Skip to main content

Table 5 Datasets used in the study and the corresponding experimental details

From: ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone

Dataset name Number of specimens Fragment size, primer information Extraction/PCR setup PCR cleanup ONT Library Preparation kit/Flow cell used
R10.3 Datasets
 Mixed Diptera (see Srivathsan et al. [33])
- Sanger barcodes available
511 (257 mixed Diptera, 254 Dolichopodidae)
17 negatives
658 bp HCO2198, LCO1490 [80] Extraction Method: QuickExtract
PCR Mix:
Total volume: 20 μl
10× buffer: 2 μl
dNTPs (2.5 mM): 1.5 μl
Taq polymerase: 0.2 μl
BSA (1 mg/ml): 2 μl
Primer (5 μM): 2 μl each
DNA:2 μl
Ampure beads (Beckman Coulter) SQK-LSK110/FLO-MIN111
 Afrotropical Phoridae (see Srivathsan et al. [35])
- Illlumina mini-barcodes available
4275 (Phoridae)
45 negatives
658 bp HCO2198, LCO1490 [75] Extraction Method: QuickExtract
PCR Mix:
Total volume: 15.16 μl
Mastermix (CWBio): 10 μl
25 mM MgCl2: 0.16 μl
BSA (1 mg/ml): 2 μl
Primer (10 μM): 1 μl each
DNA: 1 μl
Sera-Mag beads (GE Healthcare Life Sciences) in PEG SQK-LSK109/FLO-MIN111
 Palaearctic Phoridae (658) 9929 (Phoridae)
105 negatives
658 bp jgHCO2198, LCO1490 [80, 81] Extraction Method: HotSHOT
PCR Mix:
Total volume: 16 μl
Mastermix (CWBio): 7 μl
BSA (1 mg/ml): 1 μl
Primer (10 μM): 1 μl each
DNA: 6 μl
Ampure beads (Beckman Coulter) SQK-LSK110/FLO-MIN111
 Palaearctic Phoridae (313) 9932 (Phoridae)
106 negatives
313 bp m1COlintF, jgHCO2198 [79, 81] Extraction Method: HotSHOT
PCR Mix:
Total volume: 14 μl
Mastermix (CWBio): 7 μl
BSA (1 mg/ml): 1 μl
Primer (10 μM): 1 μl each
DNA: 4 μl
Ampure beads (Beckman Coulter) SQK-LSK110/FLO-MIN111
Flongle datasets
 Mixed Diptera subsample (see Srivathsan et al. [33])
- Sanger barcodes available
257
7 negatives
See “Mixed Diptera” entry for R10.3 See “Mixed Diptera” entry for R10.3 Ampure beads (Beckman Coulter) SQK-LSK109/Flongle
 Chironomidae 191 (Chironomidae)
1 negative
313 bp m1COlintF, jgHCO2198 [74, 76] Extraction Method: HotSHOT
PCR Mix:
Total volume: 14 μl
Mastermix (CWBio): 7 μl
BSA (1 mg/ml): 1 μl
Primer (10 μM): 1 μl each
DNA: 4 μl
Ampure beads (Beckman Coulter) SQK-LSK109/Flongle