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Sample GSM2308746 Query DataSets for GSM2308746
Status Public on Sep 10, 2016
Title Choroidal_melanocytes_M3_21% oxygen_passage2_rep1
Sample type RNA
Source name Primary choroidal melanocyte cells M3, cultured at 21% oxygen, passage 2, replicate 1
Organism Homo sapiens
Characteristics tissue: Primary human Melanocyte cells
gender: male
age: 83 years
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Toronto, ON) from Primary choroidal melanocyte cells isolated from normal eyes supplied by the National Eyes Bank from the CHU de Québec (QC, Canada).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Toronto, ON). Dye incorporation and cRNA yield were checked with the Nanophotometer pearl(Montréal Biotech).
Hybridization protocol 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.
Scan protocol Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
Data processing The scanned images were analyzed with Feature Extraction Software 10,7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Submission date Sep 09, 2016
Last update date Sep 10, 2016
Contact name Solange Landreville
Organization name Université Laval
Department Ophthalmology
Street address 1050 chemin Sainte-Foy, Room H2-02
City Quebec
State/province Quebec
ZIP/Postal code G1S4L8
Country Canada
Platform ID GPL13607
Series (1)
GSE86789 Differential responses of choroidal melanocytes and uveal melanoma cells to low oxygen conditions

Data table header descriptions
VALUE Gmean signal intensity

Data table
1 4.769258e+004
2 3.462500e+001
3 3.692500e+001
4 4.131163e+002
5 7.278571e+002
6 6.534146e+001
7 7.085952e+003
8 9.579048e+002
9 4.597619e+001
10 5.026829e+001
11 3.872093e+001
12 1.054233e+003
13 2.849047e+003
14 4.873023e+002
15 6.088429e+003
16 3.041026e+001
17 2.824545e+002
18 3.759091e+001
19 4.270732e+001
20 6.509767e+002

Total number of rows: 62976

Table truncated, full table size 1219 Kbytes.

Supplementary file Size Download File type/resource
GSM2308746_SG11400001_252800415601_S002_ext_072015_GE1_107_Sep09_1_3.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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