NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM461226 Query DataSets for GSM461226
Status Public on Dec 20, 2009
Title benign nevus, 7
Sample type RNA
 
Source name FFPE benign nevus
Organism Homo sapiens
Characteristics tissue: Benign nevus
Treatment protocol Formalin-fixed paraffin-embedded (FFPE) tissues.
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol All samples contained at least 75% hyperplasia tissues without necrosis, which was confirmed by pathologist. The RecoverAll total RNA Isolation kit (Ambion, Streetsville, Canada) was used to extract total RNA (including miRNA) from FFPE samples.
Label Cy3
Label protocol 100ng total RNA was dephosphorylated in the presence of calf intestine alkaline phsphatase, then a Cy3-pCp molecule was ligated to the 3' end of the RNA molecule according to Agilent miRNA protocol version 1.5.
 
Hybridization protocol Labeled RNA was hybridized to Agilent miRNA array (8 arrays per slide) at 55°C for 22h in rotisserie in a hybridization oven. Disassembled arrays were washed in GE wash buffer 1&2 for 5 minutes each.
Scan protocol Images were scanned with Agilent scanner at 5µm resolution.
Description JC-16
Data processing The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate Gene View file, providing expression data for each gene probed on the array. Features interogating same miRNA were summarized together based on their weight. No interarray normalization method was employed.
 
Submission date Oct 09, 2009
Last update date Jan 29, 2010
Contact name Harriet Feilotter
Organization name Queen's University
Department Pathology and molecular department
Lab microarray facility
Street address 88 Stuart St
City Kingston
State/province Ontario
ZIP/Postal code K7L 3N6
Country Canada
 
Platform ID GPL9081
Series (2)
GSE18509 miR-193b represses cell proliferation and regulates cyclin D1 in melanoma: benign nevi and metastatic melanoma
GSE18512 miR-193b represses cell proliferation and regulates cyclin D1 in melanoma

Data table header descriptions
ID_REF
VALUE Unnormalized Gene View data

Data table
ID_REF VALUE
hsa-let-7a 2593.08
hsa-let-7b 4695.61
hsa-let-7c 571.67
hsa-let-7d 344.505
hsa-let-7e 440.558
hsa-let-7f 783.451
hsa-let-7g 157.508
hsa-let-7i 86.7073
hsa-miR-1 -2.82574
hsa-miR-100 227.106
hsa-miR-101 38.3348
hsa-miR-103 244.765
hsa-miR-105 -1.43128
hsa-miR-106a 93.2676
hsa-miR-106b 18.1592
hsa-miR-107 101.031
hsa-miR-10a 21.2145
hsa-miR-10b 59.9985
hsa-miR-122a -0.776928
hsa-miR-124a -1.56044

Total number of rows: 470

Table truncated, full table size 9 Kbytes.




Supplementary file Size Download File type/resource
GSM461226.txt.gz 1.5 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap