Array and Probe Design
- conveniently select genes of interest from febit’s validated libraries or import/design and validate probes which are in your focus
This module allows you to import validated probe sets from febit’s libraries or to design entirely new array templates and probes with a few mouse-clicks. You are enabled to directly control all relevant probe parameters. febit’s software will save their configurations in its database for easy access and network exchange with other scientists.
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1. Choosing an Array Typeclick „add“.
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2. Choosing a Control GroupControl groups are sets of probes used to monitor the quality of synthesis and hybridization. Select from various control groups according to your experimental needs and the characteristics of your probes.
On the left side of the screen, select the control group(s) which best suits your experiment. Just drag your choice and drop it in on right side of the screen or click „add“.
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3. Choosing a Probe Parameter SetMade to provide you with maximum flexibility, Geniom software supports both standard probes and specific probes tailored according to your specific needs. All parameters like GC content or melting temperatures can be freely adjusted and stored in probe parameter sets. The sets are established once for each kind of experiment and then stored in the Geniom database.
Informations in an expression profiling parameter set:
- Probe length
- Maximum overlap
- Dirty probes yes/no
- Revert probe yes/no
- Complementary probes yes/no
- Preferred melting point
- Buffer sodium concentration
- Base composition criteria for whole probes and islands within: GC/AT content; G/C or A/T bases in a row
- Parameter weighting predetermines: probe specificity, binding score (of competing sequences), distance from 3' end, bases in row, melting point, loop rate
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4. Choosing sequencesChoose the genes, exons or PCR fragments for which probes will be synthesized on the array.
Nucleic acid fragments for expression profiling are categorized according to following tree branches:
- Artificial gene
- Organism
- User-defined category
- Functional group
- Further user-defined branches
Select probes from the Geniom sequence database that is organized just like the Windows explorer - or import your own sequence data (capture probes, oligonucleotides,…).
Indicators monitor the composition of your array as it builds up
- Tolerance level
- Array fill rate
- Number of chosen probes and controls
Control spot configuration
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5. Validating ProbesValidation of the chosen probes and gene fragments to make sure that for all chosen fragments at least
- as many probes as defined in the probe parameter set have been calculated.
- as many probes as defined in the spots per fragment setting have been calculated.
After the validation has finished, its results are displayed below the progress bar.
The probes selected are displayed.
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6. Validating ProbesThe probes selected are displayed.
Probe mapping:
- View the location of each probe in the gene.
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7. Assessing Array ParametersThe summary of array data lists
- the genetic items that will be synthesized on the array
- the configuration of the array: e.g. numbers of features, control spots etc.
- the resulting array design parameters, like feature spots per fragment, the size of the spots etc.
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8. Saving the Array LayoutYou can visually check the layout of probe and control spots on your array.
The array is displayed as a plane with colour-coded spots.
After completing the array layout, save it in the Geniom client database as a template for synthesis.
The array layout will be as saved as a complete set of all data that Geniom needs to reproducibly synthesize the array.
