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Sample GSM951049 Query DataSets for GSM951049
Status Public on Jun 23, 2012
Title Case two: ductal carcinoma in situ
Sample type RNA
Source name Mastectomy
Organism Homo sapiens
Characteristics gender: female
age: 36 years
tissue origin: breast
tissue: ductal carcinoma in situ
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)
Data processing Fluorescent signal intensities were extracted from the images with the Feature Extraction 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
VALUE normalised signal intensities for the miRNA

Data table
Blank -8.384743
NC1_00000197 -8.384743
NC1_00000215 -8.384743
NC2_00079215 -8.384743
NC2_00092197 -8.384743
NC2_00106057 -8.384743
NC2_00122731 -8.384743
NegativeControl -8.384743
bkv-miR-B1-3p -8.384743
bkv-miR-B1-5p -8.384743
dmr_285 5.307434
dmr_3 7.8848715
dmr_308 -8.384743
dmr_316 -8.384743
dmr_31a 4.3109293
dmr_6 6.567771
ebv-miR-BART1-3p -8.384743
ebv-miR-BART1-5p -8.384743
ebv-miR-BART10 -8.384743
ebv-miR-BART10* -8.384743

Total number of rows: 1368

Table truncated, full table size 31 Kbytes.

Supplementary file Size Download File type/resource
GSM951049_0604_ICR_253118111842_S01_miRNA_107_Sep09_1_2.txt.gz 7.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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