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Sample GSM419058 Query DataSets for GSM419058
Status Public on Nov 17, 2009
Title Amygdala left animal 7
Sample type other
 
Channel 1
Source name Amygdala left hand side
Organism Rattus norvegicus
Characteristics strain: Sprague-Dawley
gender: male
developmental stage: Adult
tissue: amygdala
hemisphere: Left
molecule: microRNA
Growth protocol Animals were kept under normal day/night and dairy conditions with unlimited access to food and water.
Extracted molecule other
Extraction protocol RNeasy Lipid Tissue Mini Kit (Qiagen) following manufacturer's instructions
Label Alexa Fluor® 5 fluorophor
Label protocol 600 ng microRNA sample were poly-A tailed and tagged with the sequence tag for the Alexa Fluor® 5 fluorophor using the NCode™ miRNA Labeling System (Invitrogen). Universal reference were labeled with Alexa Fluor® 3.
 
Channel 2
Source name universal brain reference
Organism Rattus norvegicus
Characteristics sample type: Invitrogen universal brain reference small RNA (>200 nt in length)
Extracted molecule other
Extraction protocol RNeasy Lipid Tissue Mini Kit (Qiagen) following manufacturer's instructions
Label Alexa Fluor® 5 fluorophor
Label protocol 600 ng microRNA sample were poly-A tailed and tagged with the sequence tag for the Alexa Fluor® 5 fluorophor using the NCode™ miRNA Labeling System (Invitrogen). Universal reference were labeled with Alexa Fluor® 3.
 
 
Hybridization protocol Samples were hybridized against the reference overnight to NCode™ Multi-Species miRNA Microarrays (Invitrogen, Carlsbad, CA, USA) using the NCode™ Multi-Species miRNA Microarrays Kit (Invitrogen, Carlsbad, CA, USA) following the instructions given by the manufacturer. Arrays were then hybridized on a MAUI hybridization station (BioMicro Systems, Inc, Salt Lake City, UT, USA) with Alexa Fluor® 3 and Alexa Fluor® 5 capture reagents and washed.
Scan protocol Scanned using an Agilent DNA microarray scanner.
Images were processed using GenePix Pro software (Molecular Devices, Sunnyvale, CA, USA).
Description Biological replicate 2 of 4.
Data processing Background adjusted using “normexp” with an offset of 50. Print-tip-loess normalization was used to adjust data within each array and subsequent Gquantile normalization to allow comparisons between arrays. Thelimma package from BioConductor was used in R.
 
Submission date Jun 19, 2009
Last update date Nov 17, 2009
Contact name Thomas Werge
Phone +45 4633 4968
Organization name Psychiatric Center, Sct. Hans Hospital
Department Institute of biological Psychiatry
Street address Boserupvej 2
City Roskilde
ZIP/Postal code Dk-4000
Country Denmark
 
Platform ID GPL8745
Series (1)
GSE16725 Regional brain expression maps for microRNAs in rats

Data table header descriptions
ID_REF
VALUE gquantile normalized log 2 ratio (test sample/universal reference)

Data table
ID_REF VALUE
1030 -2.498151492
1231 -0.032226374
1431 -0.804960127
1268 -0.099782421
1085 0.01035373
1421 -1.246765593
1033 -1.423677801
1064 -1.661442993
1297 -0.03450017
1164 -0.004089684
1163 -0.586455537
1072 -0.382304328
1213 -0.360149435
1377 2.131043457
1384 0.808443115
1106 0.141463344
1253 -0.03629007
1225 2.521138956
1272 -1.68310369
1031 -1.237631722

Total number of rows: 236

Table truncated, full table size 4 Kbytes.




Supplementary file Size Download File type/resource
GSM419058.gpr.gz 373.0 Kb (ftp)(http) GPR
Processed data included within Sample table

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