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