|
| Status |
Public on Feb 15, 2011 |
| Title |
Cervical cancer-lymph node positive-38-57 |
| Sample type |
RNA |
| |
|
| Source name |
Early stage cervical cancer
|
| Organism |
Homo sapiens |
| Characteristics |
pelvic lymph nodes: Positive
age at diagnosis: 34.2
figo stage: 1b2
|
| Treatment protocol |
Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.
|
| Label |
Biotin
|
| Label protocol |
For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.
|
| |
|
| Hybridization protocol |
Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.
|
| Scan protocol |
After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.
|
| Description |
Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis
|
| Data processing |
Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.
|
| |
|
| Submission date |
Jan 10, 2011 |
| Last update date |
Feb 15, 2011 |
| Contact name |
Maartje Noordhuis |
| E-mail(s) |
m.noordhuis@og.umcg.nl
|
| Organization name |
University Medical Center Groningen
|
| Department |
Gynecologic Oncology
|
| Street address |
PObox 30.001
|
| City |
Groningen |
| ZIP/Postal code |
9700RB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE26511 |
Involvement of the TGF-β and β-catenin pathways in pelvic lymph node metastasis in early stage cervical cancer |
|
