Experiment Overview
| Repository ID: | FR-FCM-ZY8F | Experiment name: | Aptamer binding to different bacterial species | MIFlowCyt score: | 86.00% |
| Primary researcher: | Jennifer Soundy | PI/manager: | Darren Day | Uploaded by: | Jennifer Soundy |
| Experiment dates: | 2016-07-18 - 2017-01-20 | Dataset uploaded: | Jul 2017 | Last updated: | Jul 2017 |
| Keywords: | [] [Bacteria] [Aptamer binding] [Pseudomonas aeruginosa] [SELEX progression] [FAM labelled aptamer] | Manuscripts: | |||
| Organizations: |
Victoria University of Wellington, School of Biological Sciences, Wellington, Wellington (New Zealand)
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| Purpose: | The purpose of this experiment was to investigate whether the isolated Pseudomonas aptamers had binding cross reactivity with other bacterial species, or whether they were specific for Pseudomonas. A range of gram-negative and one gram positive bacteria was tested. Salmonella enterica serovar Typhi (ATCC 19430), Klebsiella pneumoniae (ATCC 13883), Enterobacter cloacae (ATCC 13047), Listeria innocua (ATCC 33090) and Escherichia coli DH5? were used, as well as P. aeruginosa 692 (PA692) (ATCC 14502) and P.aeruginosa PAO1 (ATCC 15692). | ||||
| Conclusion: | We found that all of the aptamers were selective for P. aeruginosa with minimal cross reactivity to the tested bacteria. Small amounts of cross reactivity that can be seen could be due to similar outer membrane proteins between bacterial species. | ||||
| Comments: | ANALYSIS WAS DONE EXTERNAL TO CYTOBANK USING FLOWING SOFTWARE, FIND FILES ATTACHED SHOWING THE ANALYSIS PROCESS. Each type of bacteria was tested with one concentration of FAM labelled aptamer - 250 nM, and the resulting fluorescence was plotted and compared between bacterial species. Analysis was done using the gated geomean of control cells and then minusing this from the gated fluorescence of aptamer treated cells. | ||||
| Funding: | Not disclosed | ||||
| Quality control: | The same flow cytometer and settings are used for all experiments. The PBS used as flow buffer to re-suspend the bacteria in was run on its own to check for contamination or particulate that shows up as the same size as our target bacteria | ||||
Experiment variables
| Conditions | |
|---|---|
| · JN08 | JN08_692_027.fcs · JN08_DH5a_029.fcs · JN08_Entero_025.fcs · JN08_Kleb_023.fcs · JN08_List_026.fcs · JN08_Salm_024.fcs · JN08_pao1_028.fcs |
| · JN27 | JN27_692_013.fcs · JN27_DH5a_015.fcs · JN27_Entero_011.fcs · JN27_Kleb_009.fcs · JN27_List_012.fcs · JN27_Salm_010.fcs · JN27_pao1_014.fcs |
| · JN08.SH | JN08-SH_692_034.fcs · JN08-SH_DH5a_036.fcs · JN08-SH_Entero_032.fcs · JN08-SH_Kleb_030.fcs · JN08-SH_List_033.fcs · JN08-SH_Salm_031.fcs · JN08-SH_pao1_035.fcs |
| · JN27.SH | JN27-SH_692_020.fcs · JN27-SH_DH5a_022.fcs · JN27-SH_Entero_018.fcs · JN27-SH_Kleb_016.fcs · JN27-SH_List_019.fcs · JN27-SH_Salm_017.fcs · JN27-SH_pao1_021.fcs |
| · JN17.SH | JN17-SH_692_041.fcs · JN17-SH_DH5a_043.fcs · JN17-SH_Entero_039.fcs · JN17-SH_Kleb_037.fcs · JN17-SH_List_040.fcs · JN17-SH_Salm_038.fcs · JN17-SH_pao1_042.fcs |
| · JN21.SH | JN21-SH_692_048.fcs · JN21-SH_DH5a_050.fcs · JN21-SH_Entero_046.fcs · JN21-SH_Kleb_044.fcs · JN21-SH_List_047.fcs · JN21-SH_Salm_045.fcs · JN21-SH_pao1_049.fcs |
| · St21Lp17 | st21lp17_Ecoli_023.fcs · st21lp17_PA692_029.fcs · st21lp17_PAO1_027.fcs · st21lp17_entero_024.fcs · st21lp17_klebsiella_028.fcs · st21lp17_listeria_025.fcs · st21lp17_salmonella_026.fcs |
| · St17lp21 | st17lp21_Ecoli_030.fcs · st17lp21_PA692_036.fcs · st17lp21_PAO1_034.fcs · st17lp21_entero_031.fcs · st17lp21_klebsiella_035.fcs · st17lp21_listeria_032.fcs · st17lp21_salmonella_033.fcs |
| · St08Lp17 | st08lp17_Ecoli_037.fcs · st08lp17_PA692_043.fcs · st08lp17_PAO1_041.fcs · st08lp17_entero_038.fcs · st08lp17_klebsiella_042.fcs · st08lp17_listeria_039.fcs · st08lp17_salmonella_040.fcs |
| · No treatment | Control cells_692_005.fcs · Control cells_DH5a_007.fcs · Control cells_Ecoli_004.fcs · Control cells_Entero_003.fcs · Control cells_Kleb_008.fcs · Control cells_List_004.fcs · Control cells_PA692_002.fcs · Control cells_PAO1_003.fcs · Control cells_PBS_001.fcs · Control cells_PBS_001.fcs-(1) · Control cells_Salm_002.fcs · Control cells_entero_008.fcs · Control cells_klebsiella_006.fcs · Control cells_listeria_007.fcs · Control cells_pao1_006.fcs · Control cells_salmonella_005.fcs |
| Sample Type | |
|---|---|
| · PAO1 | Control cells_PAO1_003.fcs · Control cells_pao1_006.fcs · JN08-SH_pao1_035.fcs · JN08_pao1_028.fcs · JN17-SH_pao1_042.fcs · JN21-SH_pao1_049.fcs · JN27-SH_pao1_021.fcs · JN27_pao1_014.fcs · st08lp17_PAO1_041.fcs · st17lp21_PAO1_034.fcs · st21lp17_PAO1_027.fcs |
| · PA692 | Control cells_692_005.fcs · Control cells_PA692_002.fcs · JN08-SH_692_034.fcs · JN08_692_027.fcs · JN17-SH_692_041.fcs · JN21-SH_692_048.fcs · JN27-SH_692_020.fcs · JN27_692_013.fcs · st08lp17_PA692_043.fcs · st17lp21_PA692_036.fcs · st21lp17_PA692_029.fcs |
| · Listeria | Control cells_List_004.fcs · Control cells_listeria_007.fcs · JN08-SH_List_033.fcs · JN08_List_026.fcs · JN17-SH_List_040.fcs · JN21-SH_List_047.fcs · JN27-SH_List_019.fcs · JN27_List_012.fcs · st08lp17_listeria_039.fcs · st17lp21_listeria_032.fcs · st21lp17_listeria_025.fcs |
| · E. coli | Control cells_DH5a_007.fcs · Control cells_Ecoli_004.fcs · JN08-SH_DH5a_036.fcs · JN08_DH5a_029.fcs · JN17-SH_DH5a_043.fcs · JN21-SH_DH5a_050.fcs · JN27-SH_DH5a_022.fcs · JN27_DH5a_015.fcs · st08lp17_Ecoli_037.fcs · st17lp21_Ecoli_030.fcs · st21lp17_Ecoli_023.fcs |
| · Salmonella | Control cells_Salm_002.fcs · Control cells_salmonella_005.fcs · JN08-SH_Salm_031.fcs · JN08_Salm_024.fcs · JN17-SH_Salm_038.fcs · JN21-SH_Salm_045.fcs · JN27-SH_Salm_017.fcs · JN27_Salm_010.fcs · st08lp17_salmonella_040.fcs · st17lp21_salmonella_033.fcs · st21lp17_salmonella_026.fcs |
| · Klebsiella | Control cells_Kleb_008.fcs · Control cells_klebsiella_006.fcs · JN08-SH_Kleb_030.fcs · JN08_Kleb_023.fcs · JN17-SH_Kleb_037.fcs · JN21-SH_Kleb_044.fcs · JN27-SH_Kleb_016.fcs · JN27_Kleb_009.fcs · st08lp17_klebsiella_042.fcs · st17lp21_klebsiella_035.fcs · st21lp17_klebsiella_028.fcs |
| · Enterobacter | Control cells_Entero_003.fcs · Control cells_entero_008.fcs · JN08-SH_Entero_032.fcs · JN08_Entero_025.fcs · JN17-SH_Entero_039.fcs · JN21-SH_Entero_046.fcs · JN27-SH_Entero_018.fcs · JN27_Entero_011.fcs · st08lp17_entero_038.fcs · st17lp21_entero_031.fcs · st21lp17_entero_024.fcs |
