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Sample GSM1198239 Query DataSets for GSM1198239
Status Public on Jul 31, 2013
Title Retina_Au 20_7days_rep3
Sample type RNA
 
Channel 1
Source name retina, PBS, 7 days
Organism Mus musculus
Characteristics gender: male
strain: C57BL/6
tissue: retina
developmental stage: adult
treatment: PBS
Treatment protocol Retinal tissues were prepared from the enucleated eyes. Four retinal tissues were pooled into 1 test tube.
Growth protocol We intravitreally injected PBS or nanoparticles (gold and silicate nanoparticles with the diameter of 20 and 100 nm) into the right eyes of 5-week-old male C57BL/6 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, Au20, 7 days
Organism Mus musculus
Characteristics treatment: 20 nM Au
gender: male
age: 5-week-old
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 PBS or nanoparticles (gold and silicate nanoparticles with the diameter of 20 and 100 nm) into the right eyes of 5-week-old male C57BL/6 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 Jul 30, 2013
Last update date Jul 31, 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)
GSE49371 Investigation of Alterations in Gene Expression in the Retina Induced by Intravitreal Injection of gold and silicate nanoparticles

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

Data table
ID_REF VALUE
A_51_P100034 -0.213996729
A_51_P100174 0.026568501
A_51_P100208 -0.731892535
A_51_P100289 -0.018110823
A_51_P100298 0.156422894
A_51_P100309 0.22917825
A_51_P100327 -0.84314107
A_51_P100347 -0.104113748
A_51_P100519 0.254778933
A_51_P100537 0.170645271
A_51_P100573 -0.193843161
A_51_P100624 0.237797663
A_51_P100625 0.549881457
A_51_P100768 0.158251575
A_51_P100776 0.086910506
A_51_P100787 0.320250362
A_51_P100828 0.108642611
A_51_P100852 -0.215058878
A_51_P100991 -0.356153228
A_51_P100997 0.134224095

Total number of rows: 39429

Table truncated, full table size 998 Kbytes.




Supplementary file Size Download File type/resource
GSM1198239_Con_vs_Au_20-3_252665514754_1_1.txt.gz 4.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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