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Sample GSM675695 Query DataSets for GSM675695
Status Public on Feb 16, 2011
Title SIL_M0016_1Mb_aCGH
Sample type genomic
 
Channel 1
Source name Test, microdissected cervical squamous intraepithelial lesion
Organism Homo sapiens
Characteristics tissue: cervix
histopathological tumour grade: high grade squamous intraepithelial lesion
hpvtype: 16
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
 
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 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 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

Data table header descriptions
ID_REF
VALUE log2 normalized ratio test/ref

Data table
ID_REF VALUE
RP11-71L20 -0.043967062
RP11-501A10 -0.12441039
RP11-330C23 -0.229106151
RP11-424F11 -0.200635485
RP11-309F8 -0.09423941
RP11-524P14 -0.082668303
RP11-500O4 -0.451467148
RP11-509D1 -0.070091762
RP11-354M13 -0.169872691
RP11-454I4 -0.196962075
RP11-541B22 -0.294350516
RP11-385E19 -0.219311955
RP11-363O10 -0.131728339
RP11-433F8 -0.396710918
RP11-558C17 0.043541055
RP11-521J23 0.111458889
RP11-289P9 -0.106924635
RP11-523P24 -0.263381772
RP11-306D6 -0.155436758
RP11-502B15 -0.096782707

Total number of rows: 4632

Table truncated, full table size 108 Kbytes.




Supplementary file Size Download File type/resource
GSM675695_54M0016Cy5.gpr.gz 1.1 Mb (ftp)(http) GPR
Processed data included within Sample table
Processed data are available on Series record

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