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Sample GSM491106 Query DataSets for GSM491106
Status Public on Oct 18, 2010
Title Ref2.2 (LC)
Sample type RNA
 
Source name Total RNA with small fraction
Organism Mus musculus
Characteristics sample: Reference 2
sample type: pool of equal parts RNA from heart, lung and liver
microarray barcode: 251911910767
Extracted molecule total RNA
Extraction protocol Total RNA containing the small fraction was isolated from each sample using the miRVana miRNA Isolation Kit (Ambion), Streetsville, ON, Canada). Quality was confirmed using the Agilent 2100 Bioanalyzer and RNA Nano 6000 chips.
Label Cy3
Label protocol LC Sciences arrays were performed in one colour by the company at the LC Sciences Headquarters (Houston, TX) using two replicates of each reference pool. Briefly, 1 ug of total reference RNA was extracted with Trizol reagent (Invitrogen) and size fractionated using a YM-100 Microcon filter (Millipore). Small RNAs less than 300 nucleotides in length were extended with a poly(A) tail using poly(A) polymerase. Poly(A) tails were ligated with an oligonucleotide tag for subsequent dye staining.
 
Hybridization protocol Hybridizations were carried out overnight on µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) using 100 µL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34°C overnight. Each detection probe on the microfluidic chip consisted of a chemically-modified nucleotide coding segment complementary to target microRNA or other RNA (control sequences), and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. After RNA hybridization, tag-conjugating Cy3 and Cy5 dyes were circulated through the microfluidic chip for dye staining.
Scan protocol Images were acquired using a GenePix 4000B (Molecular Device) laser scanner by LC Sciences. Intensity data were collected using Array-Pro image analysis software (Media Cybernetics) with a scan resolution of 10 microns and PTM between 480 and 540V.
Description Reference RNA was developed from FirstChoice® mouse Total RNA including the small fraction (Catalogue # AM7800-AM7828, Ambion, Streetsville, ON)
Data processing Analysis was conducted on background subtracted signal intensities. Background was determined using a regression-based background mapping method. Spots yielding true signal (i.e., present) had signal intensities higher than 3×(background standard deviation) and standard deviation/signal intensity < 0.5. CV is calculated by (standard deviation)/(signal intensity). Probes repeated multiple times on an array were called present if the signals from at least 50% of the probes were above detection level.
 
Submission date Dec 28, 2009
Last update date Oct 18, 2010
Contact name Andrew Williams
Organization name Health Canada
Street address 50 Columbine
City Ottawa
State/province ON
ZIP/Postal code K1A OK9
Country Canada
 
Platform ID GPL8530
Series (1)
GSE19669 Cross-platform correlation analysis of global microRNA expression technologies

Data table header descriptions
ID_REF
VALUE cyclic lowess normalized signal intensity

Data table
ID_REF VALUE
1 NULL
2 NULL
3 NULL
4 NULL
5 NULL
6 NULL
7 NULL
8 NULL
9 NULL
10 NULL
11 NULL
12 NULL
13 NULL
14 NULL
15 NULL
16 NULL
17 NULL
18 NULL
19 NULL
20 NULL

Total number of rows: 3968

Table truncated, full table size 32 Kbytes.




Supplementary file Size Download File type/resource
GSM491106_04_M13.0_091782-0921-Yauk-Ref#2_2-390_Data.xls.gz 364.4 Kb (ftp)(http) XLS
Processed data included within Sample table

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