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Sample GSM651838 Query DataSets for GSM651838
Status Public on Feb 15, 2011
Title Cervical cancer-lymph node negative-08-32
Sample type RNA
 
Source name Early stage cervical cancer
Organism Homo sapiens
Characteristics pelvic lymph nodes: Negative
age at diagnosis: 47.4
figo stage: 1b1
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 no 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) [email protected]
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

Data table header descriptions
ID_REF
VALUE Gene expressions were normalized and log-transformed

Data table
ID_REF VALUE
AFFX-BioB-5_at 8.86729
AFFX-BioB-M_at 9.47577
AFFX-BioB-3_at 8.60689
AFFX-BioC-5_at 9.88421
AFFX-BioC-3_at 9.97798
AFFX-BioDn-5_at 10.1567
AFFX-BioDn-3_at 12.0766
AFFX-CreX-5_at 12.9554
AFFX-CreX-3_at 13.4614
AFFX-DapX-5_at 4.10262
AFFX-DapX-M_at 3.75225
AFFX-DapX-3_at 4.13778
AFFX-LysX-5_at 3.53994
AFFX-LysX-M_at 4.61561
AFFX-LysX-3_at 4.98052
AFFX-PheX-5_at 3.86831
AFFX-PheX-M_at 3.82493
AFFX-PheX-3_at 5.97148
AFFX-ThrX-5_at 4.49904
AFFX-ThrX-M_at 3.79597

Total number of rows: 54675

Table truncated, full table size 998 Kbytes.




Supplementary file Size Download File type/resource
GSM651838.CEL.gz 8.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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