GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1129464 Query DataSets for GSM1129464
Status Public on Apr 26, 2013
Title Retina_CON_rep3
Sample type RNA
Source name retina, 7 days
Organism Mus musculus
Characteristics treatment: control
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 7241.34
A_51_P100174 1194.423
A_51_P100208 115.3564
A_51_P100289 1590.595
A_51_P100298 2370.2542
A_51_P100309 6.363864
A_51_P100327 44.039818
A_51_P100347 96.77331
A_51_P100519 4.871621
A_51_P100537 42.379562
A_51_P100573 358.9704
A_51_P100624 4.178191
A_51_P100625 12.088211
A_51_P100768 25.22173
A_51_P100776 219.12729
A_51_P100787 5937.9424
A_51_P100828 3012.95
A_51_P100852 24.90715
A_51_P100991 106.6459
A_51_P100997 145.94147

Total number of rows: 39429

Table truncated, full table size 866 Kbytes.

Supplementary file Size Download File type/resource
GSM1129464_CON_3_252665514767_1_3.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap