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Sample GSM238496 Query DataSets for GSM238496
Status Public on Oct 19, 2007
Title ERbKO mouse aorta with placebo, biological rep3
Sample type RNA
 
Source name 2.5-4.5 month old ovarioectomized female mouse
Organism Mus musculus
Characteristics Strain: C57BL/6
Extracted molecule total RNA
Extraction protocol Total aortic RNA was isolated by homogenization in RNA STAT-60 (Tel-Test, Inc., Friendswood, TX) and purification by chloroform extraction, with a yield of approximately 6 ug total RNA per aorta. Quantity and quality of each samples was measured at the spectrophotometer (OD 260, 280, 260/280) and RNA integrity checked with the use of a Bioanalyzer (18s and 28s peaks) confirming good quality of the samples (Agilent 2100 Bioanalyzer, Agilent Technologies, Palo Alto, CA).
Label biotin
Label protocol Total RNA (5 ug; a separate aortic sample per microarray) was used for labeling (One-Cycle Eukaryotic Target Labeling Assay (Affymetrix P/N900493, Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions. Total RNA was reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
 
Hybridization protocol Unamplified, labeled cRNA (15 ug) was hybridized to whole mouse genome 430 2.0 microarrays(Affymetrix) according to the manufacturer's instructions. Affymetrix GeneChip® Operating Software (GCOS) was used for the control of GeneChip® Fluidics Stations for automated washing, staining, and scanning.
Scan protocol Affymetrix GeneChip® Operating Software (GCOS) was used for the control of GeneChip® Scanners were used for scanning and data acquisition, according to the manufacturer's instructions.
Description Gene expression data from ovarioectomized mouse aortae treated with estrogen or placebo.
Data processing The gene expression values for each probe set were first estimated from the hybridization intensities using the corrected for GC content Robust Multichip Analysis (GCRMA) method as implemented in Bioconductor (61–63). Gene expression values for each sample were estimated using the linear model of the data as implemented by the LIMMA package in BioConductor (63). The differences in log (base 2) expression levels were evaluated by the t test as implemented by the LIMMA package in BioConductor by comparing distribution of expression values between different sample categories.
 
Submission date Oct 18, 2007
Last update date Aug 28, 2018
Contact name Ulla Hansen
E-mail(s) uhansen@bu.edu
Organization name Boston University
Department Biology
Lab Hansen Lab
Street address 5 Cummington St
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL1261
Series (1)
GSE9371 Estrogen receptors alpha and beta mediation of gene expression in mouse vascular tissue
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE GCRMA-calculated signal intensity, log2 transformed.

Data table
ID_REF VALUE
1415670_at 8.44419344
1415671_at 9.563571649
1415672_at 9.755743626
1415673_at 6.988985944
1415674_a_at 7.449854424
1415675_at 7.606570806
1415676_a_at 10.21693196
1415677_at 9.157303178
1415678_at 8.92195036
1415679_at 9.693039929
1415680_at 7.681113049
1415681_at 7.539136086
1415682_at 5.532847573
1415683_at 8.357779454
1415684_at 6.822821861
1415685_at 8.054270889
1415686_at 8.679488951
1415687_a_at 12.01475935
1415688_at 8.670881417
1415689_s_at 6.731865758

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM238496.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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