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| Status |
Public on Jan 08, 2016 |
| Title |
Transcriptome Sequencing (RNAseq) enables utilization of Formalin-Fixed, Paraffin-Embedded Biopsies with Clear Cell Renal Cell Carcinoma for Exploration of Disease Biology and Biomarker Development |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Formalin-fixed, paraffin-embedded (FFPE) tissues are an underused resource for molecular analyses. This proof of concept study aimed to compare RNAseq results from FFPE biopsies with the corresponding RNAlater® (Qiagen, Germany) stored samples from clear cell renal cell carcinoma (ccRCC) patients, to enable the decision of whether or not it is feasible to apply RNAseq technology to archival tissue. Core biopsies were obtained with a 16g needle from 16 patients undergoing partial or full nephrectomy. The RNA sequencing libraries were generated applying the new Illumina TruSeq® Access library preparation protocol.
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| Overall design |
*** Access to raw data can be requested from submitters ***
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| Contributor(s) |
Eikrem O, Beisland C, Hjelle KM, Flatberg A, Scherer A, Landolt L, Skogstrand T, Leh SM, Beisvag V, Marti H |
| Citation(s) |
26901863 |
| |
| Submission date |
Dec 21, 2015 |
| Last update date |
Mar 27, 2019 |
| Contact name |
Philipp Strauss |
| E-mail(s) |
Philipp.Strauss@uib.no
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| Organization name |
University of Bergen
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| Street address |
Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst
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| City |
Bergen |
| ZIP/Postal code |
5020 |
| Country |
Norway |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (64)
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| GSM1976481 |
non-cancerous, FFPE, Patient 9, renal biopsy |
| GSM1976482 |
cancerous, FFPE, Patient 9, renal biopsy |
| GSM1976483 |
non-cancerous, RNAlater, Patient 9, renal biopsy |
| GSM1976484 |
cancerous, RNAlater, Patient 9, renal biopsy |
| GSM1976485 |
non-cancerous, FFPE, Patient 10, renal biopsy |
| GSM1976486 |
cancerous, FFPE, Patient 10, renal biopsy |
| GSM1976487 |
non-cancerous, RNAlater, Patient 10, renal biopsy |
| GSM1976488 |
cancerous, RNAlater, Patient 10, renal biopsy |
| GSM1976489 |
non-cancerous, FFPE, Patient 11, renal biopsy |
| GSM1976490 |
cancerous, FFPE, Patient 11, renal biopsy |
| GSM1976491 |
non-cancerous, RNAlater, Patient 11, renal biopsy |
| GSM1976492 |
cancerous, RNAlater, Patient 11, renal biopsy |
| GSM1976493 |
non-cancerous, FFPE, Patient 13, renal biopsy |
| GSM1976494 |
cancerous, FFPE, Patient 13, renal biopsy |
| GSM1976495 |
non-cancerous, RNAlater, Patient 13, renal biopsy |
| GSM1976496 |
cancerous, RNAlater, Patient 13, renal biopsy |
| GSM1976497 |
non-cancerous, FFPE, Patient 15, renal biopsy |
| GSM1976498 |
cancerous, FFPE, Patient 15, renal biopsy |
| GSM1976499 |
non-cancerous, RNAlater, Patient 15, renal biopsy |
| GSM1976500 |
cancerous, RNAlater, Patient 15, renal biopsy |
| GSM1976501 |
non-cancerous, FFPE, Patient 16, renal biopsy |
| GSM1976502 |
cancerous, FFPE, Patient 16, renal biopsy |
| GSM1976503 |
non-cancerous, RNAlater, Patient 16, renal biopsy |
| GSM1976504 |
cancerous, RNAlater, Patient 16, renal biopsy |
| GSM1976505 |
non-cancerous, FFPE, Patient 18, renal biopsy |
| GSM1976506 |
cancerous, FFPE, Patient 18, renal biopsy |
| GSM1976507 |
non-cancerous, RNAlater, Patient 18, renal biopsy |
| GSM1976508 |
cancerous, RNAlater, Patient 18, renal biopsy |
| GSM1976509 |
non-cancerous, FFPE, Patient 19, renal biopsy |
| GSM1976510 |
cancerous, FFPE, Patient 19, renal biopsy |
| GSM1976511 |
non-cancerous, RNAlater, Patient 19, renal biopsy |
| GSM1976512 |
cancerous, RNAlater, Patient 19, renal biopsy |
| GSM1976513 |
non-cancerous, FFPE, Patient 21, renal biopsy |
| GSM1976514 |
cancerous, FFPE, Patient 21, renal biopsy |
| GSM1976515 |
non-cancerous, RNAlater, Patient 21, renal biopsy |
| GSM1976516 |
cancerous, RNAlater, Patient 21, renal biopsy |
| GSM1976517 |
non-cancerous, FFPE, Patient 22, renal biopsy |
| GSM1976518 |
cancerous, FFPE, Patient 22, renal biopsy |
| GSM1976519 |
non-cancerous, RNAlater, Patient 22, renal biopsy |
| GSM1976520 |
cancerous, RNAlater, Patient 22, renal biopsy |
| GSM1976521 |
non-cancerous, FFPE, Patient 24, renal biopsy |
| GSM1976522 |
cancerous, FFPE, Patient 24, renal biopsy |
| GSM1976523 |
non-cancerous, RNAlater, Patient 24, renal biopsy |
| GSM1976524 |
cancerous, RNAlater, Patient 24, renal biopsy |
| GSM1976525 |
non-cancerous, FFPE, Patient 27, renal biopsy |
| GSM1976526 |
cancerous, FFPE, Patient 27, renal biopsy |
| GSM1976527 |
non-cancerous, RNAlater, Patient 27, renal biopsy |
| GSM1976528 |
cancerous, RNAlater, Patient 27, renal biopsy |
| GSM1976529 |
non-cancerous, FFPE, Patient 29, renal biopsy |
| GSM1976530 |
cancerous, FFPE, Patient 29, renal biopsy |
| GSM1976531 |
non-cancerous, RNAlater, Patient 29, renal biopsy |
| GSM1976532 |
cancerous, RNAlater, Patient 29, renal biopsy |
| GSM1976533 |
non-cancerous, FFPE, Patient 31, renal biopsy |
| GSM1976534 |
cancerous, FFPE, Patient 31, renal biopsy |
| GSM1976535 |
non-cancerous, RNAlater, Patient 31, renal biopsy |
| GSM1976536 |
cancerous, RNAlater, Patient 31, renal biopsy |
| GSM1976537 |
non-cancerous, FFPE, Patient 32, renal biopsy |
| GSM1976538 |
cancerous, FFPE, Patient 32, renal biopsy |
| GSM1976539 |
non-cancerous, RNAlater, Patient 32, renal biopsy |
| GSM1976540 |
cancerous, RNAlater, Patient 32, renal biopsy |
| GSM1976541 |
non-cancerous, FFPE, Patient 33, renal biopsy |
| GSM1976542 |
cancerous, FFPE, Patient 33, renal biopsy |
| GSM1976543 |
non-cancerous, RNAlater, Patient 33, renal biopsy |
| GSM1976544 |
cancerous, RNAlater, Patient 33, renal biopsy |
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| Relations |
| BioProject |
PRJNA306624 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE76207_Eikrem_et_al_count_matrix.txt.gz |
2.1 Mb |
(ftp)(http) |
TXT |
| GSE76207_Eikrem_et_al_logcpm_matrix_filtered.txt.gz |
3.3 Mb |
(ftp)(http) |
TXT |
| Processed data are available on Series record |
| Raw data not provided for this record |
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