|
| Status |
Public on Feb 16, 2011 |
| Title |
SCC_G16_1Mb_aCGH |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Test, cervical carcinoma tissue, minimum 95% tumour
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cervix
histopathological diagnosis: squamous cell carcinoma
histopathological tumour grade: grade III / late stage
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Following mechanical disaggregation, gDNA was extracted using proteinase K phenol / choloroform method.
|
| Label |
Cy3, Cy5
|
| Label protocol |
gDNA was labelled using Invitrogen Bioprime aCGH labelling kit, according to manufactures protocols
|
| |
|
| Channel 2 |
| Source name |
Ref, peripheral blood lymphocytes
|
| Organism |
Homo sapiens |
| Characteristics |
pbl: pooled random donor samples
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Following mechanical disaggregation, gDNA was extracted using proteinase K phenol / choloroform method.
|
| Label |
Cy5, Cy3
|
| Label protocol |
gDNA was labelled using Invitrogen Bioprime aCGH labelling kit, according to manufactures protocols
|
| |
|
| |
| Hybridization protocol |
aCGH probes were hybridised to template slides according to Centre for Microarray Resources (Cambridge University, Pathology Department) methods
|
| Scan protocol |
Stringency washed array slides were scanned using an Axon 4100B microarray scanner
|
| Description |
Dye swapped hybridisations. Filename suffix (e.g. Cy3 or Cy5) indicates Test gDNA dye. Ratios are always Test / Ref. Average Log 2 ratios were computed by inverting dye swapped values.
|
| Data processing |
R using snapCGH bioconductor package
Mean pixel values are background subtracted, median normalized, with replicate spots averaged. Dye swapped experiments were inverted prior to combining, and averaging.
|
| |
|
| Submission date |
Feb 15, 2011 |
| Last update date |
Feb 16, 2011 |
| Contact name |
Ian Roberts |
| E-mail(s) |
ian.roberts@cantab.net
|
| Phone |
0044 1223 763 279
|
| Organization name |
Hutchison MRC Research Centre
|
| Department |
Cancer Cell Unit
|
| Lab |
Coleman
|
| Street address |
Hills Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0XZ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13177 |
| Series (2) |
| GSE27332 |
Gain of the oncostatin M receptor in cervical squamous cell carcinoma is associated with adverse clinical outcome [camb1Mb data] |
| GSE27333 |
Gain of the oncostatin M receptor in cervical squamous cell carcinoma is associated with adverse clinical outcome |
|
