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Sample GSM701889 Query DataSets for GSM701889
Status Public on Nov 30, 2011
Title brain_bg RA_rep3
Sample type RNA
 
Source name Ac song nucleus budgerigar
Organism Melopsittacus undulatus
Characteristics brain area: arcopallium song nucleus
gender: Male
age: Adult
Extracted molecule total RNA
Extraction protocol After laser capture the samples, the cap membrane with nuclei were carefully removed and placed in a 0.65 ml tube of the PicoPure RNA isolation kit which contained 50ul of disruption buffer (Molecular Devices). Tubes were placed on a 42oC heat block for 30 min then placed in a -80 oC freezer until all desired samples were captured. Total RNA was then isolated according to the remaining protocol steps in the PicoPure isolation kit instructions (Molecular Devices). The concentration and integrity of total RNA were measured on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA USA) using the RNA Pico 6000 kit according to manufacturer instructions (Agilent Technologies).
Label Cy3
Label protocol Samples were labeled with Cy3-dCTP using the uMACS SuperAmp Kit (Miltenyi Biotec).
 
Hybridization protocol From the amplified cDNA reactions, 1.5 mg of amplified labeled product (probe) was denatured and hybridized to our custom designed songbird oligo spotted arrays (Agilent Technologies; Whitney et al, in preparation) containing oligos designed from over 44,000 relatively unique cDNA transcripts, including some splice variants. More detailed information on the arrays is available at http://aviangenomes.org/main/zebrafincholigoarray.
Scan protocol After hybridization, the microarrays were scanned with the Axon GenePix 4000B scanner to acquire and analyze the expression data (Molecular Devices).
Description gene expression brain
Data processing For analysis, signal intensity on an axon array scanner was obtained in Agilent oligoarray format. The data was extracted in R using the Agi4x44PreProcess Bioconductor library.The values were normalized using median centered log2 transformation. Raw and normalized expression distributions were evaluated for sample quality control using the normalization centering profile, the normalization factor, and a cross-sample correlation analysis. Normalization was evaluated with VSN (variance stabilization normalization)-Scale Factor package in R (R Foundation for Statistical Computing, Vienna, Austria). VSN-Scale Factor was chosen because it performed the least manipulation of the original intensity profiles, and normalizes samples among themselves.
 
Submission date Apr 05, 2011
Last update date Nov 30, 2011
Contact name Erina Hara
Organization name Duke University Medical Center
Street address Rm 449 Bryan Research Building
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
 
Platform ID GPL9856
Series (1)
GSE28395 Avian arcopallium

Data table header descriptions
ID_REF
VALUE Normalized log2 transformation

Data table
ID_REF VALUE
0205P0030B17 107
0202P0024M14 624
0205P0028D09 72
0202P0019C06 117
0203P0050F15 261
0206P0012J11 88
0203P0070P07 70
0202P0043B09 68
0106P0001D01 119
0203P0043A22 217
0206P0018B06 427
0202P0038K07 778
0206P0020E24 228
0057P0001C12 21419
0106P0009G08 101
0202P0008C24 360
0203P0022P10 65
0206P0021I07 1972
0106P0001B01 164
0063P0031D01 85

Total number of rows: 43125

Table truncated, full table size 707 Kbytes.




Supplementary file Size Download File type/resource
GSM701889_2317_4964_CU_073_AgilentSongbird2_21_GE1-v5_95_Feb07_1_1.txt.gz 6.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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