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Sample GSM849520 Query DataSets for GSM849520
Status Public on Nov 02, 2012
Title PCMM_5
Sample type RNA
Source name melanoma biopsy
Organism Homo sapiens
Characteristics tissue: skin
gender: male
age: 84
Treatment protocol All cutaneous specimens were harvested in the operating room, immediately stored in RNAlater (Quiagen, Hilden, Germany) and kept at - 80 °C until RNA isolation.
Extracted molecule total RNA
Extraction protocol Total RNA including miRNAs was isolated using the miRNeasy Mini Kit (Quiagen, Hilden, Germany) according to the manufacturer’s protocol. RNA concentration and purity was determined by NanoDrop ND-1000 spectral photometer (Peqlab, Erlangen, Germany). RNA integrity control (RIN) was determined by means of capillary electrophoresis with the 2100 Bioanalyzer and the RNA 6000 NanoLabCHip Kits (both Agilent Technologies, Santa Clara, USA).
Label Cy3
Label protocol For assessment of labeling and hybridization efficiencies total RNA samples were spiked with in-vitro synthesized oligonucleotides by using the MicroRNA Spike-In Kit (Agilent Technologies, Santa Clara, USA). A total of 100 ng total RNA per sample were introduced into a labeling reaction. The spiked total RNA was treated with alkaline calf intestine phosphatase (CIP). The dephosphorylated RNA was labeled with the miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, USA) according to the manufacturer´s instructions using T4 RNA ligase, incorporating Cyanine 3-Cytidine biphosphate (pCp). The Cyanine-3-labeled miRNA samples were prepared for One-Color based hybridization with Complete miRNA Labeling and Hyb Kit (Agilent Technologies, Santa Clara, USA) according to the manufacturer´s instructions.
Hybridization protocol Labeled miRNA samples were hybridized at 55°C for 20 hrs on separate Human miRNA Microarrays Release 16.0 (8x60K format, (Agilent Technologies, Santa Clara, USA). Afterwards, microarrays were washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies, Santa Clara, USA) followed by drying with acetonitrile (Sigma-Aldich, St.Louis, USA).
Scan protocol Fluorescent signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies, Santa Clara, USA) on the Agilent DNA Microarray Scanner.
Description RS-227_06.txt
Data processing Fluorescent signal intensities were extracted from the images using Feature Extraction Software (Agilent Technologies, Santa Clara, USA). All the steps described were carried out according to the manufacturer´s instructions.
Submission date Dec 14, 2011
Last update date Nov 02, 2012
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 GPL15019
Series (1)
GSE34460 Comparative microarray analysis of microRNA expression profiles in primary cutaneous malignant melanoma, cutaneous malignant melanoma metastases and benign melanocytic naevi

Data table header descriptions
VALUE Normalized signal intensity

Data table
Blank -3.321954
NC1_00000197 -3.321954
NC1_00000215 -3.321954
NC2_00079215 -3.321954
NC2_00092197 -3.321954
NC2_00106057 -3.321954
NC2_00122731 -3.321954
NegativeControl -3.321954
bkv-miR-B1-3p -3.321954
bkv-miR-B1-5p -3.321954
dmr_285 5.742437
dmr_3 13.109493
dmr_308 -3.321954
dmr_316 -3.321954
dmr_31a 3.9939883
dmr_6 11.631886
ebv-miR-BART1-3p -3.321954
ebv-miR-BART1-5p -3.321954
ebv-miR-BART10 -3.321954
ebv-miR-BART10* -3.321954

Total number of rows: 1368

Table truncated, full table size 31 Kbytes.

Supplementary file Size Download File type/resource
GSM849520.txt.gz 7.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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