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Sample GSM1936727 Query DataSets for GSM1936727
Status Public on Apr 13, 2016
Title HCS_6 (SCC control) [lncRNA]
Sample type RNA
 
Source name skin
Organism Homo sapiens
Characteristics gender: Male
tissue: non-lesional skin (control)
Treatment protocol Punch biopsies (4 mm) were obtained under local anaesthesia and immediately put in RNAlater (Qiagen, Hilden, Germany) and stored at - 80 °C until RNA extraction.
Growth protocol A total of three patients with cSCC were biopsied. A total of three control (non-lesional skin) were biopsied.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with TRIzol (Life Technologies, Carlsbad, USA) following the manufacturers protocol. RNA quantity and quality was determined with NanoDrop ND-1000 and RNA integrity with standard denaturing agarose gel electrophoresis. To purify mRNA from total RNA, rRNA was removed with mRNA-ONLY™ Eukaryotic mRNA Isolation Kit (Epicentre, Omaha, USA).
Label CY3
Label protocol The samples were amplified with a mixture of oligo (dT) and random priming method (Arraystar Flash RNA Labeling Kit, Arraystar) and transcribed in fluorescent cRNA which was purified by RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers protocol. Concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) was measured with NanoDrop ND-1000. Next, to 1 μg of each labeled cRNA, 5 μl 10 × Blocking Agent (Agilent Technology, Santa Clara, USA) and 1 μl of 25 × Fragmentation Buffer was added (Agilent Technology, Santa Clara, USA). The mixture was heated at 60 °C for 30 min and 25 μl 2 × GE Hybridization buffer (Agilent Technology, Santa Clara, USA) was added to dilute the labeled cRNA.
 
Hybridization protocol For hybridization 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarrays which were incubated in an Agilent hybridization oven (Agilent Technology, Santa Clara, USA) for 17 hours at 65°C.
Scan protocol Finally, arrays were washed, fixed and scanned with Agilent DNA Microarray Scanner G2505C (Agilent Technologies, Santa Clara, USA).
Description We identified 1516 significantly up- and 2586 down-regulated lncRNAs (FC ≥2 and p<0.05) in cSCC compared to skin (control)
Data processing Quantile normalization which was applied to raw data and further data processing was performed with GeneSpring GX v12.0 software package (Agilent Technologies, Santa Clara, USA). Only lncRNAs and mRNAs that at least in 3 out of 6 samples have flags in Marginal or Present (“All Targets Value”) were chosen for further data analysis. Hierarchical clustering was performed with R software (version 2.15, http://www.r-project.org/) in order to arrange samples into groups based on their expression levels.
 
Submission date Nov 10, 2015
Last update date Apr 13, 2016
Contact name Michael Sand
Organization name Ruhr-University Bochum
Department Depatment of Dermatology, Venereology and Allergology
Street address Gudrunstr. 56
City Bochum
State/province NRW
ZIP/Postal code 44791
Country Germany
 
Platform ID GPL16956
Series (1)
GSE74859 Long non-coding RNAs in cutaneous squamous cell carcinoma

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
ASHGA5P041796 13.090287
ASHGA5P031496 7.8046575
ASHGA5P047663 6.0772853
ASHGA5P026943 4.639778
ASHGA5P018786 9.036506
ASHGA5P023786 4.4329386
ASHGA5P021269 7.0009
ASHGA5P000239 3.6170783
ASHGA5P057058 6.849548
ASHGA5P017384 5.575436
ASHGA5P058077 4.678117
ASHGA5P013553 8.842979
ASHGA5P032168 9.407621
ASHGA5P048339 11.492133
ASHGA5P031073 17.880253
ASHGA5P033848 7.499239
ASHGA5P040353 6.114977
ASHGA5P022755 6.0256596
ASHGA5P039495 12.634695
ASHGA5P025630 7.6595016

Total number of rows: 20321

Table truncated, full table size 465 Kbytes.




Supplementary file Size Download File type/resource
GSM1936727_6_Skin.txt.gz 2.7 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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