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

1. Pre-lab (front-end) processing
Different collections have different standards
Challenge is to transform this into a standard
lab-compatible format
Core labs operate in 96-well plate format
which require compatible front-end solutions
If this is not addressed collection processing may become the bottleneck in the analytical chain
which could hamper large-scale barcoding projects.

2. Logistical problems: lots and specimens
Barcoding – 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. Unique voucher number
Label with
voucher nr.
OM2035

4. Pre-lab (front-end) processing
1. Arraying
Unprocessed Formatted
specimens 2. Databasing
data records
Labeling
4 Main steps required to transform
specimen collections into lab-ready 3. Imaging
96-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. SAMPLING KITS
Dispatched by core analytical facilities; To streamline sample submission
1. Sampling plates 2. Sampling instructions 3. CD with templates for
data entry
4. BMTA & Data Policy
Agreement (iBOL)

6. Specimen arraying + sampling
CONCEPT: Grouping of specimens in an arrangement that is compatible
with 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. Specimen/sample arraying: Examples
Direct 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. Specimen/sample arraying: Examples
A1
H
12
Plant box
Tissue sampling – line-up the samples
Correct (1 & 2) and incorrect (3 & 4)
tissue sampling
Arraying Databasing Imaging Sampling

9. Field data
Transferred to specimen data sheet
Measurements
Compulsory fields Include if available
Collecting number Genus
Date of collection Species
Country/province
GPS
Field identification
Family
Field observations Total length
Picture numbers
Collectors
Measurements
Weight
Sex Fork length
Arraying Databasing Imaging Sampling

10. Data collection: BOLD requirements
Arraying Databasing Imaging Sampling

11. Data collection: BOLD requirements
Arraying Databasing Imaging Sampling

12. BOLD specimen data spreadsheet
MS Exel based – 4 tabs/pages
Voucher Information
Arraying Databasing Imaging Sampling

13. BOLD specimen data spreadsheet
Taxonomy
Arraying Databasing Imaging Sampling

14. BOLD specimen data spreadsheet
Specimen details
Arraying Databasing Imaging Sampling

15. BOLD specimen data spreadsheet
Collection Data
Arraying Databasing Imaging Sampling

16. Specimen Imaging
Important 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. 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. Key stages of front-end processing
1 2 3
Sampling &
Field data
4
NEXT STEP IN THE PIPELINE
PCR
Sequencing