Pre-lab (front-end) processingDifferent collections have different standardsChallenge is to transform this into a standard...
Logistical problems: lots and specimensBarcoding – Specimen based  BATCH 09/10/2010    Multiple taxa from the same        ...
Unique voucher number            Label with            voucher nr.             OM2035
Pre-lab (front-end) processing                                             1. Arraying            Unprocessed             ...
SAMPLING KITS        Dispatched by core analytical facilities; To streamline sample submission1. Sampling plates          ...
Specimen arraying + samplingCONCEPT: Grouping of specimens in an arrangement that is compatiblewith a 96-well format used ...
Specimen/sample arraying: ExamplesDirect sampling                                                      Subsample right amo...
Specimen/sample arraying: Examples                                                          A1                            ...
Field dataTransferred to specimen data sheet                                                                   Measurement...
Data collection: BOLD requirements     Arraying   Databasing   Imaging   Sampling
Data collection: BOLD requirements     Arraying   Databasing   Imaging   Sampling
BOLD specimen data spreadsheetMS Exel based – 4 tabs/pages                       Voucher Information            Arraying  ...
BOLD specimen data spreadsheet                Taxonomy     Arraying   Databasing   Imaging   Sampling
BOLD specimen data spreadsheet               Specimen details    Arraying     Databasing   Imaging   Sampling
BOLD specimen data spreadsheet               Collection Data    Arraying     Databasing   Imaging   Sampling
Specimen ImagingImportant in the barcoding process – can serve as an electronic voucher    • .jpg format    • High resolut...
Specimen Imaging    Framing/Orientation                       Display maximum diagnostic characters•   Leave as little mar...
Key stages of front-end processing         1               2               3Sampling &Field data                          ...
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Michelle Van der Bank - Front-end processing

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Specimen arraying, databasing, imaging, sampling. Pre-lab challenges and solutions: individual tracking of collection specimens, avoiding human error when working with large batches of specimens, streamlining front-end processing of large specimen batches

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Michelle Van der Bank - Front-end processing

  1. 1. Pre-lab (front-end) processingDifferent collections have different standardsChallenge is to transform this into a standard lab-compatible format Core labs operate in 96-well plate formatwhich require compatible front-end solutionsIf this is not addressed collection processing may become the bottleneck in the analytical chainwhich could hamper large-scale barcoding projects.
  2. 2. Logistical problems: lots and specimensBarcoding – Specimen based BATCH 09/10/2010 Multiple taxa from the same collecting event Unique voucher number Single collection voucher with data link to the original batch number
  3. 3. Unique voucher number Label with voucher nr. OM2035
  4. 4. Pre-lab (front-end) processing 1. Arraying Unprocessed Formatted specimens 2. Databasing data records Labeling4 Main steps required to transformspecimen collections into lab-ready 3. Imaging96-well microplates Formatted images 4. Sampling/ Subsampling Lab-ready 96 well microplate Core lab procedure LIMS BOLD Systems (www.boldsystems.org)LIMS – Lab information management system Pre-conference Short Course on DNA Barcoding Methods
  5. 5. SAMPLING KITS Dispatched by core analytical facilities; To streamline sample submission1. Sampling plates 2. Sampling instructions 3. CD with templates for data entry 4. BMTA & Data Policy Agreement (iBOL)
  6. 6. Specimen arraying + samplingCONCEPT: Grouping of specimens in an arrangement that is compatiblewith a 96-well format used by most labs Specimen aggregate matching plate map 12 x 8 format 95 samples + 1 negative control Arraying Databasing Imaging Sampling
  7. 7. Specimen/sample arraying: ExamplesDirect sampling Subsample right amount of tissue 1drop/30μl 95- 100% ethanol Specimens order to match plate map Work sterile!  Excessive tissue might inhibit DNA extraction Enter corresponding sample ID in CCDB record Ensure all cap strips are firmly into the wells Arraying Databasing Imaging Sampling
  8. 8. Specimen/sample arraying: Examples A1 H 12 Plant boxTissue sampling – line-up the samples Correct (1 & 2) and incorrect (3 & 4) tissue sampling Arraying Databasing Imaging Sampling
  9. 9. Field dataTransferred to specimen data sheet MeasurementsCompulsory fields Include if availableCollecting number GenusDate of collection SpeciesCountry/provinceGPSField identificationFamilyField observations Total lengthPicture numbersCollectorsMeasurementsWeightSex Fork length Arraying Databasing Imaging Sampling
  10. 10. Data collection: BOLD requirements Arraying Databasing Imaging Sampling
  11. 11. Data collection: BOLD requirements Arraying Databasing Imaging Sampling
  12. 12. BOLD specimen data spreadsheetMS Exel based – 4 tabs/pages Voucher Information Arraying Databasing Imaging Sampling
  13. 13. BOLD specimen data spreadsheet Taxonomy Arraying Databasing Imaging Sampling
  14. 14. BOLD specimen data spreadsheet Specimen details Arraying Databasing Imaging Sampling
  15. 15. BOLD specimen data spreadsheet Collection Data Arraying Databasing Imaging Sampling
  16. 16. Specimen ImagingImportant in the barcoding process – can serve as an electronic voucher • .jpg format • High resolution pictures up to 20 megapixels • Maximum of 10 images per specimen Arraying Databasing Imaging Sampling
  17. 17. Specimen Imaging Framing/Orientation Display maximum diagnostic characters• Leave as little margins as possible Flower/Bud Fruit Stem and spines• Do not cut off parts of specimen• Scale bar can be useful Background• BOLD allows batch comparison– orientation must be the same Colour backgrounds are impractical Arraying Databasing Imaging Sampling
  18. 18. Key stages of front-end processing 1 2 3Sampling &Field data 4 NEXT STEP IN THE PIPELINE PCR Sequencing

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