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Sample GSM1499920 Query DataSets for GSM1499920
Status Public on Sep 09, 2014
Title Uveal_melanoma_derivative_cell_line_T143_passage4_rep1
Sample type RNA
 
Source name Uveal melanoma derivative cell line T143, passage 4,replicate 1
Organism Homo sapiens
Characteristics cell type: Uveal melanoma derivative cell line
gender: male
age: 55y
Extracted molecule total RNA
Extraction protocol Total RNA was isolated directly from two UM primary tumors (patients 142 and 143) and the corresponding cell lines (T142 and T143) cultured to near 100% confluency at passages P4, P20 and P60 using the RNeasy Mini Kit (QIAGEN, Toronto, ON).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color LLowInput 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%).
Description Gene expression after 4 cell passages
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 08, 2014
Last update date Sep 09, 2014
Contact name Karine Zaniolo
E-mail(s) karine.zaniolo@gmail.com
Organization name Centre de recherche du CHU de Québec
Department CUO-Recherche
Lab Sylvain Guérin
Street address 1050 Chemin Sainte-Foy
City Québec
State/province Québec
ZIP/Postal code G1S 4L8
Country Canada
 
Platform ID GPL13607
Series (1)
GSE61228 Effects of Long-term Serial Passaging on the Characteristics and Properties of Cell Lines Derived From Uveal Melanoma Primary Tumors.

Data table header descriptions
ID_REF
VALUE Gmean signal intensity

Data table
ID_REF VALUE
1 1.150917e+004
2 3.265854e+001
3 3.636364e+001
4 7.947609e+002
5 3.834146e+001
6 4.152381e+001
7 1.438478e+002
8 1.514047e+003
9 4.040476e+001
10 2.187381e+002
11 4.070455e+001
12 1.303721e+002
13 3.692857e+001
14 8.557442e+002
15 3.346512e+001
16 4.011364e+001
17 4.519512e+001
18 4.378571e+001
19 3.764444e+001
20 3.965854e+001

Total number of rows: 62976

Table truncated, full table size 1219 Kbytes.




Supplementary file Size Download File type/resource
GSM1499920_SG11400001_252800415603_S001_GE1_107_Sep09_2_2.txt.gz 12.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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