|
| Status |
Public on May 03, 2012 |
| Title |
Esophageal squamous cell carcinoma 123 |
| 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: Male
tumor stage: IV
|
| 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 |
|
