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Sample GSM321631 Query DataSets for GSM321631
Status Public on Oct 27, 2008
Title Functionally-regressed Late luteal phase CL, biological rep 4
Sample type RNA
 
Source name Corpus luteum collected between days 14-16 after the midcycle LH surge from animal with serum concentrations of progesterone <0.5 ng/ml at time of CL collection
Organism Macaca mulatta
Characteristics Gender:female, Tissue: Corpus luteum, reproductive state:normal menstrual cyclicity
Biomaterial provider Oregon National Primate Research Center
Treatment protocol Blood samples were collected daily by saphenous venipuncture starting six days after onset of menses. Serum was separated and samples were assayed daily for estradiol concentrations. Following the midcycle estradiol surge, the first day of low serum estradiol (< 100pg/ml) corresponds with the day after the LH surge (LH surge = day 0). On the appropriate day following the midcycle LH surge, the CL was collected during aseptic midline laparotomy, immediately flash frozen in liquid nitrogen, and stored at -80°C until total RNA was extracted.
Extracted molecule total RNA
Extraction protocol Trizol (Invitrogen) extraction of total RNA was performed according to the manufacturer's instructions, and total RNA obtained by Trizol extraction was further purified using RNeasy spin columns (Qiagen) following manufacturer instructions.
Label Biotin
Label protocol Messenger RNA is amplified and labeled from 2 micrograms of total RNA in two steps according to the standard Affymetrix one-cycle cDNA protocol (Expression Analysis Technical Manual Rev.4). 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-UTP (Affymetrix). Following removal of free nucleotides, target yield is measured by UV260 absorbance.
 
Hybridization protocol Labeled target is fragmented at 95C 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 micrograms of target is hybridized for 16 hours at 45C to the GeneChip Rhesus Macaque Genome array (Affymetrix), 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 GeneChips were scanned using the GeneChip Scanner 3000 with the 7G upgrade (Affymetrix) and GCOS version 1.4.0 software (Affymetrix), yielding cell fluorescence intensity (.CEL files). Image inspection was performed manually immediately following each scan.
Description Gene expression data from CL that are undergoing functional regression. Luteolysis (CL death) is subdivided into two steps: 1) a decrease in progesterone secretion (functional regression), and 2) apoptosis and structural remodeling of luteal tissue (structural regression). This stage corresponds to CL in the first stage of luteolysis (functional regression). They have, or are about to, quit producing progesterone, but the tissue has not yet started to degenerate.
Data processing The processed image files (.CEL) were normalized across arrays using the robust multichip average (RMA) algorithm and log-transformed (base 2).After normalization, GeneSifter (VizX Labs) microarray expression analysis software was used to analyze the resultant data.
 
Submission date Sep 16, 2008
Last update date Oct 27, 2008
Contact name Randy Lloyd Bogan
E-mail(s) boganr@ohsu.edu
Phone (503)614-3751
Fax (503)690-5563
Organization name Oregon National Primate Research Center
Department Reproductive Sciences
Lab Hennebold Lab
Street address 505 NW 185th Ave
City Beaverton
State/province OR
ZIP/Postal code 97123
Country USA
 
Platform ID GPL3535
Series (1)
GSE12807 Gene expression data throughout spontaneous functional regression of the rhesus macaque corpus luteum.

Data table header descriptions
ID_REF
VALUE Quantification

Data table
ID_REF VALUE
AFFX-BioB-5_at 7.06493
AFFX-BioB-M_at 7.77661
AFFX-BioB-3_at 7.17565
AFFX-BioC-5_at 8.69291
AFFX-BioC-3_at 9.1121
AFFX-BioDn-5_at 10.1905
AFFX-BioDn-3_at 11.3925
AFFX-CreX-5_at 12.6656
AFFX-CreX-3_at 12.6537
AFFX-DapX-5_at 2.98507
AFFX-DapX-M_at 3.1753
AFFX-DapX-3_at 2.97442
AFFX-LysX-5_at 2.91633
AFFX-LysX-M_at 3.14615
AFFX-LysX-3_at 2.86049
AFFX-PheX-5_at 3.06323
AFFX-PheX-M_at 2.89133
AFFX-PheX-3_at 4.26105
AFFX-ThrX-5_at 3.24428
AFFX-ThrX-M_at 3.08914

Total number of rows: 52865

Table truncated, full table size 1518 Kbytes.




Supplementary file Size Download File type/resource
GSM321631.CEL.gz 4.4 Mb (ftp)(http) CEL
GSM321631.CHP.gz 358.0 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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