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Sample GSM1958830 Query DataSets for GSM1958830
Status Public on Jun 01, 2016
Title total RNA from adjacent normal tissue of OT8 [WG-DASL]
Sample type RNA
 
Source name OT8_N
Organism Homo sapiens
Characteristics patient id: OT8
disease: Oral tongue squamous cell carcinomas (OTSCC)
tissue type: adjacent normal tissue
patient age: 37
patient gender: M
patient survival status: Dead
patient overall survival (months): 1.1
patient disease-free survival (months): 0.0666666666666667
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 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 GPL18281
Series (2)
GSE75538 A minimal DNA 5-methylcytosine signature of oral tongue squamous cell carcinoma [HumanHT-12 WG-DASL V4.0]
GSE75540 A minimal DNA 5-methylcytosine signature of oral tongue squamous cell carcinoma

Data table header descriptions
ID_REF
VALUE transformed, normalized and batch-corrected
Detection Pval

Data table
ID_REF VALUE Detection Pval
7A5 8.50 0.00
A1BG 6.78 0.01
A1CF 6.13 0.96
A26C3 6.56 0.84
A2BP1 7.26 0.01
A2LD1 7.50 0.00
A2M 12.52 0.00
A2ML1 11.58 0.00
A3GALT2 6.33 0.18
A4GALT 10.86 0.00
A4GNT 6.14 0.04
AAA1 6.23 0.38
AAAS 7.71 0.00
AACS 8.95 0.00
AADAC 6.79 0.00
AADACL1 8.94 0.00
AADACL2 6.58 0.00
AADACL4 6.24 0.14
AADAT 7.95 0.00
AAGAB 10.83 0.00

Total number of rows: 20818

Table truncated, full table size 345 Kbytes.




Supplementary data files not provided
Processed data are available on Series record

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