Dataset: Study for evaluating the effect of cold ischemic time and RNA stabilization method on RNA integrity and gene expression measurements
Time series of eleven breast cancer samples subjected to different cold ischemic stress of up to 3 hr post tumor excision. A different...
Time series of eleven breast cancer samples subjected to different cold ischemic stress of up to 3 hr post tumor excision. A different 2x2 factorial within this study evaluated the effect of stabilization method (RNAlater vs snap freezing) and stablization delay (0 and 40 min) at room temperature. Tissue samples were collected at surgery, cut into 1-2 mm pieces and divided into 8 portions. Portions were put in RNAlater or fresh frozen at baseline, 20, 40, 60, 120, and 180 minutes thereafter, or snap frozen in dry ice in a pre-chilled sample vial at baseline and 40 minutes thereafter.
- Species:
- human
- Samples:
- 86
- Source:
- E-GEOD-25011
- PubMed:
- 22034635
- Updated:
- Dec.12, 2014
- Registered:
- Jun.18, 2014
Factors:
(via ArrayExpress)
| Sample | RNA_260_280 | RNA_CONCENTRATION_NGPUL | STABILIZATION | TRUE_COLD_ISCHEMIC_TIME_MIN | PASSEDQC | EXTRA_COLD_ISCHEMIC_TIME_MIN | PATIENT ID | RNA_INTEGRITY_NUMBER (AS REPORTED BY THE AGILLENT BIOANALYZER) |
|---|---|---|---|---|---|---|---|---|
| GSM614476 | 2.04 | 254.9 | FlashFrozen | 86 | Y | 40 | MD71 | 7.3 |
| GSM614475 | 2.04 | 376.5 | FlashFrozen | 46 | Y | 0 | MD71 | 7.1 |
| GSM614474 | 2.07 | 689.6 | RNAlater | 226 | Y | 180 | MD71 | 8.5 |
| GSM614473 | 2.05 | 242.1 | RNAlater | 168 | Y | 120 | MD71 | 9.2 |
| GSM614472 | 2.1 | 600.4 | RNAlater | 106 | Y | 60 | MD71 | 8.4 |
| GSM61447 | 2 | 465.3 | RNAlater | 86 | Y | 40 | MD71 | 8.7 |
| GSM614470 | 2 | 451.6 | RNAlater | 66 | Y | 20 | MD71 | 8.9 |
| GSM614469 | 2.03 | 387.9 | RNAlater | 46 | Y | 0 | MD71 | 9.2 |
| GSM614468 | 2.06 | 229 | FlashFrozen | 74 | Y | 40 | MD69 | 7 |
| GSM614467 | 2.09 | 155.5 | FlashFrozen | 34 | Y | 0 | MD69 | 6.8 |
| GSM614466 | 2.08 | 831 | RNAlater | 214 | Y | 180 | MD69 | 8.8 |
| GSM614465 | 2.04 | 342.7 | RNAlater | 154 | Y | 120 | MD69 | 6.9 |
| GSM614464 | 2.01 | 121.8 | RNAlater | 96 | Y | 60 | MD69 | 7.9 |
| GSM614463 | 2.02 | 460.6 | RNAlater | 74 | Y | 40 | MD69 | 8.8 |
| GSM614462 | 2.03 | 420.1 | RNAlater | 54 | Y | 20 | MD69 | 8.6 |
| GSM61446 | 2.07 | 569.1 | RNAlater | 34 | Y | 0 | MD69 | 8.5 |
| GSM614460 | 2.03 | 336.1 | FlashFrozen | 85 | Y | 40 | MD67 | 7.8 |
| GSM614459 | 2.05 | 255.5 | FlashFrozen | 45 | Y | 0 | MD67 | 8.6 |
| GSM614458 | 2.04 | 345.4 | RNAlater | 225 | Y | 180 | MD67 | 8.3 |
| GSM614457 | 2 | 414.8 | RNAlater | 165 | Y | 120 | MD67 | 8.8 |
| GSM614456 | 2.03 | 383.8 | RNAlater | 105 | Y | 60 | MD67 | 8 |
| GSM614455 | 2.01 | 456.4 | RNAlater | 85 | Y | 40 | MD67 | 8.3 |
| GSM614454 | 2.05 | 765.7 | RNAlater | 65 | Y | 20 | MD67 | 7.9 |
| GSM614453 | 2.06 | 728 | RNAlater | 45 | Y | 0 | MD67 | 8.5 |
| GSM614452 | 2.1 | 39.7 | FlashFrozen | 88 | N | 40 | MD66 | 4.9 |
| GSM61445 | 2.02 | 29 | FlashFrozen | 45 | N | 0 | MD66 | 4.7 |
| GSM614450 | 2.05 | 211.5 | RNAlater | 225 | Y | 180 | MD66 | 7.3 |
| GSM614449 | 2.07 | 267.5 | RNAlater | 165 | Y | 120 | MD66 | 6.6 |
| GSM614448 | 2.06 | 154 | RNAlater | 105 | Y | 60 | MD66 | 6.7 |
| GSM614447 | 2.1 | 153.5 | RNAlater | 88 | Y | 40 | MD66 | 6.1 |
| GSM614446 | 2.04 | 354.7 | RNAlater | 66 | Y | 20 | MD66 | 6.4 |
| GSM614445 | 2.04 | 308.8 | RNAlater | 45 | Y | 0 | MD66 | 6.3 |
| GSM614444 | 1.98 | 211.1 | FlashFrozen | 77 | Y | 40 | MD52 | 9.1 |
| GSM614443 | 2.02 | 125 | FlashFrozen | 37 | Y | 0 | MD52 | 8.7 |
| GSM614442 | 1.97 | 144.9 | RNAlater | 217 | Y | 180 | MD52 | 9 |
| GSM61444 | 1.85 | 140.6 | RNAlater | 157 | Y | 120 | MD52 | 5.4 |
| GSM614440 | 1.98 | 108.2 | RNAlater | 97 | Y | 60 | MD52 | 6.1 |
| GSM614439 | 1.92 | 128.6 | RNAlater | 77 | Y | 40 | MD52 | 7.7 |
| GSM614438 | 1.94 | 321.2 | RNAlater | 57 | Y | 20 | MD52 | 4.3 |
| GSM614437 | 2.02 | 268.1 | RNAlater | 37 | Y | 0 | MD52 | 8.6 |
| GSM614436 | 2.03 | 310.9 | FlashFrozen | 75 | Y | 40 | MD50 | 8.2 |
| GSM614435 | 2.03 | 357.2 | FlashFrozen | 35 | Y | 0 | MD50 | 7.9 |
| GSM614434 | 2.11 | 587 | RNAlater | 215 | Y | 180 | MD50 | 8.4 |
| GSM614433 | 2.1 | 646.5 | RNAlater | 155 | Y | 120 | MD50 | 8.7 |
| GSM614432 | 2.03 | 247.9 | RNAlater | 95 | Y | 60 | MD50 | 8.4 |
| GSM61443 | 2.02 | 392.9 | RNAlater | 75 | Y | 40 | MD50 | 8.8 |
| GSM614430 | 1.99 | 462.4 | RNAlater | 55 | Y | 20 | MD50 | 8.6 |
| GSM614429 | 2.02 | 319.3 | RNAlater | 35 | Y | 0 | MD50 | 8.6 |
| GSM614428 | 2.05 | 128.7 | FlashFrozen | 63 | Y | 40 | MD49 | 7 |
| GSM614427 | 2.07 | 129.2 | FlashFrozen | 23 | Y | 0 | MD49 | 6.9 |
| GSM614426 | 2.03 | 354.3 | RNAlater | 203 | Y | 180 | MD49 | 6.7 |
| GSM614425 | 2.03 | 367.6 | RNAlater | 143 | Y | 120 | MD49 | 6.9 |
| GSM614424 | 2.02 | 399.1 | RNAlater | 83 | Y | 60 | MD49 | 7.2 |
| GSM614423 | 2.01 | 465 | RNAlater | 63 | Y | 40 | MD49 | 7.1 |
| GSM614422 | 2.02 | 401.1 | RNAlater | 43 | Y | 20 | MD49 | 6.9 |
| GSM61442 | 2.08 | 544.8 | RNAlater | 23 | Y | 0 | MD49 | 7.1 |
| GSM614420 | 2.02 | 687 | RNAlater | 215 | Y | 180 | MD40 | 8 |
| GSM614419 | 2 | 361.6 | RNAlater | 155 | Y | 120 | MD40 | 7.4 |
| GSM614418 | 2.07 | 676.5 | RNAlater | 95 | Y | 60 | MD40 | 8.7 |
| GSM614417 | 1.99 | 428.8 | RNAlater | 75 | Y | 40 | MD40 | 8.5 |
| GSM614416 | 2.04 | 611.4 | RNAlater | 55 | Y | 20 | MD40 | 8.6 |
| GSM614415 | 2.06 | 704.7 | RNAlater | 35 | Y | 0 | MD40 | 8.6 |
| GSM614414 | 2.15 | 101.5 | FlashFrozen | 84 | Y | 40 | MD64 | 6.4 |
| GSM614413 | 2.12 | 112.6 | FlashFrozen | 44 | Y | 0 | MD64 | 6.7 |
| GSM614412 | 2.07 | 807.5 | RNAlater | 224 | Y | 180 | MD64 | 7.1 |
| GSM6144 | 2.04 | 361.7 | RNAlater | 164 | Y | 120 | MD64 | 7 |
| GSM614410 | 2.08 | 552.4 | RNAlater | 104 | Y | 60 | MD64 | 8.7 |
| GSM614409 | 2.09 | 560.6 | RNAlater | 84 | Y | 40 | MD64 | 7.9 |
| GSM614408 | 2.06 | 785.2 | RNAlater | 64 | Y | 20 | MD64 | 7.8 |
| GSM614407 | 2.04 | 414.1 | RNAlater | 44 | Y | 0 | MD64 | 8.3 |
| GSM614406 | 2.09 | 201.9 | FlashFrozen | 67 | Y | 40 | MD57 | 3.3 |
| GSM614405 | 2.08 | 174.1 | FlashFrozen | 27 | Y | 0 | MD57 | 5.5 |
| GSM614404 | 2.09 | 826.2 | RNAlater | 207 | Y | 180 | MD57 | 6.8 |
| GSM614403 | 2.02 | 425.4 | RNAlater | 147 | Y | 120 | MD57 | 6.5 |
| GSM614402 | 2.02 | 463.4 | RNAlater | 87 | Y | 60 | MD57 | 6.5 |
| GSM61440 | 2.08 | 567.1 | RNAlater | 67 | Y | 40 | MD57 | 7.2 |
| GSM614400 | 2.09 | 796.5 | RNAlater | 47 | Y | 20 | MD57 | 6.9 |
| GSM614399 | 2.07 | 907.3 | RNAlater | 27 | Y | 0 | MD57 | 7.1 |
| GSM614398 | 2.05 | 364.6 | FlashFrozen | 75 | N | 40 | MD53 | 5 |
| GSM614397 | 2.03 | 360.8 | FlashFrozen | 35 | Y | 0 | MD53 | 5 |
| GSM614396 | 2.08 | 740.8 | RNAlater | 215 | Y | 180 | MD53 | 6.4 |
| GSM614395 | 1.98 | 333.3 | RNAlater | 155 | N | 120 | MD53 | 6.5 |
| GSM614394 | 1.99 | 436.3 | RNAlater | 95 | Y | 60 | MD53 | 6.7 |
| GSM614393 | 2.08 | 952.5 | RNAlater | 75 | Y | 40 | MD53 | 6.6 |
| GSM614392 | 2.08 | 915.2 | RNAlater | 55 | Y | 20 | MD53 | 7 |
| GSM61439 | 2.07 | 650.6 | RNAlater | 35 | Y | 0 | MD53 | 7.7 |