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Sample GSM1122680 Query DataSets for GSM1122680
Status Public on Apr 16, 2013
Title Retina_SH-42_7days_rep2
Sample type RNA
 
Channel 1
Source name retina, 7 days
Organism Mus musculus
Characteristics gender: male
strain: C57BL/6
tissue: retina
developmental stage: adult
treatment: SH-42
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, SH-42, or SH-80 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 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label
 
Channel 2
Source name retina, 7 days
Organism Mus musculus
Characteristics treatment: control
cell line: 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, SH-42, or SH-80 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 Cy5
Label protocol 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label
 
 
Hybridization protocol Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
Scan protocol Scanned on an Agilent G2565AA scanner.
Data processing Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.
 
Submission date Apr 15, 2013
Last update date Apr 16, 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)
GSE46057 Investigation of Alterations in Gene Expression in the Retina Induced by Intravitreal Injection of SH-42 and SH-80

Data table header descriptions
ID_REF
VALUE The averages of normalized ratios were calculated by dividing the average of normalized test signal channel intensity by the average of normalized control channel intensity.

Data table
ID_REF VALUE
A_51_P100034 -0.136495216
A_51_P100174 -0.054249233
A_51_P100208 0.314267046
A_51_P100289 0.163586708
A_51_P100298 0.027283025
A_51_P100309 -1.848637628
A_51_P100327 -0.253766874
A_51_P100347 0.08707119
A_51_P100519 -1.320097611
A_51_P100537 -0.498040177
A_51_P100573 -0.179558282
A_51_P100624 -2.502513734
A_51_P100625 -0.999133201
A_51_P100768 -1.251406869
A_51_P100776 0.420121677
A_51_P100787 0.347400788
A_51_P100828 -0.074047052
A_51_P100852 -1.4289758
A_51_P100991 -0.335685924
A_51_P100997 0.066860305

Total number of rows: 39429

Table truncated, full table size 1003 Kbytes.




Supplementary file Size Download File type/resource
GSM1122680_Con_vs._SH-42_2_252665514765_1_1.txt.gz 4.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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