|
| Status |
Public on Feb 16, 2011 |
| Title |
SIL_M0076_1Mb_aCGH |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Test, microdissected cervical squamous intraepithelial lesion
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cervix
histopathological tumour grade: low grade squamous intraepithelial lesion
hpvtype: other
|
| Growth protocol |
SCC cell lines were grown in 10% FCS + 90% GMEM + antibiotics
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was extracted using proteinase K phenol / choloroform method.
|
| Label |
Cy3
|
| 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 |
reference: pooled random donor samples peripheral blood lymphocytes
|
| Growth protocol |
SCC cell lines were grown in 10% FCS + 90% GMEM + antibiotics
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was extracted using proteinase K phenol / choloroform method.
|
| Label |
Cy5
|
| 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 Pennsylvania
|
| 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.
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.
|
| |
|
| 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 |
GPL13176 |
| Series (2) |
| GSE27331 |
Gain of the oncostatin M receptor in cervical squamous cell carcinoma is associated with adverse clinical outcome [penn1Mb data] |
| GSE27333 |
Gain of the oncostatin M receptor in cervical squamous cell carcinoma is associated with adverse clinical outcome |
|
