NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM904951 Query DataSets for GSM904951
Status Public on Jan 02, 2013
Title PAA (array)
Sample type RNA
 
Source name PAA liver, brain and muscle
Organism Squalius alburnoides
Characteristics genome composition: PAA
tissue: liver, brain, muscle
developmental stage: adult
Extracted molecule total RNA
Extraction protocol Fishes were sacrificed by overdose on anaesthetic MS222, and the respective tissues/organs were dissected and preserved in RNAlatter® (Ambion) at -20ºC. Total RNA was extracted from liver, muscle and brain using the Tri-Reagent® (Ambion) following the supplier's instructions. Contaminant DNA was eliminated by the addition of TURBO™ DNase (Ambion) followed by purification with phenol/chloroform. Ethanol, Glycogen and Sodium Acetate (NaOAc) were used to achieve RNA precipitation. RNA quantity and quality was assessed using the Nanodrop and Agilent 2100 Bioanalyzer systems, respectively. Samples with a RIN number above 7 were used.
Label Cy3
Label protocol Total RNA from all samples was labeled using the ULS microRNA labeling kit (Kreatech) according to the manufacturer’s instructions. Briefly, 2 ug of total RNA from each sample were incubated with Cy3-ULS for 15 min at 85ºC. The labeled RNAs were purified to remove non-reacted Cy-ULS to produce a fluorescently-labeled RNA sample for microarray analysis. Dye incorporation was monitored by UV-visible spectroscopy.
 
Hybridization protocol PREHYBRIDIZATION: 1. Make 100 ml prehybridization buffer (for a maximum of 4 slides) containing 1M Tris-HCL pH=9 pre-heated at 50ºC, 100mM ethanolamide and 0.1% SDS. 2. Warm the prehybridization solution to 50 ºC in a 100 ml Coplin Jar. 3. Place slides to be analyzed into the pre-warmed pre-hybridization buffer. Incubate for 20 minutes at 50 ºC with constant agitation, if possible. 4. Wash thoroughly by inverting or gently shaking the container with nuclease-free water constantly for 1 minute. Decant the water and repeat this rising step with fresh nuclease-free water. 5. Allow the slides to dry by centrifuging 3 minute 800 rpm. Slides should be used immediately following prehybridization.
HYBRIDIZATION: Pre-heat 3x hybridization solution (Ambion) to 65 ºC for at least 5 min to overcome SDS precipitation. Combine labeled RNA with hybridization buffer (preheated to 65 ºC). Heat at 95 ºC for 3 minutes. Immediately put on ice for at least 1 min. Spin-down briefly. Add 4x blocking reagent (Kreatech). Incubate on dark for 1 minute at room temperature. Using Agilent gasket slides (G2534-60003), Agilent SureHyb hybridization chambers (G2534A) and hybridization oven (G2545A), see Agilent User Manual for instructions: 1. For each array, put a gasket slide onto a SureHyb chamber and add a total of 250 ul target as 1 dot in the center of the chamber. 2. Put a microarray slide on the gasket slide by holding it in place with your fingertips, towards the top edge of the gasket chamber. 3. Gently (!) allow the microarray slide to drop onto the gasket chamber by lowering it with the aid of your other hand. Do not move the microarray slide after it is in place. 4. Place the SureHyb chamber into the hybridization oven at 42 ºC for 16 hours.
Scan protocol Slides were scanned using the Agilent G2565AA DNA microarray scanner: Resolution: 10, Red laser PMT= 0, Green laser PMT= 100.
Data processing Microarray images were analyzed using Quantarray v3.0 software (PerkinElmer). Manually flagged bad spots were eliminated and the Cy3 median pixel intensity values were background subtracted, followed by the averaging of quadruplicate features on the array. Data points were removed when intensity values were below 200% background. A global median normalization of miRNA microarray data was applied using BRB-ArrayTools v3.4.0 software. Cy3 intensities were obtained.
 
Submission date Mar 28, 2012
Last update date Jan 02, 2013
Contact name Angela Inácio
E-mail(s) mainacio@fc.ul.pt
Organization name centro de Biologia Ambiental
Street address Campo Grande
City Lisbon
ZIP/Postal code 1749-16
Country Portugal
 
Platform ID GPL14672
Series (2)
GSE36894 miRNA expression profile in the Squalius alburnoides complex
GSE38799 miRNA expression profile and small RNA transcriptome in the Squalius alburnoides complex

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
cel-let-7 359.0264966
dme-miR-124 226.5756795
dme-miR-184* 187.6320024
dme-miR-7 276.2938689
dme-miR-9a 4099.236868
dre-let-7d 111.4047089
dre-let-7g 302.341468
dre-let-7h 184.4075486
dre-let-7i 139.990832
dre-let-7j 226.4412216
dre-miR-1 1364.706792
dre-miR-101b 151.1979672
dre-miR-10a 221.4702178
dre-miR-10a* 592.3386896
dre-miR-10b 222.8644357
dre-miR-10c 218.8896262
dre-miR-10d 397.7668898
dre-miR-10d* 217.9318274
dre-miR-122 356.5382138
dre-miR-125a 328.333758

Total number of rows: 241

Table truncated, full table size 5 Kbytes.




Supplementary file Size Download File type/resource
GSM904951_PAA.txt.gz 213.4 Kb (ftp)(http) TXT
Processed data included within Sample table

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