|
| Status |
Public on Mar 05, 2011 |
| Title |
SCC_71_05_aCGH |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Squamous cell carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Uterine cervix
histology: High grade, late stage
ID: 71_05
|
| Growth protocol |
Cell lines were cultured in 10% FCS + 90% GMEM + antibiotics, according to standard maintenance procedures
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was extracted by mechanical disaggregation, followed by 2 hr incubtaion in 1 mg / ml proteinase K at 55oC. gDNA recovery involved phenol chloroform extraction, ethanol precipitation and RNAse A digestion. gDNA was quality chked and quantified by Nanodrop spectophotometric assessment and Invitrogen picogreen measurement
|
| Label |
Alexa 532 dUTP
|
| Label protocol |
gDNA was labelled using Invitrogen Bioprime aCGH labelling kit, according manufacturers recommendations
|
| |
|
| Channel 2 |
| Source name |
Peripheral blood lymphocytes
|
| Organism |
Homo sapiens |
| Characteristics |
reference: pooled random donor blood sample
|
| Growth protocol |
Cell lines were cultured in 10% FCS + 90% GMEM + antibiotics, according to standard maintenance procedures
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was extracted by mechanical disaggregation, followed by 2 hr incubtaion in 1 mg / ml proteinase K at 55oC. gDNA recovery involved phenol chloroform extraction, ethanol precipitation and RNAse A digestion. gDNA was quality chked and quantified by Nanodrop spectophotometric assessment and Invitrogen picogreen measurement
|
| Label |
Alex 635 dUTP
|
| Label protocol |
gDNA was labelled using Invitrogen Bioprime aCGH labelling kit, according manufacturers recommendations
|
| |
|
| |
| Hybridization protocol |
Hybridisation and stringency washing was conducted acording to Agilents' own protocols.
|
| Scan protocol |
Arrays were scanned on an Axon 41000 B using GenePix Pro 6.0
|
| Description |
Ref gDNA pool contains 10-15 male samples
|
| Data processing |
Data was processed in R using snapCGH Bioconductor packages and in house scripts.
The aCGH ratio is taken as log 2 {(median Ch1 foreground - median Ch1 background) / (median Ch2 foreground - mediumn Ch2 background)}
|
| |
|
| Submission date |
Mar 03, 2011 |
| Last update date |
Mar 05, 2011 |
| Contact name |
Ian Roberts |
| E-mail(s) |
[email protected]
|
| 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 |
GPL9128 |
| Series (2) |
| GSE27333 |
Gain of the oncostatin M receptor in cervical squamous cell carcinoma is associated with adverse clinical outcome |
| GSE27673 |
An integrated genomics approach for novel biomarker discovery in squamous cell cervical carcinoma |
|
