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Sample GSM467099 Query DataSets for GSM467099
Status Public on Dec 01, 2010
Title Control replicate 2 at 48 hpf
Sample type mixed
 
Channel 1
Source name Total RNA from Zebrafish embroys, control treated
Organism Danio rerio
Characteristics developmental stage: 48 hpf
sample type: miRNAs and control RNAs from Zebrafish fish embroys
tissue: embryo
Treatment protocol Embryos are collected from the mating cages and kept in an incubator at 28.5º C. Embroys are treated with 10nM Morphine sulphate , and 5hpto sacrifice time.
Growth protocol A natural breeding system has been used to obtain zebrafish embryos. This natural breeding is based on the photoperiod exhibited by the zebrafish in such a way that the egg laying is done during the first light of the day, so it can be controlled with artificial light.
Extracted molecule total RNA
Extraction protocol Trizol® reagent (Invitrogen) was used to extract total RNA from cells
Label DY547
Label protocol Total RNA was ligated to a synthetic linker, 5’-pCU-DY547-3’. Reference DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs were combined and labeled with a ULYSIS® Alexa Fluor® 647 kit.
 
Channel 2
Source name Reference DNA
Organism Homo sapiens
Characteristics sample type: synthetic DNA oligos corrresponding to human miRNAs
Treatment protocol Embryos are collected from the mating cages and kept in an incubator at 28.5º C. Embroys are treated with 10nM Morphine sulphate , and 5hpto sacrifice time.
Growth protocol A natural breeding system has been used to obtain zebrafish embryos. This natural breeding is based on the photoperiod exhibited by the zebrafish in such a way that the egg laying is done during the first light of the day, so it can be controlled with artificial light.
Extracted molecule other
Extraction protocol Trizol® reagent (Invitrogen) was used to extract total RNA from cells
Label Alexa Fluor® 647
Label protocol Total RNA was ligated to a synthetic linker, 5’-pCU-DY547-3’. Reference DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs were combined and labeled with a ULYSIS® Alexa Fluor® 647 kit.
 
 
Hybridization protocol A mixture of labeled RNA and DNA was hybridized to a miRNA microarray (Thomson et al), inside a MAUI mixer in a MAUI hybridization system (BioMicro® System, Inc, Salt Lake City, UT, USA). Thomson, J.M., Parker, J., Perou, C.M., and S.M. Hammond. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1: 47-53. Epub 2004 Sep 29.
Scan protocol Slides were scanned with a ScanArray 5000 machine (Perkin Elmer®, Waltham, MA, USA).
Description n/a
Data processing BlueFuse (BlueGenome, Cambridge, UK) was used to quantify pixel intensities. GeneSpring GX 7.3.1 (Agilent Technologies) was used for data normalization.
 
Submission date Nov 02, 2009
Last update date Jun 21, 2010
Contact name Xiaoxiao Zhang
E-mail(s) zhang688@umn.edu
Organization name University of Minnesota
Street address 312 Church St. SE
City Minneapolis
ZIP/Postal code 55455
Country USA
 
Platform ID GPL9517
Series (1)
GSE18847 microRNA expression and opioid regulation in the zebrafish

Data table header descriptions
ID_REF
VALUE log2 normalized ratio (test/reference) to the 80th percentile in Genespring

Data table
ID_REF VALUE
1 -0.7060
2 -2.0770
3 -0.8599
4 -3.5312
5 -0.6781
6 -4.0589
7 0.0922
8 -0.4131
9 -3.4391
10 -0.3076
11 -0.1392
12 -0.2898
13 -2.8059
14 -0.7226
15 -0.2934
16 -0.4620
17 -0.5249
18 -0.0101
19 -1.2934
20 -0.7226

Total number of rows: 1147

Table truncated, full table size 13 Kbytes.




Supplementary file Size Download File type/resource
GSM467099_control_48h_#2.txt.gz 77.7 Kb (ftp)(http) TXT
Processed data included within Sample table

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