These instructions explain how to use One Codex Reformat Tubes to prepare your samples for microbiome analysis at One Codex.
One Codex Reformat Tubes enable reproducible processing of samples originally collected in a variety of formats with enhanced traceability. For more details about One Codex Reformat Tubes, see FAQ: What is a One Codex Reformat Tube?. One Codex Reformat Tubes are not designed to be used as sample collection devices.
NOTE: If you have already collected samples in OMNIgene•GUT collection devices, there is no need to reformat your samples. We process these devices directly.
1. Follow your preferred procedure for collecting stool samples.
2. Go to app.onecodex.com/register-samples. You will need to log into the account that placed the order. Download the Sample Metadata template sheet for this order. This sheet contains the One Codex Reformatting Tube Barcode IDs associated with your order.
3. Use the Sample Metadata template sheet to plan which samples should be put in each pre-barcoded One Codex Reformatting Tube.
When you are ready to reformat your samples, choose the appropriate instructions below, depending on how your samples are stored.
Aliquoting from OMNIgene•Gut tubes
If your samples are collected in OMNIgene•Gut tubes, but you do not wish to send us the entire OMNIgene•Gut device, please reach out to the team directly, either via email (firstname.lastname@example.org) or through the chat box at the bottom-right of your screen. We will provide you with specific cryovials (without buffer) for aliquoting.
If you are aliquoting from OMNIgene•Gut tubes into our cryovials (without buffer), we require a minimum of 250 µL of stool in OMNIgene•Gut buffer. We recommend that you send 1000 µL of stool in OMNIgene•Gut to allow for additional extractions. However, we request that you do not provide more than 1000 µL in these tubes, as it can result in overfill/spillage through the automated process.
Without stabilization solution
1. Process fresh stool samples immediately when they arrive to the lab. Thoroughly homogenize the sample.
NOTE: Frozen samples should be thawed over ice prior to homogenization and reformatting.
2. Carefully weigh 150 mg solid or 150 µL of liquid stool and transfer to a One Codex Reformatting Tube.
3. Vortex the samples for 15 seconds or until homogenized. Some particles may not dissolve.
In Norgen Stool Preservative, Invitrogen RNAlater, or ethanol
NOTE: If your sample is stored in a different solution or you have questions about reformatting, contact us at email@example.com.
1. Calculate what volume of sample is equivalent to 150 mg of stool.
For example, DNA/RNA Shield-Fecal Collection Tubes are designed to collect 1 g of stool in 9 ml of DNA/RNA Shield.
Thus, 1.4 ml of sample in DNA/RNA Shield-Fecal Collection Tubes is equivalent to 150 mg of stool.
2. Thoroughly homogenize the sample by vortexing or pipetting. Aliquot the volume of sample equivalent to 150 mg of stool into new centrifuge tube.
3. Centrifuge the sample at 13,000 x g for 5 minutes. Carefully remove all the supernatant.
4. (Optional) Wash the pellet with cold sterile 1X PBS. Then, centrifuge at 13,000 x g for 5 minutes. Carefully remove all the supernatant.
5. Resuspend the pellet in buffer from a One Codex Reformatting Tube. Transfer all of the sample to a One Codex Reformatting Tube.
6. Vortex the samples for 15 seconds or until homogenized. Some particles may not dissolve.
1. Collect and store the One Codex Reformatting Tubes until you’re ready to ship all the samples to our lab for processing.
NOTE: If you expect to store the samples in your lab for longer than one week, we recommend storing the tubes at -20° C until shipping. Please do not freeze the sample box that was used to ship the One Codex Reformat Tubes to you.
If you have additional questions, please send us an email at firstname.lastname@example.org or through the chat box at the bottom-right of your screen.