Laura’s Notebook: QuantSeq – inventory of finished libraries

Library prep is complete! However, I will need to redo many 😦 Based on Bioanalyzer results, any libraries with concentration <1.0 ng/uL will need to be re-done. Out of the total 132 samples that I prepped, 34 had concentrations that were LOW or <1.0 ng/uL (according to Qubit). That’s about a 25% incompletion rate. Here is the final inventory.

Next step – redo the 34 samples. Need to decide whether I should re-isolate RNA, or just try to re-do the library generation. This is a question for lab meeting tomorrow.

Ctenidia

Cohort pCO2 HOMOGENATE TUBE # TISSUE TYPE TISSUE SAMPLE # [RNA] after Dnase treatment (ng/uL) End Point PCR cycles ds cDNA concentration
Dabob Bay High 291 CTENIDIA HL10-10 158.0 15 LOW
Dabob Bay High 292 CTENIDIA HL10-11 29.6 15 1.32
Dabob Bay High 293 CTENIDIA HL10-12 39.6 16 1.03
Dabob Bay High 294 CTENIDIA HL6-10 110.0 16 1.95
Dabob Bay High 295 CTENIDIA HL6-11 34.8 18 LOW
Dabob Bay High 296 CTENIDIA HL6-12 180.0 15 3.46
Dabob Bay High 298 CTENIDIA HL6-14 182.0 15 3.08
Dabob Bay High 299 CTENIDIA HL6-15 50.4 15 2.46
Dabob Bay Ambient 301 CTENIDIA HL10-19 75.8 15 2.82
Dabob Bay Ambient 302 CTENIDIA HL10-20 62.4 14 4.90
Dabob Bay Ambient 306 CTENIDIA HL10-21 136.0 18 LOW
Dabob Bay Ambient 304 CTENIDIA HL6-19 200.0 15 2.80
Dabob Bay Ambient 305 CTENIDIA HL6-20 75.2 16 2.96
Dabob Bay Ambient 303 CTENIDIA HL6-21 95.2 14 2.40
Dabob Bay Ambient 307 CTENIDIA HL6-16 89.4 TOO LOW TOO LOW
Dabob Bay Ambient 308 CTENIDIA HL6-17 73.6 16 2.48
Dabob Bay Ambient 309 CTENIDIA HL6-18 170.0 14 1.46
Oyster Bay High 311 CTENIDIA SN6-16 158.0 16 3.76
Oyster Bay High 312 CTENIDIA SN6-17 90.6 15 1.58
Oyster Bay High 313 CTENIDIA SN6-18 72.4 15 1.81
Oyster Bay High 314 CTENIDIA SN6-19 42.2 17 LOW
Oyster Bay High 315 CTENIDIA SN6-20 148.0 15 2.32
Oyster Bay High 316 CTENIDIA SN6-21 146.0 16 3.74
Oyster Bay High 317 CTENIDIA SN6-22 158.0 15 2.14
Oyster Bay High 318 CTENIDIA SN6-23 174.0 16 4.08
Oyster Bay High 319 CTENIDIA SN6-24 77.6 16 0.64
Oyster Bay Ambient 321 CTENIDIA SN6-25 148.0 15 3.64
Oyster Bay Ambient 322 CTENIDIA SN6-26 44.6 16 NOT QUANTIFIED
Oyster Bay Ambient 323 CTENIDIA SN6-27 102.0 15 3.70
Oyster Bay Ambient 324 CTENIDIA SN6-28 172.0 16 0.78
Oyster Bay Ambient 325 CTENIDIA SN6-29 180.0 14 2.92
Oyster Bay Ambient 326 CTENIDIA SN6-30 130.0 15 4.04
Oyster Bay Ambient 327 CTENIDIA SN6-31 85.2 15 1.97
Oyster Bay Ambient 328 CTENIDIA SN6-32 156.0 14 2.12
Oyster Bay Ambient 329 CTENIDIA SN6-33 162.0 15 0.33
Fidalgo Bay High 331 CTENIDIA NF6-16 42.2 16 LOW
Fidalgo Bay High 332 CTENIDIA NF6-17 65.8 17 LOW
Fidalgo Bay High 333 CTENIDIA NF6-18 78.6 15 2.98
Fidalgo Bay High 334 CTENIDIA NF6-19 64.8 17 LOW
Fidalgo Bay High 335 CTENIDIA NF6-20 180.0 15 2.58
Fidalgo Bay High 336 CTENIDIA NF6-21 94.8 20 LOW
Fidalgo Bay High 337 CTENIDIA NF6-22 194.0 15 4.02
Fidalgo Bay High 338 CTENIDIA NF6-23 81.6 16 2.74
Fidalgo Bay High 339 CTENIDIA NF6-24 77.2 16 1.91
Fidalgo Bay Ambient 341 CTENIDIA NF6-25 89.6 14 1.31
Fidalgo Bay Ambient 342 CTENIDIA NF6-26 162.0 15 1.78
Fidalgo Bay Ambient 343 CTENIDIA NF6-27 114.0 14 2.58
Fidalgo Bay Ambient 344 CTENIDIA NF6-28 25.0 15 1.58
Fidalgo Bay Ambient 345 CTENIDIA NF6-29 190.0 14 3.50
Fidalgo Bay Ambient 346 CTENIDIA NF6-30 43.6 14 1.36
Fidalgo Bay Ambient 347 CTENIDIA NF6-31 69.0 15 LOW
Fidalgo Bay Ambient 348 CTENIDIA NF6-32 54.4 16 3.06
Fidalgo Bay Ambient 349 CTENIDIA NF6-33 82.0 15 1.90

Larvae

Spawning Tank Cohort Treatment Homo./RNA TUBE # [RNA] after Turbo Dnase treatment (ng/uL) End Point PCR cycles ds cDNA concentration
HL-10 Ambient Dabob Bay 10 Ambient 401 93.4 16 1.24
HL-10 Ambient Dabob Bay 10 Ambient 402 114.0 16 2.76
HL-10 Ambient Dabob Bay 10 Ambient 403 136.0 14 4.16
HL-10 Ambient Dabob Bay 10 Ambient 404 112.0 15 2.92
HL-10 Low Dabob Bay 10 Low 411 72.6 16 3.08
HL-10 Low Dabob Bay 10 Low 412 31.2 17 LOW
HL-10 Low Dabob Bay 10 Low 413 130.0 15 1.97
HL-10 Low Dabob Bay 10 Low 414 168.0 15 0.86
HL-6 Ambient Dabob Bay 6 Ambient 421 57.6 14 1.63
HL-6 Low Dabob Bay 6 Low 431b 83.0 16 3.36
HL-6 Low Dabob Bay 6 Low 432 74.0 17 LOW
HL-6 Low Dabob Bay 6 Low 434 63.0 15 5.58
NF-10 Ambient A Fidalgo Bay 10 Ambient 441 16.2 15 LOW
NF-10 Ambient A Fidalgo Bay 10 Ambient 442b 69.8 17 LOW
NF-10 Ambient A Fidalgo Bay 10 Ambient 443 60.2 15 1.36
NF-10 Ambient B Fidalgo Bay 10 Ambient 444 70.6 14 4.08
NF-10 Ambient B Fidalgo Bay 10 Ambient 445 160.0 15 4.00
NF-10 Low B Fidalgo Bay 10 Low 451 68.4 14 2.24
NF-10 Low A Fidalgo Bay 10 Low 452b 97.2 16 2.68
NF-10 Low B Fidalgo Bay 10 Low 453 196.0 14 0.97
NF-6 Ambient B Fidalgo Bay 6 Ambient 461b 84.0 14 2.02
NF-6 Ambient A Fidalgo Bay 6 Ambient 462b 106.0 16 0.21
NF-6 Low B Fidalgo Bay 6 Low 471b 108.0 15 5.20
NF-6 Low B Fidalgo Bay 6 Low 472b 97.0 15 2.42
NF-6 Low B Fidalgo Bay 6 Low 473 124.0 14 2.34
NF-6 Low A Fidalgo Bay 6 Low 474 77.2 14 3.02
NF-6 Low A Fidalgo Bay 6 Low 475 27.4 14 2.44
NF-6 Low A Fidalgo Bay 6 Low 476 39.2 14 4.24
NF-6 Low A Fidalgo Bay 6 Low 477 164.0 15 2.28
SN-10 Ambient A Oyster Bay C1 10 Ambient 481 89.2 14 0.88
SN-10 Ambient B Oyster Bay C1 10 Ambient 482 22.2 14 1.42
SN-10 Ambient B Oyster Bay C1 10 Ambient 483 99.0 16 1.22
SN-10 Ambient A Oyster Bay C1 10 Ambient 484 58.4 15 1.67
SN-10 Ambient B Oyster Bay C1 10 Ambient 485 19.1 14 2.90
SN-10 Ambient A Oyster Bay C1 10 Ambient 486b 148.0 16 LOW
SN-10 Ambient B Oyster Bay C1 10 Ambient 487 118.0 16 1.27
SN-10 Ambient A Oyster Bay C1 10 Ambient 488 60.0 14 3.06
SN-10 Ambient A Oyster Bay C1 10 Ambient 489 68.0 15 3.84
SN-10 Ambient B Oyster Bay C1 10 Ambient 490 186.0 14 2.32
SN-10 Ambient B Oyster Bay C1 10 Ambient 491 58.4 15 6.64
SN-10 Ambient B Oyster Bay C1 10 Ambient 492 82.6 15 2.02
SN-10 Low B Oyster Bay C1 10 Low 41 108.0 17 LOW
SN-10 Low B Oyster Bay C1 10 Low 43 156.0 15 2.48
SN-10 Low B Oyster Bay C1 10 Low 46 98.6 18 LOW
SN-10 Low B Oyster Bay C1 10 Low 47 128.0 17 LOW
SN-10 Low A Oyster Bay C1 10 Low 44 41.4 TOO LOW TOO LOW
SN-10 Low B Oyster Bay C1 10 Low 506 29.2 15 1.63
SN-10 Low A Oyster Bay C1 10 Low 45 25.1 20 LOW
SN-6 Ambient B Oyster Bay C1 6 Ambient 35 94.4 20 LOW
SN-6 Ambient B Oyster Bay C1 6 Ambient 513 142.0 15 5.92
SN-6 Ambient B Oyster Bay C1 6 Ambient 39 89.8 15 2.04
SN-6 Ambient B Oyster Bay C1 6 Ambient 37 74.6 20 LOW
SN-6 Ambient A Oyster Bay C1 6 Ambient 34 104.0 18 LOW
SN-6 Low A Oyster Bay C1 6 Low 521 66.6 17 LOW
SN-6 Low A Oyster Bay C1 6 Low 522 32.2 16 2.42
SN-6 Low B Oyster Bay C1 6 Low 523 71.4 16 2.16
SN-6 Low B Oyster Bay C1 6 Low 524 63.0 14 3.24
SN-6 Low B Oyster Bay C1 6 Low 525 140.0 14 2.44
SN-6 Low A Oyster Bay C1 6 Low 526 138.0 14 2.20
SN-6 Low B Oyster Bay C1 6 Low 527 124.0 15 1.42
SN-6 Low B Oyster Bay C1 6 Low 528 87.6 14 4.48
SN-6 low A Oyster Bay C1 6 Low 529 56.8 15 2.86
K-10 Ambient Oyster Bay C2 10 Ambient 531 95.4 15 2.10
K-10 Ambient Oyster Bay C2 10 Ambient 532 93.6 14 2.12
K-10 Ambient Oyster Bay C2 10 Ambient 533 6.5 17 LOW
K-10 Low Oyster Bay C2 10 Low 541 44.4 15 1.40
K-10 Low Oyster Bay C2 10 Low 542 32.8 16 2.22
K-10 Low Oyster Bay C2 10 Low 543 162.0 14 5.24
K-6 Ambient Oyster Bay C2 6 Ambient 551 96.4 14 1.69
K-6 Ambient Oyster Bay C2 6 Ambient 552b 74.6 15 1.84
K-6 Ambient Oyster Bay C2 6 Ambient 553 186.0 14 3.28
K-6 Ambient Oyster Bay C2 6 Ambient 554 188.0 14 2.38
K-6 Low Oyster Bay C2 6 Low 561 28.0 17 LOW
K-6 Low Oyster Bay C2 6 Low 562 126.0 17 LOW
K-6 Low Oyster Bay C2 6 Low 563 47.0 15 0.19
K-6 Low Oyster Bay C2 6 Low 564 152.0 14 2.24
K-6 Low Oyster Bay C2 6 Low 565 31.2 17 LOW
homog. Control RNA Control 571 LOW 18 LOW
homog. Control RNA Control 572 TOO LOW TOO LOW

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