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Sample GSM510057 Query DataSets for GSM510057
Status Public on Jun 13, 2010
Title P4_Ovary_LIF_biological rep1_9GF
Sample type RNA
 
Source name P4 Ovary incubated in the presence of 50 ng/ml LIF for 48 hours
Organism Rattus norvegicus
Characteristics strain: Sprague-Dawley
gender: Female
tissue: ovary
developmental stage: day P4 incubated for 2 more days
treatment group: 50 ng/ml LIF for 48 hours
Treatment protocol For each ovary sample from which RNA was collected for microarrays, 2-3 ovaries per well were cultured with media changes every 24 hours for two days in the absence (controls) or presence (treated) of either Amh (human Anti-Mülerian hormone)(50ng/mL, R&D Systems Inc., USA), Fgf2 (rat Fibroblast growth factor 2)(50ng/mL, R&D Systems Inc., USA), Bmp4 (human Bone morphogenetic protein 4)(50ng/mL, R&D Systems Inc., USA), Gdnf (rat Glial derived neurotrophic factor)(50ng/mL, Calbiochem, USA), Fgf7 (human fibroblast growth factor 7/keratinocyte growth factor)(50ng/mL, R&D Systems Inc., USA), Kitlg (mouse Kit ligand)(50ng/mL, R&D Systems Inc., USA), Lif (rat leukemia inhibitory factor)(50ng/mL, Chemicon/Millipore, USA), Pdgf-ab (rat platelet derived growth factor AB heterodimer)(50ng/mL, R&D Systems Inc., USA), Tgfb1 (human transforming growth factor beta 1)(50ng/mL, R&D Systems Inc., USA). Two or three ovaries from the same culture well (from different rat pups out of the same litter) and receiving the same treatment were pooled and homogenized together. On any given day a culture experiment was performed, the treatment groups included untreated control ovaries and one to three different growth factor treatments.
Growth protocol Four-day old female Sprague-Dawley rats (Harlan Laboratories, Inc., USA) were euthanized according to Washington State University IACUC approved protocols and the ovaries removed and cultured whole as described previously [Dole, G., et al., 2008].
Extracted molecule total RNA
Extraction protocol RNA was isolated from whole rat ovaries (2-3 ovaries per each sample) after homogenization in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to manufacturer’s instructions.
Label biotin
Label protocol Biotin-labeled ssDNA were prepared according to the standard Affymetrix protocol from at least 300 ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, 2005-2209, Affymetrix).
 
Hybridization protocol Following fragmentation, ssDNA were hybridized on Affymetrix Rat Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 4500.
Scan protocol GeneChips were scanned using Affymetrix GeneChip® Scanner 3000.
Description Gene expression data from rat P4 Ovary incubated in the presence of 50 ng/ml LIF for 48 hours
Data processing The data were analyzed with Partek Genomic Suite 6.5 beta software (Partek Inc., St. Louis, MO) using RMA, GC-content adjusted algorithm background correction, quantile normalization, median polish methos for probesets summarization, and log values of probes signals using base 2. These VALUES were then unlogged for network analysis; the unlogged data are retained in the PRE-VALUE column below.
 
Submission date Feb 16, 2010
Last update date Feb 16, 2010
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 GPL6247
Series (1)
GSE20324 Gene Bionetwork Analysis of Ovarian Primordial Follicle Development

Data table header descriptions
ID_REF
VALUE log2 GC-RMA normalized signal intensity
PRE_VALUE RMA, GC-content adjusted algorithm pre-processed un-logged signal values

Data table
ID_REF VALUE PRE_VALUE
10701620 5.2555 38.2
10701630 4.4919 22.5
10701632 3.8580 14.5
10701636 4.2928 19.6
10701643 4.8074 28
10701648 5.2211 37.3
10701654 7.6767 204.6
10701663 6.5804 95.7
10701666 5.0400 32.9
10701668 7.0596 133.4
10701671 4.7918 27.7
10701674 5.6177 49.1
10701679 6.7170 105.2
10701684 5.8875 59.2
10701689 8.1064 275.6
10701691 4.7761 27.4
10701697 5.7142 52.5
10701699 7.2075 147.8
10701709 9.6545 805.9
10701714 4.6323 24.8

Total number of rows: 27342

Table truncated, full table size 570 Kbytes.




Supplementary file Size Download File type/resource
GSM510057.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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