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Sample GSM651840 Query DataSets for GSM651840
Status Public on Feb 15, 2011
Title Cervical cancer-lymph node negative-10-34
Sample type RNA
 
Source name Early stage cervical cancer
Organism Homo sapiens
Characteristics pelvic lymph nodes: Negative
age at diagnosis: 35.8
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 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) 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

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

Data table
ID_REF VALUE
AFFX-BioB-5_at 8.3873
AFFX-BioB-M_at 8.86946
AFFX-BioB-3_at 8.02777
AFFX-BioC-5_at 9.33629
AFFX-BioC-3_at 9.47427
AFFX-BioDn-5_at 9.59467
AFFX-BioDn-3_at 11.761
AFFX-CreX-5_at 12.5532
AFFX-CreX-3_at 13.0314
AFFX-DapX-5_at 4.12704
AFFX-DapX-M_at 4.01069
AFFX-DapX-3_at 4.42954
AFFX-LysX-5_at 3.55838
AFFX-LysX-M_at 4.88965
AFFX-LysX-3_at 4.92915
AFFX-PheX-5_at 3.85748
AFFX-PheX-M_at 3.86501
AFFX-PheX-3_at 5.89164
AFFX-ThrX-5_at 4.38882
AFFX-ThrX-M_at 3.82772

Total number of rows: 54675

Table truncated, full table size 998 Kbytes.




Supplementary file Size Download File type/resource
GSM651840.CEL.gz 8.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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