RNA QC

I have been having some discrepancies in my RNA QC data for AH’s sample. I have been getting “Sample too low” for a lot of samples on the Qubit, but when I run the same samples on the Tapestation, I get pretty solid concentrations. I wanted to compare data from past extractions that have done both Qubit and Tapestation. Erin Chille did RNA extractions for an Mcap 2018 larval experiment and a Ahya 2018 gamete experiment where she did Qubit and Tapestation QC on the samples. I compared those results in the figures and tables below.

Mcap 2018 RNA QC

These samples were embryo and larvae samples. Here’s the summary table for the Mcap 2018 experiment:

BatchNo ExtractionNo SampleNo DateCollected DateExtracted Quantity_uL Extractor Qubit_RNA TS_RNA Link Notes
1 10 218 20180615 20190301 300 Erin 99.9 45.4 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Results/  
1 11 219 20180615 20190301 300 Erin 138 85.3 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Results/  
1 12 220 20180615 20190301 300 Erin 77.7 60.2 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Results/  
1 13 230 20180615 20190301 300 Erin 93.6 53.6 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Results/  
2 14 244 20180617 20190303 300 Erin 109.5 58.7 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-2/  
2 15 243 20180617 20190303 300 Erin 105 80.9 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-2/  
2 16 363 20180622 20190303 300 Erin 243 84.5 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-2/ Got an initial TS concentration of 4.11; reran and got TA concentration of 84.5
2 17 310 20180618 20190303 300 Erin 85.7 101 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-2/  
3 18 367 20180622 20190318   Erin 30.3 20.3 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-3/  
3 19 321 20180620 20190318 300 Erin 73.5 49.3 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-3/  
3 20 232 20180616 20190318 300 Erin 43.3 36.7 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-3/  
3 21 322 20180620 20190318 300 Erin 74.9 40.8 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-3/  
4 22 312 20180618 20190322 300 Erin 81 80.3 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-4/  
4 23 231 20180616 20190322 300 Erin 82.9 78.2 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-4/  
4 24 379 20180622 20190322   Erin 83.9 72.4 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-4/  
4 25 371 20180622 20190322   Erin 59.4 54 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-4/  
5 26 311 20180618 20190329 300 Erin 129 98.4 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-5/  
5 27 375 20180622 20190329   Erin 52.5 54.5 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-5/  
5 28 359 20180622 20190329   Erin 131.5 107 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-5/  
5 29 323 20180620 20190329 300 Erin 91.9 88.6 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-5/  
5 30 242 20180617 20190329 300 Erin 144.5 110 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-5/  
6 31 360 20180622 20190412   Erin NA NA https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-6/ Qubit too low; No associated TS value
6 32 364 20180622 20190412   Erin NA NA https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-6/ Qubit too low; No associated TS value
6 33 372 20180622 20190412   Erin NA NA https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-6/ Qubit too low; No associated TS value
7 34 361 20180622 20190425   Erin 68.7 79.2 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-7/  
7 35 365 20180622 20190425   Erin 99.8 57.4 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-7/  
7 36 373 20180622 20190425   Erin 35.5 14.9 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-7/  
8 37 156 20180613 20190426 300 Erin 266 221 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-8/  
8 38 182 20180614 20190426 300 Erin 109.5 94.3 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-8/  
8 39 165 20180614 20190426 300 Erin 179 103 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-8/  
8 40 164 20180614 20190426 300 Erin 129 118 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-8/  
8 41 130 20180613 20190426 300 Erin 306 295 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-8/  
8 42 154 20180613 20190426 300 Erin 53.2 99.6 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-8/ Hard to see the TS concentration number in the image
8 43 181 20180614 20190426 300 Erin 138 121 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-8/  
8 44 163 20180614 20190426 300 Erin 140 120 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-8/  
9 45 133 20180613 20190429 300 Erin 79.9 71.8 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-9/  
9 46 153 20180613 20190429 300 Erin 47.2 62.5 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-9/  
9 47 155 20180613 20190429 300 Erin 216 201 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-9/  
9 48 158 20180613 20190429 300 Erin 129 86 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-9/  
9 49 160 20180613 20190429 300 Erin 45.4 35.2 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-9/  
9 50 166 20180614 20190429 300 Erin 79 99.9 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-9/  
9 51 169 20180614 20190429 300 Erin 34.6 37.6 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-9/  
10 52 127 20180613 20190506 300 Erin 32.9 38 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-10/  
10 53 129 20180613 20190506 300 Erin 38.5 30.4 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-10/  
10 54 132 20180613 20190506 300 Erin 20.2 19.7 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-10/  
10 55 162 20180614 20190506 300 Erin 47.1 NA https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-10/ No associated TS value
10 56 167 20180614 20190506 300 Erin 28.9 28.3 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-10/  
10 57 168 20180614 20190506 300 Erin 23.6 14.3 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-10/  
10 58 179 20180614 20190506 300 Erin 28.3 24.7 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-10/  
10 59 185 20180614 20190506 300 Erin 36.6 31.6 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-10/  
11 60 128 20180613 20190507 300 Erin & Emma 158 232 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-11/  
11 61 131 20180613 20190507 300 Erin & Emma 131.5 117 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-11/  
11 62 134 20180613 20190507 300 Erin & Emma 118 109 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-11/  
11 63 157 20180613 20190507 300 Erin & Emma 76.1 69.7 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-11/  
11 64 159 20180613 20190507 300 Erin & Emma 212 197 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-11/  
11 65 180 20180614 20190507 300 Erin & Emma 105 103 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-11/  
12 66 183 20180614 20190517 300 Erin 52 36 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-12/  
12 67 184 20180614 20190517 300 Erin 77.3 48.3 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-12/  
12 68 186 20180614 20190517 300 Erin 118 76.9 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-12/  
12 69 215 20180614 20190517 300 Erin 192 89.1 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-12/  
12 70 212 20180614 20190517 300 Erin 74 41.7 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-12/  
12 71 121 20180615 20190517 300 Erin 55.3 27.8 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-12/  
12 72 221 20180613 20190517 300 Erin 43.5 23 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Montipora-Larvae-DNA-RNA-Extraction-Batch-12/  
                     
            Min 20.2 14.3    
            Max 306 295    
            Mean 97.59333333 80.25423729    
            Median 81.95 72.4    
            SD 61.89514333 55.84537249    

Here’s the chart plotting the TS RNA concetrations on the y-axis and Qubit RNA concetrations on the x-axis:

R-squared value is 0.735.

Ahya 2018 RNA QC

These samples were either egg or sperm samples. Here’s the summary table for the Ahya 2018 experiment:

BatchNo ExtractionNo SampleNo DateCollected DateExtracted Quantity_uL Extractor Content Qubit_RNA TS_RNA Link Notes
1 1 796 20180411 20190524 100 Erin Eggs 44.7 52.4 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-1/  
1 2 161 20180211 20190524 100 Erin Sperm NA NA https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-1/  
1 3 227 20180211 20190524 100 Erin Eggs 179 157 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-1/  
1 4 203 20180211 20190524 100 Erin Eggs 64.3 53.9 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-1/  
1 5 13 20180111 20190524 100 Erin Sperm NA NA https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-1/  
1 6 179 20180211 20190524 100 Erin Eggs 26.4 25.3 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-1/  
1 7 191 20180211 20190524 100 Erin Eggs 74 54.6 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-1/  
1 8 197 20180211 20190524 100 Erin Sperm NA NA https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-1/  
1 9 778 20180411 20190524 100 Erin Sperm NA NA https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-1/  
1 10 209 20180211 20190524 100 Erin Sperm NA NA https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-1/  
2 11 784 20180411 20190528 100 Erin & Emma Eggs 96.6 76.9 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-2/  
2 12 215 20180211 20190528 100 Erin & Emma Eggs 101 86.6 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-2/  
2 13 760 20180411 20190528 100 Erin & Emma Eggs 109 88.4 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-2/  
2 14 790 20180411 20190528 100 Erin & Emma Sperm 10.2 24.4 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-2/  
2 15 19 20180111 20190528 100 Erin & Emma Eggs 153 113 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-2/  
2 16 185 20180211 20190528 100 Erin & Emma Sperm NA 38.8 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-2/ No Qubit value, but TS value
2 17 173 20180211 20190528 100 Erin & Emma Sperm NA 18 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-2/ No Qubit value, but TS value
2 18 754 20180411 20190528 100 Erin & Emma Sperm 11 36.1 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-2/  
2 19 167 20180211 20190528 100 Erin & Emma Eggs 121 84.2 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-2/  
2 20 221 20180211 20190528 100 Erin & Emma Sperm 12.1 NA https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-2/ No associated TS value
3 21 14 NA 20190820 100 Erin Sperm NA NA https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-3/  
3 22 755 NA 20190820 100 Erin Sperm 34.4 76.5 https://echille.github.io/E.-Chille-Open-Lab-Notebook/Acropora-Larvae-DNA-RNA-Extraction-Batch-3/  
                       
              Min 10.2 18    
              Max 179 157    
              Mean 74.05 65.74    
              Median 69.15 54.6    
              SD 54.48872502 37.57053937    

Here’s the chart plotting the TS RNA concetrations on the y-axis and Qubit RNA concetrations on the x-axis:

R-squared value is 0.856.

Written on October 7, 2023