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Sample GSM289424 Query DataSets for GSM289424
Status Public on May 20, 2008
Title small_follicle_granulosa_cell_rep2
Sample type RNA
 
Source name granulosa cells of small follicles (< or = 5 mm)
Organism Bos taurus
Characteristics granulosa cells of small follicles (< or = 5 mm) from follicular stage ovaries of young nonpregnant cycling heifers
granulosa cells were isolated by dissection (i.e. scraped and flushed) from the fresh tissue as previously described (Skinner and Osteen, 1988). Cell preparations have been characterized cytochemically to be greater that 98% pure and contain less than 1% contamination with endothelial cells.
Treatment protocol Bovine ovaries were obtained from of young nonpregnant cycling heifers less then 10 min after death. Ovaries were delivered fresh on ice to laboratory. Only follicular stage ovaries were used as assessed by morphological criteria that include the absence of a corpus luteum and the presence of developing large antral follicles.
Extracted molecule total RNA
Extraction protocol Cells from 20-40 follicles of the same size were pooled to make each RNA sample. RNA was extracted using the Trizol reagent according to manufacturers instructions (Sigma, St. Louis, MO).
Label biotin
Label protocol standard Affymetrix procedures
 
Hybridization protocol standard Affymetrix procedure
Scan protocol standard Affymetrix procedure
Description RNA from theca cell of small follicles
Data processing Auto-scale ON (1-1000). Scaling = all probe sets, Target Signal 125. The microarray chip image data were converted to numerical data with GeneChip Operating Software (Affymetrix) using MAS-5 preprocessing algorithm.
The absolute analysis from MAS was imported into GeneSpring 7.3 software (Silicon Genetics, Redwood City, CA). The developing follicle data were normalized within GeneSpring using the default/recommended normalization methods. These include setting of signal values below 0.01-0.01, total chip normalization to the 50th percentile, and normalization of each gene to the median.
 
Submission date May 19, 2008
Last update date May 19, 2008
Contact name Michael K Skinner
E-mail(s) skinner@mail.wsu.edu
Organization name WSU
Department SBS
Street address Abelson 507
City Pullman
State/province WA
ZIP/Postal code 99163
Country USA
 
Platform ID GPL2112
Series (1)
GSE11495 Regulation of granulosa and theca cell transcriptomes during ovarian antral follicle development.

Data table header descriptions
ID_REF Affymetrix Probe set ID
DETECTION P-VALUE t-test p-value
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
VALUE GCOS-calculated signal intensities, target signal 125.

Data table
ID_REF DETECTION P-VALUE ABS_CALL VALUE
AFFX-BioB-3_at 0.98408204 P 137.7
AFFX-BioB-5_at 0.9591388 P 153.1
AFFX-BioB-M_at 0.91740316 P 180.4
AFFX-BioC-3_at 0.8683582 P 586.5
AFFX-BioC-5_at 0.8126075 P 438.4
AFFX-BioDn-3_at 0.53691024 P 1911.3
AFFX-BioDn-5_at 0.986705 P 930.1
AFFX-Bt-A00196-1_s_at 0.60461175 A 13.7
AFFX-Bt-AB076373-1_at 0.89477587 A 9.7
AFFX-Bt-actin-3_at 0.085846454 P 744.9
AFFX-Bt-actin-5_at 0.05776253 P 187.6
AFFX-Bt-actin-M_at 0.04068733 P 341.7
AFFX-Bt-AF292559-1_at 0.43105605 A 1.1
AFFX-Bt-AF292559-2_s_at 0.7717568 A 7.3
AFFX-Bt-AF292559-3_s_at 0.52374893 A 3.8
AFFX-Bt-AF292559-4_s_at 0.40594748 A 0.6
AFFX-Bt-AF292560-1_s_at 0.39119303 A 0.4
AFFX-Bt-AF298789-1_at 0.48106375 A 2.6
AFFX-Bt-AF323980-1_at 0.39913842 A 0.5
AFFX-Bt-AJ002682-1_s_at 0.42680752 A 1

Total number of rows: 24128

Table truncated, full table size 805 Kbytes.




Supplementary file Size Download File type/resource
GSM289424.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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