomic Analysis
How do I best start my genomic project?
In general, it is best to contact us first. Together, we can design your study, decide about the best possible platform, discuss how analysis will be performed and what you can expect.

How long does it take until I get my results?
For smaller microarray projects (<24 samples), you can expect to receive your data 3 weeks after sample and orderform delivery. For special arrays, Affymetrix and NimbleGen can take longer for array delivery.
       For sequencing projects, no specific time frame can be given for several reasons: Illumina does not store consumables in Europe - therefore, and for other Illumina-internal reasons, our orders can take weeks and weeks....
       Please be also aware that a run of the sequencer processes 8 samples in parallel. All of them have to be the same read-length and either single-end or paired-end reads. We have to have the complete flow cell filled to provide the price indicated in our orderforms. This means: either you fill the entire flow cell with your samples or you have to wait until others want to do something similar.

Which organisms can be analyzed?
Any organisms with a well annotated genome (or transcriptome) can be analyzed.
        In the field of microarrays, standard arrays can be purchased for many organisms. Affymetrix covers over 20 organisms, NimbleGen over 100. Arrays can also be customized for your favorite organism. This is usually easier with NimbleGen than with Affymetrix.
       In the field of Next Generation Sequencing, a reference genome of the organism must be available. Sequences are mapped to this reference genome.

How do I best prepare my samples?
In general, a combination of organic phase extraction (phenol) with column purification (e.g. Qiagen) works best. These two completely different purification principles remove all kind of impurities. Protocols can be found on our Downloads page.
       For miRNA analysis, do not use columns. Almost all of them remove short RNAs.
      For very small samples (a few thousand cells), specific protocols are necessary; you find them on our Downloads page too.

I have doubts about the quality of my samples. Should I still submit them for analysis?
Before we start any expensive experiment like arrays or sequencing, we perform a broad range of quality controls. These include Nanodrop testing of purity, RNA integrity test on the Bioanalyzer, DNA or RNA specific quantification using the Qubit assays. If we have doubts about the samples, we will contact you for your decision "No or Go".
             

Alteration of Gene Expression
Who can request clones?
IRB has a single-use contract with Sigma and Open Biosystems, i.e. only IRB researchers and IBMB-CSIC researchers have access to the Sigma libraries; only IRB researchers have access to the Open Biosystems library. If you work outside of IRB, please contact Sigma and IRB administration to find out if these contracts can be modified to include your institution.

For which genes do you have shRNA or ORF clones?
Our shRNA clones cover approximately 75% of human and mouse refseq mRNAs, the ORF clones cover the same percentage of human genes. In our Downloads page, you find the complete lists of available clones and corresponding genes. 

I cannot open the clone lists because they are in xlsx-format.
The libraries contain more than 65,535 clones. Therefore, one needs Excel 2007 to show more than 65,535 rows.

I cannot find my favorite gene in your clone lists.
Our lists contain the official gene names as available on the NCBI website. At NCBI, go to the search field, click on gene and check if you used the official name.

How long does it take until I receive my clones?
Send us an email with your clone request, we tell you when tubes for bacterial inocculation should be delivered and you will receive the clones the same day of tube delivery. In toto, this takes 3 days max.