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Sample GSM666016 Query DataSets for GSM666016
Status Public on May 03, 2012
Title Esophageal squamous cell carcinoma 27
Sample type RNA
 
Channel 1
Source name Esophageal squamous cell carcinoma, fresh frozen tissue
Organism Homo sapiens
Characteristics tissue: Esophageal squamous cell carcinoma tumor
biomaterial: Fresh frozen tissue
gender: Female
tumor stage: III
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol (Invitrogen) according to the manufacures recommendations. RNA integrity was checked on a Bioanalyzer (Agilent).
Label Cy3
Label protocol Direct labeled by random priming (Promega, Pronto)
 
Channel 2
Source name Human Reference RNA (Stratagene), pool of ten cell lines
Organism Homo sapiens
Characteristics biomaterial: Pool of 10 different cell lines
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol (Invitrogen) according to the manufacures recommendations. RNA integrity was checked on a Bioanalyzer (Agilent).
Label Cy5
Label protocol Direct labeled by random priming (Promega, Pronto)
 
 
Hybridization protocol Hybridizations were performed in 4 x SSC, 0.1% SDS, 0,5 NOTE human 0,8-1,0 µg/µl Cot-1 DNA at 42degC overnight. Arrays were washed three times 4xSSC RT, twice 2xSSC / 0.1% SDS at 42degC, one time 0.2xSSC, and one time 0.1xSSC RT.
Scan protocol Arrays were scanned in Agilent scanner (Agilent Technologies)
Description Esophageal cancer
Data processing Image analysis was performed using Genepix v4.0. Result files were uploaded into BASE where they were filtered and normalized.
Correction of background intensities of Cy3 and Cy5 were calculated by means of a median-feature and median-local background intensities of the uploaded files. The intensity ratios for the individual probes were calculated as intensity of the background-corrected tumor channel (Cy3) divided with the intensity of the background-corrected reference channel (Cy5). Low-quality spots flagged during image analysis, and spots with a signal-to-noise ratio (SNR) of <1.5 and >10% saturation were excluded from further analysis. To compensate for dye bias and local background effects, data were normalized by a lowess algorithm in BASE
 
Submission date Feb 03, 2011
Last update date May 03, 2012
Contact name Anna Isinger Ekstrand
E-mail(s) anna.ekstrand@med.lu.se
Organization name Clinical Sciences
Department Oncology
Street address Barngatan 2b
City Lund
ZIP/Postal code 221 85
Country Sweden
 
Platform ID GPL5886
Series (1)
GSE27040 Dermatan sulfate is involved in the tumorigenic properties of Esophagus Squamous Cell Carcinoma

Data table header descriptions
ID_REF
VALUE normalized log2ratio (ch1/ch2)

Data table
ID_REF VALUE
3738 -0.048168867
11739 0.40625512
14864 -0.480728781
26779 1.360436739
26853 -0.542326776
27409 1.597738681
6798 3.129795386
9951 0.01423125
26501 -0.680908587
6112 1.59953888
13551 0.038354575
5387 -0.215671283
17999
26049
20979 -0.49462188
6233
22361 -0.197653712
9976 0.831866207
7755 0.701977909
14366 -0.561067903

Total number of rows: 18785

Table truncated, full table size 258 Kbytes.




Supplementary file Size Download File type/resource
GSM666016_27_GI.txt.gz 2.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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