NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM951048 Query DataSets for GSM951048
Status Public on Jun 23, 2012
Title Case two: normal breast tissue
Sample type RNA
 
Source name Mastectomy
Organism Homo sapiens
Characteristics gender: female
age: 36 years
tissue origin: breast
tissue: normal breast tissue
Treatment protocol Mastectomised breast and the axillary lymph nodes kept in formalin
Extracted molecule total RNA
Extraction protocol Twenty μm thick FFPE sections were cut and mounted on PALM Membrane Slides. Under direct microscopic visualization, tissues of interest were micro-dissected using PALM non-contact Laser catapulsion instrument (P.A.L.M. Microlaser Technologies, Carl Zeiss Ltd). Total RNA, including miRNAs, was extracted with the TRIzol reagent (Invitrogen, supplied by Fisher Scientific UK Ltd) according to the manufacturer’s instructions. Total RNA was quantified with Quant-iT RiboGreen RNA Quantitation Kit (Fisher Scientific UK Ltd), which is an accurate method of measuring total RNA with a detection limit of 0.001-1ng/µl. RNA purity and RNA integrity number (RIN) were determined on an Agilent 2100 Bioanalyzer and RNA 6000 NanoLabChip Kits (both Agilent Technologies, Santa Clara, USA).
Label Cy3
Label protocol MiRNAs extracted from laser microdissected tissue components were profiled using Agilent microRNA microarray profiling system (Agilent Technologies, Santa Clara, USA). Total RNA samples were spiked using the MicroRNA Spike-In Kit (Agilent Technologies, Santa Clara, USA) to evaluate efficiencies of labelling and hybridisation. Total RNA was treated with Calf Intestinal Alkaline Phosphatase (CIP), and then 100 ng of total RNA was used per sample to initiate a labelling reaction. Ligation master mix for T4 RNA ligase, which includes Cyanine 3-Cytidine biphosphate (Cyanine 3-pCp) (Complete miRNA Labelling and Hyb Kit, Agilent Technologies, Santa Clara, USA) was used to label the dephosphorylated RNA.
 
Hybridization protocol Cyanine-3-labelled miRNA samples were hybridised to human miRNA microarrays (Release 16.0, 8x60K) (Agilent Technologies, Santa Clara, USA) at 55°C for 20 hrs. Microarray slides were washed with increasing stringency (Gene Expression Wash Buffers, Agilent Technologies, Santa Clara), and subsequently dried with acetonitrile (Sigma-Aldrich, St. Louis, USA).
Scan protocol Fluorescent signal intensities were detected on an Agilent Microarray Scanner (Agilent Technologies, Santa Clara, USA) using the Scan Control A.8.4.1 Software (Agilent Technologies, Santa Clara, USA).
Description miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[2734-1]
Data processing Fluorescent signal intensities were extracted from the images with the Feature Extraction 10.7.3.1 Software (Agilent Technologies, Santa Clara, USA). The raw signal values were 'normalized to the 90th percentile' when importing the FE files into GeneSpring (the analysis software). Only the top 20% of probes on the array typically had any detectable signal so shifting to the 90th percentile meant the median line was around the centre of this expressed set.
 
Submission date Jun 21, 2012
Last update date Jun 23, 2012
Contact name Sarkawt Khoshnaw
Organization name University of Nottingham
Street address Queens Medical Centre
City Nottingham
ZIP/Postal code NG7 2UH
Country United Kingdom
 
Platform ID GPL15019
Series (1)
GSE38867 MicroRNAs expression profiling during breast cancer progression

Data table header descriptions
ID_REF
VALUE normalised signal intensities for the miRNA

Data table
ID_REF VALUE
Blank -8.224733
NC1_00000197 -8.224733
NC1_00000215 -8.224733
NC2_00079215 -8.224733
NC2_00092197 -8.224733
NC2_00106057 -8.224733
NC2_00122731 -8.224733
NegativeControl -8.224733
bkv-miR-B1-3p -8.224733
bkv-miR-B1-5p -8.224733
dmr_285 5.6928344
dmr_3 8.107908
dmr_308 -8.224733
dmr_316 -8.224733
dmr_31a 4.693523
dmr_6 6.774284
ebv-miR-BART1-3p -8.224733
ebv-miR-BART1-5p -8.224733
ebv-miR-BART10 -8.224733
ebv-miR-BART10* -8.224733

Total number of rows: 1368

Table truncated, full table size 31 Kbytes.




Supplementary file Size Download File type/resource
GSM951048_0604_ICR_253118111842_S01_miRNA_107_Sep09_1_1.txt.gz 7.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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