20220125 Re-QCing DNA and RNA samples from the E5 Project

Rechecking the DNA and RNA from the E5 project

Troubleshooting problematic coral samples from each of the four timepoints

QC Date: January 25, 2022

DNA Samples

Tube number Timepoint Species Colony ID Extraction date
711 Nov Porites POR-93 20210903
475 March Porites POR-78 20210921
97 January Porites POR-367 20210923
149 January Porites POR-365 20210924
625 Sept Porites POR-387 20210924
637 Sept Porites POR-72 20210930
21 January Porites POR-235 20211001
131 January Porites POR-357 20211004
201 January Porites POR-76 20211005
819 Nov Acopora ACR-374 20211005
163 Sept Porites POR-340 20211007
537 March Pocillopora POC-255 20211007
769 Nov Porites POR-71 20211007
23 January Porites POR-236 20211008
177 January Porites POR-78 20211020
185 January Porites POR-82 20211020
483 March Porites POR-81 20211020
739 Nov Porites POR-70 20211028
175 January Porites POR-70 20211101
243 January Porites POR-81 20211102

RNA Samples

Tube number Timepoint Species Colony ID Extraction date
1 January Porites POR-266 20210824
347 March Acropora ACR-350 20210831
353 March Porites POR-353 20210831
775 Nov Acropora ACR-173 20210902
217 January Acropora ACR-187 20210903
717 Nov Acropora ACR-175 20210903
19 January Porites POR-224 20210903
263 January Acropora ACR-187 20210910
111 January Porites POR-381 20210920
835 January Porites POR-79 20211130
153 January Porites POR-72 20210903
291 March Pocillopora POC-257 20211112
249 March Porites POR-235 20211104
169 March Porites POR-340 20210903
543 March Porites POR-385 20211102
817 March Porites POR-83 20211122
687 Sept Pocillopora POC-377 20210903
843 Sept Porites POR-362 20211112
157 Sept Porites POR-71 20211115
885 Nov Porites POR-354 20211105
239 Nov Porites POR-349 20211118
81 January Porites POR-262 20211105
867 January Porites POR-245 20211105
343 January Porites POR-341 20210902
219 January Porites POR-355 20211108
927 January Porites POR-383 20211112
213 January Porites POR-349 20211129
85 January Porites POR-71 20211115
497 January Porites POR-75 20211129
907 January Porites POR-69 20211130
633 January Porites POR-79 20211130
271 January Porites POR-72 20210903
923 March Pocillopora POC-257 20211112
901 March Porites POR-235 20211104
151 March Porites POR-340 20210903
903 March Porites POR-385 20211102
143 March Porites POR-83 20211122
401 Sept Pocillopora POC-377 20210903
461 Sept Porites POR-362 20211112
207 Sept Porites POR-71 20211115
225 Nov Porites POR-354 20211105
229 Nov Porites POR-349 20211118

QC notes

  • These were all samples that had no detectable DNA or RNA using the Qubit BR kit, but had a band when run out on a gel

Qubit

  • Used High Sensitivity DNA or RNA Qubit Protocol
  • All samples read twice, standards only read once

DNA Qubit

Tube number RFU DNA 1 (ng/uL) DNA 2 (ng/uL) Average
Standard 1 54.14      
Standard 2 24741.95      
7   0.196 0.190 0.193
13   0.218 0.172 0.195
109   0.632 0.630 0.631
125   0.308 0.224 0.276
167   0.456 0.454 0.455
173   0.366 0.352 0.359
191   0.440 0.462 0.451
193   0.430 0.436 0.433
195   nd nd nd
209   0.258 0.322 0.290
235   0.638 0.646 0.642
267   102.0 100.0 101.0
287   0.792 0.760 0.776
409   1.20 1.20 1.20
459   0.302 0.304 0.303
469   0.430 0.524 0.477
577   10.8 10.8 10.8
601   0.312 0.286 0.299
647   0.762 0.754 0.758
795   0.304 0.290 0.297
831   1.39 1.22 1.305

Nanodrop

  • Used ThermoScientific Nanodrop 2000
  • Blanked using the Tris HCl

DNA

Tube number ng/uL 260:230
7 -0.8 1.09
13 3.1 1.46
109 -0.4 0.49
125 0.4 -4.63
167 0.9 3.58
173 1.3 2.70
191 -0.1 0.39
193 0.3 -1.15
195 -0.3 0.46
209 0.7 1.54
235 -0.5 0.95
267 127.3 1.84
287 -1.0 1.02
409 0.4 -1.21
459 0.7 2.16
469 -0.9 3.24
577 12.5 1.94
601 2.4 2.08
647 0.8 1.22
795 2.9 1.42
831 3.2 1.80

RNA 1 Qubit

Tube number RFU DNA 1 (ng/uL) DNA 2 (ng/uL) Average
Standard 1 54.14      
Standard 2 24741.95      
7   0.196 0.190 0.193
13   0.218 0.172 0.195
109   0.632 0.630 0.631
125   0.308 0.224 0.276
167   0.456 0.454 0.455
173   0.366 0.352 0.359
191   0.440 0.462 0.451
193   0.430 0.436 0.433
195   nd nd nd
209   0.258 0.322 0.290
235   0.638 0.646 0.642
267   102.0 100.0 101.0
287   0.792 0.760 0.776
409   1.20 1.20 1.20
459   0.302 0.304 0.303
469   0.430 0.524 0.477
577   10.8 10.8 10.8
601   0.312 0.286 0.299
647   0.762 0.754 0.758
795   0.304 0.290 0.297
831   1.39 1.22 1.305

Nanodrop

  • Used ThermoScientific Nanodrop 2000
  • Blanked using the Rnase Free Water

RNA 1

Tube number ng/uL 260:230
7 -0.8 1.09
13 3.1 1.46
109 -0.4 0.49
125 0.4 -4.63
167 0.9 3.58
173 1.3 2.70
191 -0.1 0.39
193 0.3 -1.15
195 -0.3 0.46
209 0.7 1.54
235 -0.5 0.95
267 127.3 1.84
287 -1.0 1.02
409 0.4 -1.21
459 0.7 2.16
469 -0.9 3.24
577 12.5 1.94
601 2.4 2.08
647 0.8 1.22
795 2.9 1.42
831 3.2 1.80

RNA 2 Qubit

Tube number RFU DNA 1 (ng/uL) DNA 2 (ng/uL) Average
Standard 1 54.14      
Standard 2 24741.95      
7   0.196 0.190 0.193
13   0.218 0.172 0.195
109   0.632 0.630 0.631
125   0.308 0.224 0.276
167   0.456 0.454 0.455
173   0.366 0.352 0.359
191   0.440 0.462 0.451
193   0.430 0.436 0.433
195   nd nd nd
209   0.258 0.322 0.290
235   0.638 0.646 0.642
267   102.0 100.0 101.0
287   0.792 0.760 0.776
409   1.20 1.20 1.20
459   0.302 0.304 0.303
469   0.430 0.524 0.477
577   10.8 10.8 10.8
601   0.312 0.286 0.299
647   0.762 0.754 0.758
795   0.304 0.290 0.297
831   1.39 1.22 1.305

Nanodrop

  • Used ThermoScientific Nanodrop 2000
  • Blanked using the Tris HCl

RNA 2

Tube number ng/uL 260:230
7 -0.8 1.09
13 3.1 1.46
109 -0.4 0.49
125 0.4 -4.63
167 0.9 3.58
173 1.3 2.70
191 -0.1 0.39
193 0.3 -1.15
195 -0.3 0.46
209 0.7 1.54
235 -0.5 0.95
267 127.3 1.84
287 -1.0 1.02
409 0.4 -1.21
459 0.7 2.16
469 -0.9 3.24
577 12.5 1.94
601 2.4 2.08
647 0.8 1.22
795 2.9 1.42
831 3.2 1.80

Addtional Notes

  • NA
Written on January 25, 2022