|
| Status |
Public on Jul 19, 2011 |
| Title |
Cervical tumor biopsy, P-130 |
| Sample type |
RNA |
| |
|
| Source name |
Cervical tumor, 3B
|
| Organism |
Homo sapiens |
| Characteristics |
histology: Squamous cell carcinoma
gene-based hypoxia: More hypoxic
imaging-based hypoxia: More hypoxic
combined hypoxia biomarker: More hypoxic
cohort (gse36562 study): DCE-MRI cohort
hypoxia score: High
tissue: cervical tumor
figo stage: 3B
cohort: basic cohort
lymph node status (gse38433 study): 1
cohort (gse38964 study): Integrative cohort
3p status: Loss
|
| Treatment protocol |
The samples were immediately snap-frozen in liquid nitrogen and stored at -80oC until used for analysis. Biopsies with more than 50% tumor cells in HE stained sections from the central part of the specimen were used further.
|
| Growth protocol |
1-4 tumor samples were collected from each patient at the time of diagnosis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent, followed by double precipitation with isopropanol and final precipitation with 5M lithium chloride. RNA from different biopsies of the same tumor was pooled. Quality control was performed with the Agilent Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Illumina protocol.
|
| |
|
| Hybridization protocol |
The samples were hybridized to the arrays at 58oC overnight, using the standard Illumina hybridization protocol.
|
| Scan protocol |
Scanning was performed with an Illumina BeadArray reader, using the standard Illumina scanning protocol.
|
| Description |
Basic cohort
P-130
|
| Data processing |
The data were normalized using quantile normalization in J-Express.
|
| |
|
| Submission date |
Feb 23, 2011 |
| Last update date |
Jun 24, 2020 |
| Contact name |
Heidi Lyng |
| E-mail(s) |
heidi.lyng@rr-research.no
|
| Phone |
4722781478
|
| Organization name |
Oslo University Hospital
|
| Department |
Department of Radiation Biology
|
| Street address |
Montebello
|
| City |
Oslo |
| ZIP/Postal code |
0310 |
| Country |
Norway |
| |
|
| Platform ID |
GPL6884 |
| Series (7)
|
| GSE27469 |
Drivers of gene expression in cervical cancer |
| GSE29817 |
Membranous Expression of Ectodomain Isoforms of the Epidermal Growth Factor Receptor (EGFR) Predicts Outcome after Chemoradiotherapy of Lymph Node Negative Cervical Cancer |
| GSE36562 |
Hypoxia-induced gene expression in chemoradioresistant cervical cancer revealed by dynamic contrast enhanced MRI |
| GSE38964 |
Identification of eight candidate target genes of the prognsotic 3p loss in cervical cancer by integrative genomic profiling |
| GSE72723 |
Integrative analysis of DCE-MRI and gene expression profiles in construction of a gene classifier for assessment of hypoxia-related risk of chemoradiotherapy failure in cervical cancer |
| GSE75034 |
Selection of reference genes for gene expression studies related to hypoxia in cervical cancer |
| GSE146114 |
Combining imaging- and gene-based hypoxia biomarkers in cervical cancer improves prediction of treatment failure independent of intratumor heterogeneity |
|
| Relations |
| Affiliated with |
GSE68339 |
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