The Process

Trust the Process.

Accounts

We use iLab to handling billing, so make sure you and your PI have active accounts there.

  1. Follow directions at iLab to create accounts
    1. UPenn clients will have dormant accounts that use PennKey credentials, go to iLab to activate your account.
    2. CHOP clients may also have dormant accounts.
    3. See iLab for other institutions.

We use the NGSC website to handle sample submission and data presentation, so you will also have to have accounts there.

  1. PI creates account if new to NGSC
  2. Investigator (grad student, post doc, staff, etc.) creates account if new to NGSC
  3. Jonathan activates accounts

Setting Up an Experiment

  1. Investigator fills in Request or Experiment and submits to the NGSC
    • Use the Standard Service Request link under Request Services to make your request.
  2. Jonathan reads request
    1. generate estimate
    2. confer with BA, PI, and Investigator to agree on charges
  3. BA, PI, and Investigator make entries in iLab to allow NGSC to charge grant
    1. UPenn clients typically use CAMS to set spending permissions which percolate to iLab overnight.
    2. All other clients should load a PO to cover the costs which we have to review and approve.
  4. Jonathan
    1. loads the study
    2. generates sample submission forms
    3. informs investigator about the form
  5. Investigator emails sample submission form to Shilpa
  6. Shilpa reviews and loads samples and informs Investigator that we can accept the samples.

Sample Submission

  1. Investigator checks the Sample Submission Calendar to see when we have drop-off hours
    • Using the website link Get Started / Calendars / Sample Submission
  2. Pre-submission
    1. Investigator fills out forms and emails to NGSC
    2. Shilpa
      1. reviews and confers with Investigator and alters if needed
      2. runs programs as needed to load, pool, check, and schedule the samples
        • loads the samples
        • creates any pools that are needed
        • makes sure the barcodes in the pool get along well with each other
        • adds the pool to the run schedule.
      3. informs Investigator that the samples are loaded.
    3. Investigator appears with samples
    4. Lab Staff and Investigator match samples with db entries
    5. Lab Staff print labels and apply to tubes
  3. Standard Submission
    1. Investigator appears with samples
    2. Lab Staff and Investigator create db entries
    3. Lab Staff print labels and apply to tubes
  4. Once the samples arrive they are scheduled for any QC requested.

Quality Checks

  1. The Lab Staff follow Trello cards
  2. Qubit
    1. perform measurements
  3. BioA
    1. perform measurements
    2. place values in core.qc
    3. export BioA data
    4. Lab Staff gives the data to Jonathan
    5. Shilpa generatess BioA reports and notifies the Investigator with comments.
  4. Kapa
    1. Lab Staff use either the 5nM dilutions or stock samples to measure concentration
    2. Sample is plated in triplicate at three different dilutions
    3. Plate is processed on QPCR machine
    4. Lab Staff reviews the raw data
    5. Shilpa loads the into the database

Pooling

We generally pool without diluting. This means we generally put a different volume of each sample into a new tube and add TRIS to dilute to the final target molarity.

We plug the Kapa-derived molarties for the ‘5nM’ dilution into a prepared spreadsheet. We pick a nominal target molarity and volume and see what sample volumes the spreadsheet indicates.