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Sample GSM5258374 Query DataSets for GSM5258374
Status Public on Apr 22, 2021
Title EyeBank_cultured_corneal_endothelial_cells_001_with TGF-beta2_rep1
Sample type RNA
Source name primary corneal endothelial cell population
Organism Homo sapiens
Characteristics disease: no corneal pathology associated
Sex: M
age: 72
treatment: TGF-beta2
cell type: primary corneal endothelial cell population
Treatment protocol At confluency, culture medium was switched for OptiMem-I, fetal bovin serum and penicilin/streptomycin supplemented or not with TGF-beta2 for 7 days.
Growth protocol [Isolation protocol] Cells were isolated from mechanically peeled Descemet's membrane using collagenase A (1mg/ml) treatment. They were then seeded in culture dishes for expansion.
Cell populations were expanded in culture medium made of OptiMem-I, 8 % fetal bovine serum, 5 ng/mL human epidermal growth factor, 20 μg/mL ascorbic acid, 0.08 % chondroitin sulfate and a 1X mix of penicilin and streptomycin. Cells were maintained in 37°C and 8% CO2 incubators.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Cat#74104)
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 50-200 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions
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 of passage 3 cells after 7 days post-confluency exposed to TGF-beta2
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.
Supplementary file processed_data.txt forms the basis of conclusions in the manuscript.
Submission date Apr 21, 2021
Last update date Apr 22, 2021
Contact name Stéphanie Proulx
Organization name Université Laval
Street address 1050 Chemin Ste-Foy
City Québec
State/province Qc
ZIP/Postal code G1S4L8
Country Canada
Platform ID GPL13607
Series (1)
GSE172573 TGF-β modulation of cell-cell and cell-extracellular matrix interactions in post-confluent corneal endothelial cells

Data table header descriptions
VALUE gPixNormIQR : The normalized Inter-quartile range of all of the inlier pixels per feature. The range is computed independently in each channel.

Data table
1 1390.3080
2 10.0076
3 8.3396
4 12.6021
5 9.6369
6 11.1195
7 21.3124
8 23.3510
9 10.3782
10 7.4130
11 9.6369
12 22.6097
13 56.1535
14 13.8994
15 11.1195
16 11.1195
17 12.2315
18 10.3782
19 5.3744
20 14.8260

Total number of rows: 62976

Table truncated, full table size 837 Kbytes.

Supplementary file Size Download File type/resource
GSM5258374_SG11400001_252800422291_S001_GE1_107_Sep09_1_2.txt.gz 12.1 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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