Pre-lab (front-end) processingDifferent collections have different standards

If this is not addressed collection processing may become the bottleneck in the analytical chain which could hamper large-scale barcoding projects.

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

Logistical problems: lots and specimens

Multiple taxa from the same collecting event

Single collection voucherwith data link to the original batch number

CD002709/10/2011Unique voucher number

BATCH 09/10/2010

Barcoding – Specimen based

Unique voucher number

Label with voucher nr.

OM2035

Unprocessedspecimens

1. Arraying

Labeling

3. Imaging

4. Sampling/ Subsampling

Lab-ready 96 well microplate

Formatted data records

2. Databasing

Formattedimages

BOLD Systems (www.boldsystems.org)

LIMSCore lab procedure

Pre-lab (front-end) processing

Pre-conference Short Course on DNA Barcoding Methods

4 Main steps required to transform specimen collections into lab-ready96-well microplates

LIMS – Lab information management system

SAMPLING KITSDispatched 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)

Specimen arraying + sampling

CONCEPT: Grouping of specimens in an arrangement that is compatible with a 96-well format used by most labs

12 x 8 format

95 samples + 1 negative control

Specimen aggregate matching plate map

Arraying Databasing Imaging Sampling

Specimen/sample arraying: Examples

1drop/30μl 95-100% ethanol

Work sterile!

Ensure all cap strips are firmly into the wells

Enter corresponding sample ID in CCDB record

Subsample right amount of tissue

Excessive tissue might inhibit DNA extraction

Direct sampling

Arraying Databasing Imaging Sampling

Specimens order tomatch plate map

Tissue sampling – line-up the samples

Plant box

A

H

1

12

Correct (1 & 2) and incorrect (3 & 4)tissue sampling

Specimen/sample arraying: Examples

Arraying Databasing Imaging Sampling

Field data

Compulsory fields Include if available

Collecting number Genus

Date of collection Species

Country/province

GPS

Field identification

Family

Field observations

Picture numbers

Collectors

Measurements

Weight

Sex

Measurements

Fork length

Total length

Arraying Databasing Imaging Sampling

Transferred to specimen data sheet

Data collection: BOLD requirements

Arraying Databasing Imaging Sampling

Data collection: BOLD requirements

Arraying Databasing Imaging Sampling

BOLD specimen data spreadsheet

Voucher Information

Arraying Databasing Imaging Sampling

MS Exel based – 4 tabs/pages

BOLD specimen data spreadsheet

Taxonomy

Arraying Databasing Imaging Sampling

BOLD specimen data spreadsheetSpecimen details

Arraying Databasing Imaging Sampling

BOLD specimen data spreadsheetCollection Data

Arraying Databasing Imaging Sampling

Specimen Imaging

• .jpg format• High resolution pictures up to 20 megapixels• Maximum of 10 images per specimen

Important in the barcoding process – can serve as an electronic voucher

Arraying Databasing Imaging Sampling

Specimen ImagingFraming/Orientation

• Leave as little margins as possible• Do not cut off parts of specimen• Scale bar can be useful• BOLD allows batch comparison–

orientation must be the same

Flower/Bud Fruit Stem and spines

Display maximum diagnostic characters

Background

Colour backgrounds are impractical

Arraying Databasing Imaging Sampling

Key stages of front-end processing

1 2 3

4

Sampling &Field data

NEXT STEP IN THE PIPELINEPCRSequencing