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Sample GSM1198238 Query DataSets for GSM1198238
Status Public on Jul 31, 2013
Title Retina_Au 20_7days_rep2
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 0.068613308
A_51_P100174 -0.15466074
A_51_P100208 -0.408387713
A_51_P100289 0.216076347
A_51_P100298 -0.04271734
A_51_P100309 0.077680117
A_51_P100327 0.369257861
A_51_P100347 0.049972374
A_51_P100519 0.231929156
A_51_P100537 -0.69638228
A_51_P100573 0.125580221
A_51_P100624 0.286131698
A_51_P100625 0.383574026
A_51_P100768 0.26303104
A_51_P100776 0.23811108
A_51_P100787 0.327782889
A_51_P100828 0.006477564
A_51_P100852 0.410915246
A_51_P100991 -0.240105423
A_51_P100997 -0.008667337

Total number of rows: 39429

Table truncated, full table size 998 Kbytes.




Supplementary file Size Download File type/resource
GSM1198238_Con_vs_Au_20-2_252665514753_1_1.txt.gz 4.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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