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Sample GSM1595872 Query DataSets for GSM1595872
Status Public on Jan 30, 2015
Title Primary human corneal epithelial cells Collagen type IV rep1
Sample type RNA
Source name Primary human corneal epithelial cells cultivated on Collagen type IV
Organism Homo sapiens
Characteristics tissue: Primary human corneal epithelial cells
gender: Sex unknown
age: 45 years
treatment: cultivated on Collagen type IV
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Toronto, ON) from HCEC isolated from normal eyes supplied by the National Eyes Bank from the CHU de Québec (QC, Canada), and cultivated on BSA, Collagen type I and Collagen tye IV matrix.
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 Jan 29, 2015
Last update date Jan 30, 2015
Contact name Karine Zaniolo
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)
GSE65421 Functional impact of collagens on the activity directed by the promoter of the a5 integrin subunit gene in corneal epithelial cells

Data table header descriptions
VALUE Gmean signal intensity

Data table
1 9.81E+04
2 4.51E+01
3 4.51E+01
4 2.68E+02
5 9.21E+02
6 1.02E+02
7 9.73E+03
8 1.99E+03
9 6.12E+01
10 9.82E+01
11 6.07E+01
12 8.64E+02
13 9.25E+02
14 6.70E+02
15 7.33E+03
16 5.14E+01
17 3.07E+02
18 5.00E+01
19 4.79E+01
20 1.32E+03

Total number of rows: 62976

Table truncated, full table size 911 Kbytes.

Supplementary file Size Download File type/resource
GSM1595872_SG11400001_252800421099_S001_GE1_107_Sep09_2_4.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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