Item | Specification | Comment |
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Technical: |
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RNA requirements | 50 microgram | total RNA preferable |
RNA QC | Agarose gel | We perform entry QC on all samples |
CAGE library deliverable | 200 nanogram | Gel purified DNA fragments |
Sequencing platform | Illumina/Solexa | |
Number of reads per channel guaranteed | 4,000,000 reads per channel | Standard conditions: 1 Channel per sample. Additional sequences can be obtained at extra charges. |
Data analysis | Extract tags from reads>>>mapping tags to genome>>>clustering tags based on genome locations and window size. | Standard approach. Mapping procedures may have to developed for genomes other than human and mouse. |
Mapping rates | About 50% of tags map to unique mapping position | One experiment should provide the customer with at least 1,000,000 useful CAGE tags. |
Description of deliverables: Sequencing data | Illumina files | Delimited text files holding sequence information and quality scores. |
Description of deliverables: Data analysis | Mapping positions | Tables/flat files: # of raw reads, # extracted tags, # of mapped tags. |
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Estimated Turn-around-times: | About 2 month | Depending on free capacities |
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Documentation: | Report on CAGE library preparation |
| Read me file to descript content of flat text files. |
