Grace’s Notebook: Day 12, cold and warm, infected, uninfected RNA extractions – RNA in 24/24 samples

Today, Sam, Steven and I met to discuss a pooling plan for libraries (details in post). From that meeting it was decided that I should extract RNA from more day 12 samples, specfically from cold, warm, and infected and uninfected treatments. All 24 samples had RNA. An updated sample summary is provided at the end of the post.

Samples extracted today:

FRP trtmnt_tank sample_day infection_status maturity tube_number
6162 cold 12 1 I 220
6163 cold 12 1 I 228
6164 cold 12 1 I 257
6172 cold 12 0 M 316
6177 cold 12 1 I 250
6178 cold 12 0 M 218
6187 cold 12 1 I 239
6188 cold 12 1 I 245
6189 cold 12 0 I 216
6196 cold 12 1 I 203
6199 cold 12 1 I 254
6231 warm 12 1 I 278
6232 warm 12 0 M 286
6233 warm 12 1 I 371
6234 warm 12 0 I 263
6235 warm 12 0 I 297
6238 warm 12 0 M 375
6245 warm 12 1 I 365
6256 warm 12 1 I 283
6257 warm 12 1 I 363
6261 warm 12 1 I 273
6262 warm 12 1 I 289
6263 warm 12 1 I 368
6266 warm 12 1 I 264

Sample preparation and extraction:

Everything went pretty smoothly, and followed same protocol as last 4 extraction days (1; 2; 3; 4).

Protocol:

img

Some notes from today:

  • After Step 1 –> Had to re-spin tube 278 becuase there was still liquid on filter
  • After Step 2 –> Had to re-spin tubes 316 and 278 because still liquid on filter
  • During Step 3 –> some dried Prep Buffer dust may have gotten into tube 220, 228, 257
  • During Step 4 –> Switched to new wash buffer that Sam had added ethanol to on tube 245

Results:

qubit_tube_conc_ng.ml original_sample_conc_ng.ul sample_vol_ul dilution_factor tube_number extraction_method ul_sample-used elution_vol_ul total-yield_ng
405 40.5 2 100 264 Zymo_microprep 35 15 526.5
166 16.6 2 100 368 Zymo_microprep 35 15 215.8
271 27.1 2 100 289 Zymo_microprep 35 15 352.3
361 36.1 2 100 273 Zymo_microprep 35 15 469.3
207 20.7 2 100 363 Zymo_microprep 35 15 269.1
190 19 2 100 283 Zymo_microprep 35 15 247
370 37 2 100 365 Zymo_microprep 35 15 481
232 23.2 2 100 375 Zymo_microprep 35 15 301.6
409 40.9 2 100 297 Zymo_microprep 35 15 531.7
266 26.6 2 100 263 Zymo_microprep 35 15 345.8
285 28.5 2 100 371 Zymo_microprep 35 15 370.5
510 51 2 100 286 Zymo_microprep 35 15 663
177 17.7 2 100 278 Zymo_microprep 35 15 230.1
284 28.4 2 100 254 Zymo_microprep 35 15 369.2
420 42 2 100 203 Zymo_microprep 35 15 546
444 44.4 2 100 216 Zymo_microprep 35 15 577.2
315 31.5 2 100 245 Zymo_microprep 35 15 409.5
203 20.3 2 100 239 Zymo_microprep 35 15 263.9
125 12.5 2 100 218 Zymo_microprep 35 15 162.5
316 31.6 2 100 250 Zymo_microprep 35 15 410.8
287 28.7 2 100 316 Zymo_microprep 35 15 373.1
272 27.2 2 100 257 Zymo_microprep 35 15 353.6
280 28 2 100 228 Zymo_microprep 35 15 364
129 12.9 2 100 220 Zymo_microprep 35 15 167.7

WHere are they now?

  • DNA columns in -20C in FTR 209 in labeled box on top shelf
  • Hemolymph pellets are back in their respective positions in the boxes in rack 14
  • Extracted RNA eluted in RNase-free water are in Rack 3, Column 4, Row 2 in the -80C

Sample Summary:

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