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Sample GSM308520 Query DataSets for GSM308520
Status Public on Jan 26, 2009
Title corpusluteum_A+LH+TRL+R5020_Rep3
Sample type RNA
 
Source name Day 12 corpus luteum, Anide + LH + TRL + R5020 treated
Organism Macaca mulatta
Characteristics Female, Antide + LH + TRL + R5020 treated days 9-11 of luteal phase, CL collected day 12
Treatment protocol See 'Young KA, Stouffer RL. Gonadotropin and steroid regulation of matrix metalloproteinases and their endogenous tissue inhibitors in the developed corpus luteum of the rhesus monkey during the menstrual cycle. Biol Reprod. 2004 Jan;70(1):244-52 (PMID: 13679308)'
Extracted molecule total RNA
Extraction protocol Invitrogen TRIzol Plus RNA Purification Kit
Label biotin
Label protocol Messenger RNA is amplified and labeled from 2 ug of total RNA in two steps. In the first step, mRNA is converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix). In the second step, amplified and labeled cRNA (the target) is produced in an in vitro transcription reaction using T7 RNA polymerase and biotin-CTP (Affymetrix.). Following removal of free nucleotides, target yield is measured by UV260 absorbance.
 
Hybridization protocol Labeled target is fragmented at 95o C in the presence of high magnesium concentration. The fragmented material is combined with biotinylated hybridization control oligomer and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer. Ten ug of target is hybridized with the GeneChip Rhesus Macaque Genome array (Affymetrix) overnight, followed by washing, staining with streptavidin-phycoerythrin (Molecular Probes), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs), and a final staining step on the Fluidics Station 450 (Affymetrix).
Scan protocol The distribution of fluorescent material on the processed array is determined using the Affymetrix 3000 GeneArray laser scanner with the 7G upgrade. Image inspection is performed manually immediately following each scan. All array scanning and data processing on the Affymetrix system is performed with GeneChip Operating System (GCOS) software.
Description Treated
Data processing The probe-level Cel file is processed with Affymetrix Microarray Suite, version 5.0 (MAS 5.0) software. The GeneChip expression arrays contain control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, CreX and species-specific actin and GAPDH). Following image processing and absolute analysis of the array pattern with MAS, six values are examined to assess overall assay performance: background, noise, average Signal, % Present, ratio of Signal values for probe sets representing the 5' and 3' ends of actin and GAPDH transcripts, and total Signal for probe sets for BioB, BioC, BioD and CreX. Assays demonstrating poor or marginal performance are flagged. Using MAS 5.0, array data is globally scaled to auniform, average target intensity for all assays prior to further analysis.
 
Submission date Jul 29, 2008
Last update date Jan 26, 2009
Contact name Cecily Vauna Bishop
E-mail(s) bishopc@ohsu.edu
Organization name Oregon National Primate Research Center
Department Division of Reproductive & Developmental Sciences
Street address 505 NW 185th Ave
City Beaverton
State/province OR
ZIP/Postal code 97006
Country USA
 
Platform ID GPL3535
Series (1)
GSE12281 The effects of LH ablation/replacement versus steroid ablation/replacement on gene expression in primate corpora lutea

Data table header descriptions
ID_REF
VALUE Calculated signal intensity (MAS 5.0)
ABS_CALL Call in an absolute analysis that indicates if the signal was present (P), absent (A), or marginal (M)
DETECTION P-VALUE p-value of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 39.5595 P 0.00933744
AFFX-BioB-M_at 105.895 P 0.000126798
AFFX-BioB-3_at 44.253 P 0.000445901
AFFX-BioC-5_at 202.223 P 7.00668e-05
AFFX-BioC-3_at 183.152 P 6.02111e-05
AFFX-BioDn-5_at 346.355 P 4.42873e-05
AFFX-BioDn-3_at 820.183 P 7.00668e-05
AFFX-CreX-5_at 2803.05 P 4.42873e-05
AFFX-CreX-3_at 3045.89 P 4.42873e-05
AFFX-DapX-5_at 7.58915 A 0.116113
AFFX-DapX-M_at 6.41174 A 0.749204
AFFX-DapX-3_at 0.690455 A 0.979978
AFFX-LysX-5_at 0.9297 A 0.794268
AFFX-LysX-M_at 1.03328 A 0.916408
AFFX-LysX-3_at 9.2137 P 0.0239288
AFFX-PheX-5_at 11.5468 A 0.165861
AFFX-PheX-M_at 1.66856 A 0.921998
AFFX-PheX-3_at 2.11613 A 0.916408
AFFX-ThrX-5_at 3.27691 A 0.749204
AFFX-ThrX-M_at 8.42488 A 0.102165

Total number of rows: 52865

Table truncated, full table size 2128 Kbytes.




Supplementary file Size Download File type/resource
GSM308520.CEL.gz 4.6 Mb (ftp)(http) CEL
GSM308520.CHP.gz 300.8 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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