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This is a validated protocol

View the validation data here

Description

This protocol orders DNA primers to be synthesized for use at Transcriptic. DNA is synthesized by IDT and will be available in your inventory once it is received and diluted per the experimental parameters.

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gBlocks

gBlocks are larger fragments of double-stranded​ DNA that can be synthesized by IDT. Currently, the Oligosynthesis protocol does not support gBlocks, however they can be ordered via IDT and shipped directly to Transcriptic.

To add gBlocks to your inventory, follow the method outlined in this video. Make a note of the individual 3 digit tube codes, and the 4 digit Accessioning number for the shipping address.

Now go to IDT and order your gBlocks as you normally would, include the 3 digit labels at the end of the gBlock name in the order form. Next for the shipping address for the order use the address below but add your accessioning number

Transcriptic, Inc.
ATTN: Accessioning (Your accession number)
3565 Haven Avenue,
Suite 3,
Menlo Park
CA 94025

Sample requirements

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This protocol does not require any sample inputs.

Required parameters

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There are two ways to import sequences to be synthesised

Single oligonucleotides can be specified in the top portion of the protocol, however if you wish to synthesize a large number of oligonucleotides a bulk upload functionality is provided.

Single Oligonucleotides

sequence specifies the sequence of DNA you wish to be synthesized, for example, ATGCGTAATCG. N is also an acceptable character for any base.

scale specifies the quantity of DNA you wish to synthesize. Options are 10 nmol, 25 nmol, 100 nmol, 250 nmol and 1 µmol.

purification specifies how you wish your synthesized oligonucleotides to be purified. Choose from Standard, HPLC and PAGE.

oligonucleotide name specifies the name of your sequence.

diluent specifies the solvent you wish your oligonucleotides to be diluted in. Choose from deionized water or TE buffer.

concentration specifies the final concentration you wish your oligonucleotides to be diluted to.

More information on scale and purification can be found on the Oligosynthesis capabilities page.

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Add additional sequences

If you wish to synthesize additional sequences click the Add Oligonucleotide link.

Bulk Upload Sequences

sequence CSV the .csv file you wish to upload that contains your sequence information. You can download a template of this here.

Universal parameters

This parameter is required for either synthesis method.

storage condition for diluted oligonucleotides the conditions that you wish your diluted oligonucleotides to be stored in. Choose from -20 or 4 degree celsius.

Protocol Outputs

This protocol out puts physical samples that will be visible in your inventory once the run completes. The storage condition of the samples will be dependent on what you specified in your protocol.

Recommended guidelines

Sequences can be difficult to synthesize for various reasons, including GC content, homopolymers, length and secondary structure. It is recommend you review synthesis guidelines from IDT to advise your sequence choices, which are accessible here

Further reading

IDT
IDT Oligonucleotide synthesis FAQ
IDT Oligonucleotide purification FAQ

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Check out the forum if you have more questions.

For further advice on your protocol please ask questions to the community at https://forum.transcriptic.com