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Sample GSM187662 Query DataSets for GSM187662
Status Public on Feb 03, 2008
Title gubernaculum_orl_GD20_male_left_A
Sample type RNA
 
Source name gubernaculum, LE/orl male fetus at gestational day 20 - fetus A
Organism Rattus norvegicus
Characteristics Strain: LE/orl
Gender: male
Age: Gestational day 20
Tissue: gubernaculum
Side: left
litter:7
fetus:25
Treatment protocol The lower half of a fetus was placed in RNAlater. After storage at 4'C for at least 24 hours, the gubernaculum was dissected and placed in lysis buffer from the RNeasy Mini Kit (Qiagen)
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the RNeasy Mini Kit (Qiagen) and contaminating DNA was removed with the RNAse-free DNase Set (Qiagen), both according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA was prepared as follows. 30 ng total RNA was amplified and labeled with the Affymetrix GeneChip Two-Cycle cDNA Synthesis Kit, according to the manufacturer's instructions.
Performed according to the standard Affymetrix protocol. This was performed at DuPont Haskell Laboratory for Health and Environmental Sciences.
 
Hybridization protocol Hybridization, washing and staining were performed according to the standard Affymetrix protocol with the Affymetrix Hybridization Oven 640 and GeneChip Fluidics Station. This was performed at DuPont Haskell Laboratory for Health and Environmental Sciences.
Scan protocol GeneChips were scanned with the Affymetix GeneArray Scanner. This was performed at DuPont Haskell Laboratory for Health and Environmental Sciences.
Description gubernaculum_orl_GD20_male_left_A
Data processing The GC-RMA algorithm was used within the AffylmGUI package of Bioconductor to calculate log2 expression values. CEL files from all samples from the same tissue in the series were input together.
 
Submission date May 07, 2007
Last update date Feb 03, 2008
Contact name Julia S. Barthold
E-mail(s) [email protected]
Organization name Nemours/AI duPont Hospital for Children
Department Urology
Street address 1600 Rockland Road
City Wilmington
State/province DE
ZIP/Postal code 19803
Country USA
 
Platform ID GPL341
Series (1)
GSE7755 Gene expression in fetal gubernaculum and testis of wildtype (LE/wt) and cryptorchid (LE/orl) rats

Data table header descriptions
ID_REF
VALUE GC-RMA expression value (log2)

Data table
ID_REF VALUE
1367452_at 11.76404421
1367453_at 7.764762571
1367454_at 9.811006109
1367455_at 11.49803702
1367456_at 11.09175796
1367457_at 9.640293363
1367458_at 3.675393117
1367459_at 11.45884146
1367460_at 11.7366989
1367461_at 10.73928867
1367462_at 8.592405429
1367463_at 8.3972227
1367464_at 9.087606557
1367465_at 9.320930092
1367466_at 10.41056919
1367467_at 8.031890398
1367468_at 2.85651318
1367469_at 13.41137259
1367470_at 13.12280815
1367471_at 9.221791927

Total number of rows: 15923

Table truncated, full table size 358 Kbytes.




Supplementary file Size Download File type/resource
GSM187662.CEL.gz 1.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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