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Sample GSM1129466 Query DataSets for GSM1129466
Status Public on Apr 26, 2013
Title Retina_AAP_rep2
Sample type RNA
 
Source name retina, 7 days
Organism Mus musculus
Characteristics treatment: peptide AAP
gender: male
strain: C57BL/6
tissue: retina
developmental stage: adult
Treatment protocol Retinal tissues were prepared from the enucleated eyes. Four retinal tissues were pooled into 1 test tube.
Growth protocol We intravitreally injected 1 μM of PBS, AAP, or HAN into the right eyes of C57BL/6 male mice. One week later, the mice were sacrificed and the eyes were enucleated.
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions.
Label Cy3
Label protocol Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).
 
Hybridization protocol After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Canine Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).
Scan protocol The hybridized images were scanned using Agilent’s DNA microarray scanner (G2565AA) and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).
Data processing All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3 (Agilent Technology, USA). The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity. Functional annotation of genes was performed according to Gene OntologyTM Consortium (http://www.geneontology.org/index.shtml) by GeneSpringGX 7.3. Gene classification was based on searches done by BioCarta (http://www.biocarta.com/), GenMAPP (http://www.genmapp.org/), DAVID (http://david.abcc.ncifcrf.gov/), and Medline databases (http://www.ncbi.nlm.nih.gov/).
 
Submission date Apr 25, 2013
Last update date Apr 26, 2013
Contact name Jeong Hun Kim
Organization name Seoul National University
Lab FARB (Fight against Angiogenesis-Related Blindness) Laboratory
Street address 101, Daehak-ro, Jongno-gu
City Seoul
ZIP/Postal code 110744
Country South Korea
 
Platform ID GPL11202
Series (1)
GSE46378 Investigation of Alterations in Gene Expression in the Retina Induced by High-Affinity Peptides targeting vascular endothelial growth factor, AAP and HAN

Data table header descriptions
ID_REF
VALUE Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

Data table
ID_REF VALUE
A_51_P100034 7398.64
A_51_P100174 1283.8066
A_51_P100208 111.6028
A_51_P100289 1431.828
A_51_P100298 1842.7722
A_51_P100309 7.5116405
A_51_P100327 41.0454
A_51_P100347 120.8618
A_51_P100519 6.563936
A_51_P100537 44.58555
A_51_P100573 358.45172
A_51_P100624 5.540945
A_51_P100625 10.506734
A_51_P100768 5.219348
A_51_P100776 248.72197
A_51_P100787 5739.793
A_51_P100828 3154.4695
A_51_P100852 13.747453
A_51_P100991 124.2455
A_51_P100997 184.67738

Total number of rows: 39429

Table truncated, full table size 866 Kbytes.




Supplementary file Size Download File type/resource
GSM1129466_AAP_2_252665514768_1_1.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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