|
| Status |
Public on Oct 01, 2006 |
| Title |
Cervical Cancer Patient 16, Biopsy 2 |
| Sample type |
RNA |
| |
|
| Source name |
Cervical Cancer Patient 16
|
| Organism |
Homo sapiens |
| Characteristics |
FIGO: 3B
Histology: SCC
Grade: WD
hp5: 25
HGB: 112
ifp: 13.325
age: 60.9
tumsizeMR: 10.5
ResponseToTherapy: NR
|
| Treatment protocol |
Flash-frozen punch biopsies were obtained from patients with cervical cancer who were undergoing examination under general anesthesia as part of their pretreatment evaluation for cervical cancer.
|
| Growth protocol |
Immediately upon removal from the patient, the specimens were bisected; one-half was placed in a storage medium (optimal cutting temperature compound) for conventional histopathologic examination, then immediately flash-frozen in liquid nitrogen. The other half of each sample was flash-frozen without any storage medium. The specimens were subsequently evaluated by a pathologist (J. Schwock) based on the morphology of the frozen H&E-stained tissue sections cut from the optimal cutting temperature–embedded material.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the Absolutely RNA Microprep Kit (Stratagene, La Jolla, CA). Briefly, tumor tissue was lysed in guanidine thiocyanate, mixed with ethanol, and RNA was captured on a silica-based fiber matrix within a microspin cup. RNA was then washed with saline buffers, DNA contamination was removed with DNase, and RNA was then eluted in RNase-free water. The quality of the purified RNA was assessed by analyzing 200 pg of each sample using a Bioanalyzer 2100 (Agilent, Palo Alto, CA). Only samples with a 28S/18S ribosomal peak ratio of 1.8 to 2.0 were considered suitable for labeling.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
A total of 1.5 ug of purified total RNA template was reverse transcribed to generate double-stranded cDNA. Following second strand cDNA synthesis, biotin-labeled antisense cRNA was generated by in vitro transcription. Next, 15 ug of each generated cRNA preparation was fragmented and hybridized to an oligonucleotide array.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
Gene expression data from cervical cancer patients
|
| Data processing |
The data were processed using GC-RMA as implemented in the gcrma package (v1.1.3) of BioConductor using default settings
|
| |
|
| Submission date |
Sep 07, 2006 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Paul C Boutros |
| E-mail(s) |
[email protected]
|
| Organization name |
Ontario Institute for Cancer Research
|
| Street address |
101 College Street, Suite 800
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 0A3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE5787 |
Survey of Intra- and Inter-Tumour Heterogeneity of Gene Expression in Cervical Cancer |
|
| Relations |
| Reanalyzed by |
GSE64985 |
| Reanalyzed by |
GSE119087 |
