Reagents | Materials | Equipment | |
Life Technologies Fast Advanced master mix (#4444557) | Microcentrifuge tubes | Biological Safety Cabinet Class 2 Type A/B3 | |
PCR grade water | ABI 96-well optical plates | Fully equipped reagent and genomic preparation clean rooms | |
IDTE 1x TE Buffer pH 8.0 | optical adhesive film | Heating Blocks | |
IS481 primers and probe | adhesive film | Pipettes (various volumes) | |
pIS1001 primers and probe | adhesive film applicator | Applied Biosystems 7500 Real-time Analyzer | |
Human Beta Globin (HBG) primers and probe | pipette tips (various volumes) | ||
Internal positive control gBlock and primers and probe | Lo-bind PCR tubes | ||
Instagene Matrix (BioRad) | tube racks | ||
HBG-IS481-pIS1001 gBlock | Discard pail and waste bags | ||
QC strain of Bordetella parapertussis organism | disposable gloves and gown | ||
Ambion Carrier RNA (thermofisher #4382878) | Clear plastic bags |
Primers | Sequence | Product Size | Final Concentration (nM) | Target | Reference | |
PPertM_mod (481-F) | CATCAAGCACCGCTTTACCC | 117 | 300 | IS481 | Modified Kamachi et al., 2015 | |
APPert_mod-R (481-R) | TGTTGGGAGTTCTGGTAGGTGTG | |||||
135U17 (F) (1001-F) | TCGAACGCGTGGAATGG | 65 | 150 | pIS1001 | Tatti et al., 2011 | |
199L20 (R) (1001-R) | GGCCGTTGGCTTCAAATAGA | |||||
HBG-F | ACCCAGAGGTTCTTTGAGTCCTTT | 82 | 100 | HBG | Mauritz et al. | |
HBG-R | TGCCATGAGCCTTCACCTTAG |
Probe | Sequence | Target | Dye/Quencher | Final Concentration (nM) | Reference | |
871U22P_MGB (481-P) | TTGCGTGAGTGGGCT | IS481 | FAM/MGB | 150 | Modified Tatti et al., 2011 | |
157U21P (1001-P) | AGACCCAGGGCGCACGCTGTC | pIS1001 | VIC/QSY | 150 | Tatti et al., 2011 | |
HBG-P | CACTCCTGATGCTGTTATG | HBG | NED/MGB | 100 | Modified Mauritz et al. | |
Pxd34_long (IPC-P) | AATGCCTGCGACAGCTACTGCAACTTCA | IPC | CY5/TAO | 100 | In-house |
Extraction Controls | Control Organism/Reagent | Comment | |
NEC: Negative Extraction Control | PCR grade water | Negative extraction control is used to test the sterility of the extraction reagents. | |
PEC: Positive Extraction Control | Material positive for Bordetella parapertussis | Positive extraction control is used to test the effectiveness of the extraction protocol with the organisms of interest |
PCR Controls | Control Organism/Reagent | Comment | |
HBG-IS481-pIS1001 gBlock | Frozen aliquots of gBlock for HBG, B. pertussis, and B. parapertussis diluted to 2.46 x 10^2 copies/uL | See below for preparation and sequence | |
NTC: No Template Control | PCR grade water | Use the same lot of water as was used in the preparation of the master mix. Tests for the sterility of the master mix reagents. |
Inhibition Control | Control Organism/Reagent | Comment | |
IPC: Internal Positive Control | IPC gBlock diluted to 1000 copies/ul and 1 uL added to each reaction | IPC control is used to test for possible PCR inhibitors present in each patient sample. See below for preparation and sequence |
Primer/Probe | Stock Concentration (uM) | Final PCR Concentration (nM) | (uL) for 1000 reactions | |
481-F | 100 | 300 | 60 | |
481-R | 100 | 300 | 60 | |
481-P | 100 | 150 | 30 | |
1001-F | 100 | 150 | 30 | |
1001-R | 100 | 150 | 30 | |
1001-P | 100 | 150 | 30 | |
HBG-F | 100 | 100 | 20 | |
HBG-R | 100 | 100 | 20 | |
HBG-P | 100 | 100 | 20 | |
IPC-P | 100 | 100 | 20 | |
IDTE Volume | 680 | |||
Final Volume | 1000 |
Reagents | 1x reaction (uL) | |
PCR grade water | 3 | |
Fast Advanced Master Mix | 10 | |
20X PERT Mix | 1 | |
IPC gBlock (1000 copies/uL) -added in genomics room- | 1 |
If | Then | |
Plate will not be run immediately | Store the plate in a 4C fridge until ready to perform PCR | |
Plate will be run immediately | Proceed to load and run the plate on the ABI 7500 |
Temperature (°C) | Time | Number of Cycles | |
50 | 2 min | Hold | |
95 | 20 sec | Hold | |
95 | 3 sec | 40 | |
60 | 30 sec |
Target | Dye | Quencher | |
HBG | NED | MGB | |
IPC | CY5 | None | |
IS481 | FAM | MGB | |
pIS1001 | VIC | None |
If Ct value for HBG is: | Then value for analysis is: | |
Any Ct value | Positive | |
Undetermined | Negative |
If Ct value for IS481 is: | Then value for analysis is: | |
35 or lower | Positive for B. pertussis or B. holmesii* | |
greater than 35 and less than or equal to 40 | Indeterminate | |
Undetermined | Negative |
If Ct value for pIS1001 is: | Then value for analysis is: | |
35 or lower | Positive for B. parapertussis | |
greater than 35 and less than or equal to 40 | Indeterminate | |
Undetermined | Negative |
If Ct value for IPC is: | Then value for analysis is: | |
Any Ct value | Positive | |
Undetermined | Negative |