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Sample GSM534496 Query DataSets for GSM534496
Status Public on Jun 01, 2010
Title FHCE1 vs IHCE1 human epididymal cells replicate 2
Sample type RNA
 
Channel 1
Source name FHCE1
Organism Homo sapiens
Characteristics cell line: FHCE1
tissue: epididymis
cell type: SV40 immortalized primary cell line
fertility status: fertile
Growth protocol Cells were grown to confluence on inserts (Corning) in a humified chamber (32°C, 5% CO2).
Extracted molecule total RNA
Extraction protocol Total cellular RNA was isolated using the Illustra RNAspin Mini kit (GE Healthcare, Buckinghamshire, Germany) according to the manufacturer’s instructions. The quality of the total RNA was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies).
Label Cy3
Label protocol Fluorescent cRNA were prepared from 500ng of total RNA using the Agilent Low RNA Input Linear Amplification Kit. As a last step of the extraction procedure, the cRNA was purified with the Rneasy Mini-Kit (Qiagen).
 
Channel 2
Source name IHCE1
Organism Homo sapiens
Characteristics cell line: IHCE1
tissue: epididymis
cell type: SV40 immortalized primary cell line
fertility status: obstructive azoospermic patient
Growth protocol Cells were grown to confluence on inserts (Corning) in a humified chamber (32°C, 5% CO2).
Extracted molecule total RNA
Extraction protocol Total cellular RNA was isolated using the Illustra RNAspin Mini kit (GE Healthcare, Buckinghamshire, Germany) according to the manufacturer’s instructions. The quality of the total RNA was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies).
Label Cy5
Label protocol Fluorescent cRNA were prepared from 500ng of total RNA using the Agilent Low RNA Input Linear Amplification Kit. As a last step of the extraction procedure, the cRNA was purified with the Rneasy Mini-Kit (Qiagen).
 
 
Hybridization protocol 0.75 mg of cRNA were hybridized to the Agilent microarrays (Agilent Human 1A Microarray (V2) G411B) using the Agilent In Situ Hybridization Kit Plus) according to the protocol provided by the manufacturer.
Scan protocol Following hybridization, microarrays were scanned with a ScanArray Express scanner (Perkin Elmer). Fluorescence ratios for array elements were extracted using the ScanArray Express Software (Perkin Elmer) and imported into the GeneSpring 6.1 software (Agilent Technologies) for further analysis.
Description Replicate 2 of 3, IHCE1 vs FHCE1, dye swap
Data processing GeneSpring Software 6.1 (Agilent) was used for analysis following LOWESS normalization. A dye swap was applied to some of the samples (CT1neg-CL1neg and CT2neg-CL2neg).
 
Submission date Apr 19, 2010
Last update date Apr 19, 2010
Contact name Daniel Cyr
E-mail(s) daniel.cyr@iaf.inrs.ca
Phone 514-630-8833
Fax 514-630-8850
Organization name INRS-Institut Armand-Frappier
Street address 245, Boulevard Hymus
City Pointe-Claire
State/province Québec
ZIP/Postal code H9R1G6
Country Canada
 
Platform ID GPL6087
Series (1)
GSE21391 Comparison of gene expression between a human epididymal cell line derived from the caput epididymidis of a fertile patient and another one derived from the caput epididymidis of an obstructive azoospermic patient

Data table header descriptions
ID_REF
VALUE lowess normalized ratio Cy5/Cy3 (IHCE1/FHCE1)

Data table
ID_REF VALUE
A_23_P347643 1.069
A_23_P6025 1.265
A_23_P60243 1.511
A_23_P35277 1.619
A_23_P113070 2.196
A_23_P109193 2.032
A_23_P78112 2.191
A_23_P62136 1.053
A_23_P33247 0.509
A_23_P215269 2.864
A_23_P23173 1.793
A_23_P96445 1.451
A_23_P331028 0.622
A_23_P116057 1.375
A_23_P208029 2.091
A_23_P96809 0.0791
A_23_P251142 0.989
A_23_P254079 2.467
A_23_P47600 0.604
A_23_P215163 2.226

Total number of rows: 20226

Table truncated, full table size 363 Kbytes.




Supplementary file Size Download File type/resource
GSM534496.gpr.gz 1.9 Mb (ftp)(http) GPR
Processed data included within Sample table

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