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| Status |
Public on Mar 05, 2011 |
| Title |
An integrated genomics approach for novel biomarker discovery in squamous cell cervical carcinoma |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by array
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| Summary |
Detection of copy number dependent gene expression profiles in epithelial tumours has lead to the discovery of genes significant in diagnosis, prognosis and of therapeutic value.
We sought to apply the technologies of gene expression profiling and copy number aberration detection by high density oligonucleotide microarray analysis to detect genes with expression profiles regulated by copy number. We surveyed copy number aberrations in 27 squamous cell carcinomas tissues and ten cervical carcinoma cell lines by Agilent 244k aCGH, and in a companion study of 77 tissues we obtained transcriptional profiles of a broader ranger of histologies.
Briefly, for normal (NAD) and squamous intraepithelial lesions (SILs), DNA and RNA were extracted from approximately 5 - 25 x 5 mm thin sections of fresh frozen cervical tissue, respectively. Epithelial were microdissected, pooled and processed as follows. For RNA extraction, tissue was collected in Trizol (Invitrogen, UK) and subject to homogenization (Polytron), total RNA was recovered following standard processes, and quality assessed by BioAnalyzer (Agilent). DNA was recovered following Proteinase K digestion, phenol chloroform extraction, and ethanol precipitation. Contaminating RNA was removed by RNAse A treatment, and a second round of phenol chloroform extraction and ethanol precipitation. For SCCs, RNA and DNA was extracted from whole tumour (>85%), following similar strategies as previously described.
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| Overall design |
This submission describes the copy number aberrations of 27 cervical SCC tissues and 10 common cervical SCC cell lines
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| Contributor(s) |
Karagavriilidou K, Roberts I, Carter S, Ng G, Gooding E, Chattopadhyay A, Pett M, Murray M, Winder D, Muralidhar B, Ward D, Stacey P, Philips M, Scarpini C, Mukherjee G, Coleman N |
| Citation(s) |
17516585 |
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| Submission date |
Mar 03, 2011 |
| Last update date |
Nov 14, 2014 |
| Contact name |
Ian Roberts |
| E-mail(s) |
ian.roberts@cantab.net
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| Phone |
0044 1223 763 279
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| Organization name |
Hutchison MRC Research Centre
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| Department |
Cancer Cell Unit
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| Lab |
Coleman
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| Street address |
Hills Road
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| City |
Cambridge |
| ZIP/Postal code |
CB2 0XZ |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL9128 |
Agilent-014693 Human Genome CGH Microarray 244A (Probe name version) |
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| Samples (37)
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| This SubSeries is part of SuperSeries: |
| GSE27333 |
Gain of the oncostatin M receptor in cervical squamous cell carcinoma is associated with adverse clinical outcome |
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| Relations |
| BioProject |
PRJNA141879 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE27673_RAW.tar |
1.2 Gb |
(http)(custom) |
TAR (of GPR) |
| GSE27673_full_matrix.txt.gz |
44.1 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
| Processed data are available on Series record |
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