10K Genes/Submission Documentation

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Genes are only useful to other people if they are well documented. In order to get genes cloned and synthesized through us, we require a few simple documents.

NOTE: WE OPENLY PUBLISH ALL INFORMATION GIVEN TO US.

What can we synthesize

  1. MoClo compatible DNA
  2. Whole DNA vectors

At the current time, we only accept submissions of MoClo compatible DNA and whole DNA vectors. This enables us to focus on high-throughput production and distribution of DNA rather than edge cases. We apologize if this is inconvenient for you.

DNA Markdown file

# Gene
1. Gene name
2. Part type

## Author
1. Name
2. Email
3. Affiliation
4. Project
5. ORCID

## Metadata
1. Uniprot URL link
2. Safety information
3. Collection #hastags
4. Other #hastags

# Sequence Submitted
ATGTAA

# Sequence Optimized
ATGTGA

# Gene Description
Please enter gene description here

# References
1. http://www.example.com/, http://www.example.org/

Above is an example markdown file. If you are not familiar with the markdown format, here is more information. The sections "Gene" and "Sequence", as well as the subsections "Author" and "Metadata", are automatically converted into a computer readable json file, so it is important that they are standardized. The sections below (including the recommended "Gene Description" and "References") are free-form, and you can modify them however you choose.


Gene

  • Gene name
- The name of your gene, meant to be human readable.
  • Part type
- This is an important section in describing what we do in subsequent steps with your gene. Currently (2017.12.18), there are 8 primitive types to choose from: Promoter, RBS, CDS, Terminator, Tag, Other, Composite, and Linker (reserved for GoldenGate linker sequences, described in more detail here). In addition, you may define your own with the standard 10K Genes type syntax.

Author

  • Name
- Your real full name. For liability reasons, we cannot accept usernames or handles.
  • Email
- Your contact email address. Please use a real email address, as we will use this to contact you with updates.
  • Affiliation
- If you are working within an institution, please name the institution you are working within. If you are working independently, you can put "Independent Research" in this section. Or, optionally, you can become creative with your affiliation.
  • Project
- What project this will be for. If these genes are for a new project, please send us a separate markdown describing the project.
  • ORCID
- Optional section. If you have an ORCID, please insert it here, if not, please fill in "NA". Do not leave blank. If you don't know what ORCID is, here is the wikipedia article.

Metadata

  • Uniprot URL link
- If your gene has a uniprot link, please insert it here, if not, please fill in "NA". Do not leave blank.
  • Safety information
- If your gene is in any way dangerous, please insert safety information here, if not, please fill in "NA". Do not leave blank.
  • Collection #hastags
- We have several official collections organized into hashtags. If your genes fit any of these categories, please insert the hashtags here for better searchability later. If you'd like to add any new categories, please edit the "Community contributions" tab on the 10K_Genes Collections page.
  • Other #hastags
- Any other hashtags you want to add. Have fun!

Sequence Submitted

Add the raw sequence that you would like synthesized. This is the original sequence submitted, unaffected from changes we make.

Sequence Optimized

This is the sequence after optimization to remove restriction enzyme sites and homopolymer regions, and it is the one that we synthesize with Twist.

Project file

In order to share information what groups of people are doing with the 10K Genes Parts, we request you supply a project markdown file with your DNA parts. This markdown should only take a few minutes but is required for synthesis. Make sure to include one file for each different project you are synthesizing for.

Bulk CSV file

Sometimes, it is much easier to create a CSV file with all the computer readable information. If you would like to do that, please download the template here {PLACEHOLDER}.

We still require a description file with each sequence. However, it doesn't require the metadata. When we process the CSV, we will automatically add that data into the final markdown file and send a copy to you for verification.

Associated files

Often, there are associated files that may be important for others that are looking to use your gene.

Genbank files

If your sequence has a genbank file with annotations, we ask that you please include that with your submission.

How to submit