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Sample GSM1129470 Query DataSets for GSM1129470
Status Public on Apr 26, 2013
Title Retina_HAN_rep3
Sample type RNA
Source name retina, 7 days
Organism Mus musculus
Characteristics treatment: peptide HAN
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 ( by GeneSpringGX 7.3. Gene classification was based on searches done by BioCarta (, GenMAPP (, DAVID (, and Medline databases (
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
VALUE Agilent Feature Extraction Software (v was used for background subtraction and LOWESS normalization.

Data table
A_51_P100034 8071.824
A_51_P100174 1444.812
A_51_P100208 145.2589
A_51_P100289 1736.574
A_51_P100298 2009.8496
A_51_P100309 32.25516
A_51_P100327 34.9583
A_51_P100347 98.74164
A_51_P100519 5.797576
A_51_P100537 52.279335
A_51_P100573 419.84702
A_51_P100624 5.337501
A_51_P100625 41.263966
A_51_P100768 5.175973
A_51_P100776 264.55142
A_51_P100787 6624.0586
A_51_P100828 4054.1333
A_51_P100852 89.37654
A_51_P100991 151.4132
A_51_P100997 301.70465

Total number of rows: 39429

Table truncated, full table size 866 Kbytes.

Supplementary file Size Download File type/resource
GSM1129470_HAN_3_252665514793_1_1.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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