| database reported |
1 |
| target species |
1 |
| software name |
1 |
| software parameters |
1 |
| how many mismatches etc. |
0 |
| where are mismatches located 3′ 5′ |
0 |
| list potential non target organisms that may cause problems |
0 |
| closely related |
0 |
| co-occurring |
0 |
| target tissue |
1 |
| tissue source |
0 |
| geographic scope |
0 |
| number of individuals the tissue was extracted from |
1 |
| tested on more than one haplotype |
0 |
| DNA concentration of the target extracts |
0 |
| primer (and probe) sequences reported |
1 |
| thermocycling conditions |
1 |
| check of amplification success |
1 |
| amplification confirmed by sequencing |
0 |
| gene / region reported |
1 |
| probe (if applicable; 5′-3′) |
1 |
| 5′ reporter dye (e.g. FAM, VIC, TET, NED) |
1 |
| internal quencher (in the middle of the probe sequence; e.g. ZEN) |
NA |
| 3′ quencher (ZEN, BHQ1, BHQ2, IBFQ, TAMARA) |
1 |
| TaqMan MGBNFQ (minor groove binder non fluorescent quencher) (yes/no) |
0 |
| volume |
1 |
| primer concentration |
1 |
| use of commercial Master Mix |
1 |
| use of custom Master Mix |
0 |
| MgCl2 concentration |
NA |
| dNTP concentration |
NA |
| buffer type and concentration |
NA |
| enzyme type and concentration |
0 |
| enhancer chemicals (additives TMAC, BSA, DIMSO….) |
0 |
| DNA extract volume in PCR |
1 |
| cycler model |
1 |
| annealing time |
1 |
| annealing temp |
1 |
| cycles |
1 |
| technical replication |
1 |
| optimization of PCR conditions |
0 |
| how many per species |
1 |
| geographic origin |
0 |
| tissue source (fresh or old) |
0 |
| non-target amplification checked via sequencing |
0 |
| DNA concentration |
0 |
| basic geographic scope |
1 |
| unidirectional lab flow |
1 |
| extensive geographic testing |
0 |
| method of extraction |
1 |
| modifications from established protocol |
0 |
| lysate volume |
0 |
| extraction negative control |
1 |
| elution volume |
0 |
| verification of DNA extraction |
0 |
| volume weight of environmental sample |
1 |
| filter type |
1 |
| pore size |
1 |
| surface area diameter |
0 |
| pressure used for filtration |
0 |
| filter preservation |
1 |
| precipitation chemicals added |
NA |
| centrifugation force and time for precipitation |
NA |
| temperature of precipitation |
NA |
| storage between collection and processing |
0 |
| “field” blanks |
1 |
| criteria to determine detection |
1 |
| sample type (e.g., water sediment) |
1 |
| artificial habitat |
0 |
| natural habitat |
1 |
| target DNA spiked into sample type |
0 |
| environmental variables recorded |
1 |
| sequence validation of positive field samples |
0 |
| determined limit of detection |
0 |
| method of establishment |
NA |
| multiple replicates of standard curve |
NA |
| multiple locations |
1 |
| site where species is not there |
0 |
| site where species is there |
1 |
| site where species was there historically |
0 |
| multiple samples at each site |
1 |
| environmental gradients (e.g., abiotic biotic conditions) |
1 |
| different known target species densities |
0 |
| testing against data from traditional methods |
1 |
| inhibition testing |
1 |
| geographic region tested |
0 |
| source of species occurrence information |
0 |
| multiple samples per species |
1 |
| geographic origin of tissue samples |
0 |
| tissue source |
0 |
| non-target amplification checked via sequencing |
0 |
| DNA concentration |
0 |
| non co-occurring closely related species checked from in silico |
0 |
| justify non-verified results from in silico (geographic realistic) |
0 |
| non-target amplification checked via sequencing |
0 |
| sampling through time |
0 |
| sampling spatially |
1 |
| statistical modelling |
0 |
| occupancy modelling |
1 |
| parameters and variables of model reported |
1 |
| know origin (e.g., shedding rate) |
0 |
| state |
0 |
| degradation rate |
0 |
| transport |
0 |
