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Sample GSM1193010 Query DataSets for GSM1193010
Status Public on Jul 20, 2013
Title Retina_PTC_7days_rep3
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: control
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 titanium dioxide nanoparticles (PTC and 10 times PTC) into the right eyes of 8-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, 7 days
Organism Mus musculus
Characteristics cell line: male
age: 8-week-old
strain: C57BL/6
tissue: retina
developmental stage: adult
treatment: PTC
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 titanium dioxide nanoparticles (PTC and 10 times PTC) into the right eyes of 8-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.
Description Con vs PTC 3_252665512821_1_1
Data processing Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.
The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity.
 
Submission date Jul 19, 2013
Last update date Jul 20, 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)
GSE49048 Investigation of Alterations in Gene Expression in the Retina Induced by Intravitreal Injection of titanium dioxide nanoparticles

Data table header descriptions
ID_REF
VALUE normalized ratio treatment/control

Data table
ID_REF VALUE
A_51_P100034 -0.11794706
A_51_P100174 0.299990258
A_51_P100208 -0.305589924
A_51_P100289 0.164642645
A_51_P100298 -0.01025125
A_51_P100309 0.135537365
A_51_P100327 0.657069765
A_51_P100347 -0.320001653
A_51_P100519 0.402140071
A_51_P100537 -0.277947432
A_51_P100573 0.202928193
A_51_P100624 0.102015477
A_51_P100625 0.051139442
A_51_P100768 0.810561805
A_51_P100776 -0.216066776
A_51_P100787 0.393951002
A_51_P100828 -0.011142
A_51_P100852 0.227253976
A_51_P100991 -0.348720077
A_51_P100997 -0.019327552

Total number of rows: 39429

Table truncated, full table size 1000 Kbytes.




Supplementary file Size Download File type/resource
GSM1193010_Con_vs_PTC_3_252665512821_1_1.txt.gz 15.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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