|
| Status |
Public on Mar 08, 2011 |
| Title |
NORM_03_normal |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
normal
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: lung
disease status: normal control
|
| Treatment protocol |
Four sample cores, each 0.6mm in diameter, from viable tumor areas from each tumor and normal specimen were taken and pooled prior to RNA isolation in order to obtain a representative sample of each patient
|
| Growth protocol |
twenty formalin-fixed and paraffin-embedded (FFPE) tumor tissue samples were obtained from patients diagnosed with stage I-IIIA at the University Hospital of Northern Norway (UNN) and Nordland Central Hospital (NLCH)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from the collected core samples by using the Recover All™ Total Nucleic Acid Isolation Kit for FFPE Tissues (Ambion, Austin, TX), according to the manufacturer’s instructions, with some minor adjustments. Xylene treatment was increased from 3 min to 8 min, and protease treatment was increased from 3 hrs to approximately 20 hrs. RNA quality and quantity was assessed by using the NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE) and further verified by an Agilent 2100 Bioanalyzer profil
|
| Label |
Cy3
|
| Label protocol |
Total RNA (700ng) from sample and reference was labelled with Hy3TM and Hy5TM fluorescent label using the miRCURYTm LNA Array power labelling kit (Exiqon, Vedbaek, Denmark)
|
| |
|
| Channel 2 |
| Source name |
common ref pool (samples s1 to s30)
|
| Organism |
Homo sapiens |
| Characteristics |
reference: common ref pool (samples s1 to s30)
|
| Treatment protocol |
Four sample cores, each 0.6mm in diameter, from viable tumor areas from each tumor and normal specimen were taken and pooled prior to RNA isolation in order to obtain a representative sample of each patient
|
| Growth protocol |
twenty formalin-fixed and paraffin-embedded (FFPE) tumor tissue samples were obtained from patients diagnosed with stage I-IIIA at the University Hospital of Northern Norway (UNN) and Nordland Central Hospital (NLCH)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from the collected core samples by using the Recover All™ Total Nucleic Acid Isolation Kit for FFPE Tissues (Ambion, Austin, TX), according to the manufacturer’s instructions, with some minor adjustments. Xylene treatment was increased from 3 min to 8 min, and protease treatment was increased from 3 hrs to approximately 20 hrs. RNA quality and quantity was assessed by using the NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE) and further verified by an Agilent 2100 Bioanalyzer profil
|
| Label |
Cy5
|
| Label protocol |
Total RNA (700ng) from sample and reference was labelled with Hy3TM and Hy5TM fluorescent label using the miRCURYTm LNA Array power labelling kit (Exiqon, Vedbaek, Denmark)
|
| |
|
| |
| Hybridization protocol |
The hybridization was performed according to the miRCURYTM LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria)
|
| Scan protocol |
The miCURYTM LNA Array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent technologies Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery Inc., USA).
|
| Description |
Hy3TM-labeled samples and a Hy5TM-labelled reference RNA sample
|
| Data processing |
The quantified signals were background corrected with offset value 10 and normalized using the global Lowess (Locally Weighted Scatterplot Smoothing) regression algorithm. Many rows were deleted because they did were not present in 80% of all the total samples. That is if over 20% of a row was flagged as non viable by the scanner the data row was removed. Criteria included signal/noise greater than 2.5, and well formed circular spot.
|
| |
|
| Submission date |
Mar 07, 2011 |
| Last update date |
Mar 08, 2011 |
| Contact name |
Chris Fenton |
| E-mail(s) |
[email protected]
|
| Phone |
776 481 96479
|
| Organization name |
UITO
|
| Department |
Microarray
|
| Lab |
Microarray
|
| Street address |
Thor Knutsen vg 6
|
| City |
Tromsø |
| ZIP/Postal code |
9007 |
| Country |
Norway |
| |
|
| Platform ID |
GPL11432 |
| Series (1) |
| GSE27705 |
Signature of MicroRNAs with Impact on Angiogenesis in Non-Small Cell Lung Cancer |
|
