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Sample GSM2310301 Query DataSets for GSM2310301
Status Public on Sep 15, 2016
Title Uveal_melanoma_derivative_cell_line_T97_rep1
Sample type RNA
 
Source name Uveal melanoma derivative cell line T97, replicate 1
Organism Homo sapiens
Characteristics cell line: T97
tissue: Uveal melanoma derivative cell line
gender: male
age: 69 years
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Toronto, ON) from the uveal melanoma cell lines T97, T98, T108, T111, T128, T131, T132, T142, T143, T151, T157 cultured from the primary tumors T97, T98, T108, T111, T128, T131, T132, T142, T143, T151, T157 of patients diagnosed with uveal melanoma .
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 14, 2016
Last update date Sep 15, 2016
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)
GSE86915 Transcription of the human 5-Hydroxytryptamine receptor 2B (HTR2B) gene is under the regulatory influence of the transcription factors NFI and RUNX1 in human uveal melanoma

Data table header descriptions
ID_REF
VALUE Gmean signal intensity

Data table
ID_REF VALUE
1 1.270393e+004
2 3.609524e+001
3 3.670455e+001
4 1.206190e+003
5 3.784091e+001
6 4.145238e+001
7 2.179048e+002
8 2.252762e+003
9 4.311628e+001
10 8.059091e+001
11 4.531250e+001
12 1.201818e+002
13 4.428261e+001
14 1.030721e+003
15 4.330952e+001
16 4.117073e+001
17 5.006977e+001
18 4.286364e+001
19 4.454762e+001
20 4.365116e+001

Total number of rows: 62976

Table truncated, full table size 1219 Kbytes.




Supplementary file Size Download File type/resource
GSM2310301_SG11400001_252800415604_S001_GE1_107_Sep09_2_1.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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