Why am I receiving a report?
The WCIC uses LIMS to help track and manage client projects. Reports are generated by LIMS and automatically sent to clients on a monthly basis. Through the monthly report, you can check-in on the progress of your contract.
** If you are receiving a report in error or if your contract has come to an end**, please “reply all” to the report email and request to be removed from the automatic send list.
Some clients have multiple contracts, and each contract will now receive a report individually. This will result in multiple report emails each month. If you would prefer an “ALL CONTRACT” report, please let us know.
What is this MSN number in the name of my report?
The University of Wisconsin Madison currently uses an MSN###### ID to uniquely identify each contract. This code system is the most efficient way to refer to the materials, the billing, and the contracts involved. This MSN code will appear on all reports and invoices pertaining to that one specific contract. If you want to inquire about a specific contract, please refer to your MSN code in the email. If you have multiple active contracts with the WCIC, you will receive multiple reports each with their own MSN code.
When will I get a report emailed to me?
The first report is emailed when progress on the contract has begun. For T0 generation contracts the first data into the report is transformation initiation (“Protocol Start Date/Time”) and for T1 generation contracts reports begin at planting (“Greenhouse Arrival Date”). Once initiated, reports will be automatically emailed to you monthly.
My report looks almost empty! Should I be concerned?
Plant transformation does take many steps to be successful so please be patient and try not panic. You will first get a (mostly empty) report indicating the date that transformation was initiated. You may get that mostly empty report sent to you 2 or 3 more times while the selection and regeneration stages are ongoing. *HOWEVER*, if it has been over 90 days since the “Protocol Start Date/Time” and there are no Event IDs listed in your report, please inquire by ‘replying all’ to the report email or by emailing “email@example.com”.
What is a WP and how can I track it back to my material?
The code that all experiments and plant tags use are the Workplan (WP). It is the T0 tag and the T1 seed ID (plus more text). The vectors are giving a name in the system. Sometimes this is generated by the client, sometimes by the vectoring team, sometimes by the associate director. It should be designed at the outset, but where negotiation and changes occur, a Rosetta stone is needed that links the client information to the WP. Feel free to ask about that if it is not clear in your report.
What information does a report hold?
The WCIC uses LIMS reports to help track the progress of client projects. Reports hold a lot of important data, however, with large projects and contracts with many constructs a report can become overwhelming.
Here is a breakdown of the columns in the report:
“Work Plan No.”: (WP) Specific code to designate each client plasmid construct.
- Each “Event ID” starts with the WP number that it was transformed with.
“Protocol Start Date/Time”: This is the date of the transformation initiation.
- In 2-4 months (depending on the crop) from this date plantlets enter the greenhouse as events (“Greenhouse Arrival Date”)
- If multiple initiations are necessary to fulfill the contract, each date will be recorded and be assigned a new “Experiment ID”
“Event ID”: WCIC generated number designated upon greenhouse arrival.
- Event progress can now be tracked per event via the “Status”.
- “nursery”: Event has just entered the greenhouse.
- May remain in nursery status for 1-4 weeks to root, grow, and become more vigorous after transplant from media to soil.
- “Greenhouse Arrival Date” is now also indicated on the report.
- Event likely sampled for DNA (“PCR Test Sample Collection Date”) during nursery
- “active growth”: Event has been re-potted from a nursery pot into a large pot.
- If the event is a dicot, then the event will only remain in active growth for 1-2 weeks before entering “short days” status.
- If the event is a monocot, the event will remain in active growth status until nearing harvest
- “Date to Large Pot” is now also indicated in the
- “short days”: Dicot eventin shade cloth enabled greenhouse to induce flowering.
- Dicot event will remain in short days status until nearing harvest.
- “Date to Short Days” is now also indicated on the report.
- “in dry down”: Event is nearing harvest.
- “harvested”: Event has been h
- Harvested seed then needs to be processed (approximately 1 week) before being ready for shipment.
- “Harvested Date” is now also indicated on the report.
“PCR Test Sample Collection Date”: Date event was sampled for genetic analysis.
- 1-2 weeks following sampling, PCR TestResults will be added to the report.
“PCR Test Result: Selection”: Qualitative analysis to ensure successful transformation.
- Marker identification performed via endpoint or qualitative PCR
- Data options: ‘Positive’ or ‘Negative’
“PCR Test Result: Copy Number”: Quantitative analysis for number of gene copies
- Marker and/or gene of interest copy number evaluated with ddPCR
- Data: numerical value
I understand that reports are coming monthly, but what should I look for between receiving reports?
The dates and new items are the most informative. The first exciting report will be when plants arrive in the greenhouse 2-4 months after “Protocol Start Date/Time”. Then the next month’s report will likely include molecular analysis data and survival notices.
- You can anticipate “Date to Large Pot” to be about 30 days after “Greenhouse Arrival Date”.
- If a plant moves status to “active growth”, it means it has been transplanted to a large pot.
- You can anticipate “Harvested Date” to be about 90-120 days after “Date to Large Pot”.
- If contracted to receive a seed shipment, please start the APHIS seed movement application when plants begin to enter the greenhouse. This allows for enough time for permit approval and any permit amendments if necessary.
What is a seed report?
About a week after harvest, seed packets will be trackable in LIMS. This information will be emailed in a seed report labelled with the specific MSN number for each contract. In the seed report you can track the number (or weight) of seeds produced per event and per workplan (WP). Seed status is important to track as it will indicate what has been “sent to customer”.