RNA extractions - more day 12 - RNA in 23 / 24

Today I extracted RNA from 24 more samples from Day 12. Mix of infection status and temperature exposures. There was RNA in 23 out of 24 samples. No obvious mistakes were made, and at the end of the post I provide an updated RNA sample summary in preparation for our crab RNA meeting tomorrow.

Samples extracted today:

FRP trtmnt_tank sample_day infection_status maturity tube_number
6136 ambient 12 0 M 321
6143 ambient 12 0 M 343
6150 ambient 12 0 M 312
6168 ambient 12 1 I 357
6201 ambient 12 1 I 341
6202 ambient 12 1 I 337
           
6128 cold 12 1 I 231
6140 cold 12 1 I 237
6141 cold 12 1 I 249
6153 cold 12 0 M 209
6157 cold 12 0 M 224
6160 cold 12 0 M 238
           
6173 cold 12 1 I 210
6174 cold 12 1 I 233
6175 cold 12 0 I 246
6223 warm 12 0 M 270
6228 warm 12 0 I 290
6230 warm 12 0 M 292
           
6240 warm 12 1 I 362
6243 warm 12 1 I 272
6244 warm 12 1 I 284
6248 warm 12 0 I 378
6253 warm 12 0 I 275
6255 warm 12 1 I 262

Sample preparation and extraction

I did everything the same as I’ve done the past three extractions (1, 2, and 3).

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
413 41.3 2 100 262 Zymo_microprep 35 15 536.9
298 29.8 2 100 275 Zymo_microprep 35 15 387.4
141 14.1 2 100 378 Zymo_microprep 35 15 183.3
276 27.6 2 100 284 Zymo_microprep 35 15 358.8
94.2 9.42 2 100 272 Zymo_microprep 35 15 122.46
134 13.4 2 100 362 Zymo_microprep 35 15 174.2
172 17.2 2 100 292 Zymo_microprep 35 15 223.6
285 28.5 2 100 290 Zymo_microprep 35 15 370.5
293 29.3 2 100 270 Zymo_microprep 35 15 380.9
207 20.7 2 100 246 Zymo_microprep 35 15 269.1
352 35.2 2 100 233 Zymo_microprep 35 15 457.6
333 33.3 2 100 210 Zymo_microprep 35 15 432.9
380 38 2 100 238 Zymo_microprep 35 15 494
192 19.2 2 100 224 Zymo_microprep 35 15 249.6
243 24.3 2 100 209 Zymo_microprep 35 15 315.9
186 18.6 2 100 249 Zymo_microprep 35 15 241.8
50.6 5.06 2 100 237 Zymo_microprep 35 15 65.78
379 37.9 2 100 231 Zymo_microprep 35 15 492.7
Out of range Out of range 2 100 337 Zymo_microprep 35 15 #VALUE!
179 17.9 2 100 341 Zymo_microprep 35 15 232.7
173 17.3 2 100 357 Zymo_microprep 35 15 224.9
142 14.2 2 100 312 Zymo_microprep 35 15 184.6
77.3 7.73 2 100 343 Zymo_microprep 35 15 100.49
117 11.7 2 100 321 Zymo_microprep 35 15 152.1

Where are they now?

  • The extracted RNA is in a new box in the -80C: Rack 3, Column 4, Row 2.
  • The hemolymph pellets were placed back where I found them in the Day 12 pelleted hemolymph boxes (Rack 14)
  • The DNA from today and the previous days were transferred to boxes that I labeled and they are on the top shelf in FTR 209 -20C freezer.

Sample Summary so far from my zymo-kit extractions:

Day Infection_status temperature Total ng of RNA for all sample tubes that had RNA # tubes with RNA out of how many were processed
9 Infected NA 5532.67 21 out of 24
9 Uninfected NA 4768.96 22 out of 24
12 Infected Cold 3039.79 11 out of 11
12 Uninfected Cold 2143.7 7 out of 7
12 Infected Ambient 1593.8 5 out of 6
12 Uninfected Ambient 1061.9 6 out of 6
12 Infected Warm 1831.96 7 out of 7
12 Uninfected Warm 2998.97 11 out of 11

This was determined by using the filtering in excel and adding up the total ng of RNA from my master spreadsheet of qubit results, and hemolymph sampling data: analyses/master-qubit-sample.csv

Written on October 31, 2019