|
| Status |
Public on Jun 01, 2016 |
| Title |
genomic RNA from tumor tissue of OT3 |
| Sample type |
RNA |
| |
|
| Source name |
OT3_T
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: OT3
disease: Oral tongue squamous cell carcinomas (OTSCC)
tissue type: tumor tissue
patient age (yrs): 45
patient gender: M
tumor stage: T3N2cM0
tumor grade: MDSCC
tumor nodal status: N2c
patient survival status: Alive
patient overall survival (months): 31.2666666666667
patient disease-free survival (months): 30.8333333333333
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using PureLink RNA mini kit (Invitrogen) and RNA quality was checked on the bioanalyzer using RNA Nano6000 chip (Agilent). RNA samples with poor RIN numbers (≤7) on the bioanalyzer chip, indicating partial degradation of RNA were processed using Illumina WGDASL assay and the ones with good RIN numbers (>7) were biotin-labelled using Illumina TotalPrep RNA Amplification kit (Ambion) as per the manufacturer’s recommendations.
|
| Label |
biotin
|
| Label protocol |
Standard Illumina hybridization protocol
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
HiScan, Illumina
|
| Data processing |
Analyzed with GenomeStudio V2011.1 Gene Expression module 1.9.0 (Illumina). Transformed and normalized using VST and LOESS methods, provided within R Bioconductor package, lumi. Batch correction was performed using ComBat
|
| |
|
| Submission date |
Dec 01, 2015 |
| Last update date |
Jun 01, 2016 |
| Contact name |
binay panda |
| E-mail(s) |
binay@ganitlabs.in
|
| Organization name |
ganit labs foundation
|
| Street address |
1649A vasant kunj
|
| City |
new delhi |
| ZIP/Postal code |
110070 |
| Country |
India |
| |
|
| Platform ID |
GPL10904 |
| Series (2) |
| GSE75539 |
A minimal DNA 5-methylcytosine signature of oral tongue squamous cell carcinoma [HumanHT-12 V4.0] |
| GSE75540 |
A minimal DNA 5-methylcytosine signature of oral tongue squamous cell carcinoma |
|
