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Sample GSM252021 Query DataSets for GSM252021
Status Public on Dec 16, 2008
Title apoE-lesion-78-weeks-3
Sample type RNA
 
Source name atherosclerotic lesion of abdominal aorta
Organism Mus musculus
Characteristics strain: B6.129P2-Apoe<tm1Unc>/J
tissue: atherosclerotic lesion of abdominal aorta
gender: male
age: 78 weeks
Treatment protocol The abdominal aorta was exposed, perfused in situ with ice-cold PBS/2mM EDTA and was removed inclusive of paraaortal lymph nodes, adipose and connective tissue. The isolated abdominal aorta was cut in half and embedded in Tissue Tec (Sakura Finetek, Zoeterwoude, NL) and was frozen at -80 centigrade. 200 unstained 10 micrometer cryo-sections of aorta abdominalis were microdissected with a Palm MicroBeam laser system (P.A.L.M. Microlaser Technologies AG, Bernried, Germany) and pooled in Trizol (Invitrogen, Carlsbad, CA).
Growth protocol ApoE-/- and wild-type mice on the C57BL/6J background were from The Jackson Laboratories (Bar Harbor, Maine). Mice were housed in SPF conditions with standard chow diet and were euthanized by carbon dioxide inhalation.
Extracted molecule total RNA
Extraction protocol RNA was extracted using a phenol/chloroform extraction according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Micro-kit (Qiagen, Hilden, Germany).
Label Biotin/SAPE with Anti Streptavidin signal amplification
Label protocol T7-High-Yield-RNA-Transcript-Labeling-Kit (Enzo, Farmingdale, NY) with an IVT of 68h
 
Hybridization protocol 60rpm, 18h, 45 centigrade in Affymetrix Hybridization Buffer
Scan protocol Affymetrix Scanner 3000, single scan
Description Staining with Fluidic Station 450 Protocol: Midi-euk2v3_450
Data processing GCOS 1.4, scaled to 500
 
Submission date Dec 19, 2007
Last update date Nov 03, 2011
Contact name Andreas Johann Richard Habenicht
E-mail(s) Andreas.habenicht@med.uni-muenchen.de
Organization name Ludwig Maximilians Universität München
Department Medicine
Lab Institute for Cardiovascular Disease Prevention
Street address Pettenkoferstraße 9a
City Munich
State/province Bavaria
ZIP/Postal code 80336
Country Germany
 
Platform ID GPL8321
Series (3)
GSE10000 Age-dependent aorta transcriptomes in wild-type and apoE-deficient C57BL/6J mice
GSE21419 Laser Capture Microdissection of Hyperlipidemic Mouse Aorta Atherosclerosis
GSE40156 Transcript atlases reveal that artery tertiary lymphoid organs but not secondary lymphoid organs control key steps of atherosclerosis T cell immunity in aged apoe-/- mice.

Data table header descriptions
ID_REF
VALUE Signal value scaled to 500 by GCOS
ABS_CALL Call by default alpha
DETECTION P-VALUE Detection p-value as calculated by GCOS

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 1179.9 P 0.00006
AFFX-BioB-M_at 1968.8 P 0.000044
AFFX-BioB-3_at 1199.3 P 0.000044
AFFX-BioC-5_at 3416 P 0.000052
AFFX-BioC-3_at 4020.6 P 0.000044
AFFX-BioDn-5_at 6272.3 P 0.000044
AFFX-BioDn-3_at 11847.4 P 0.000044
AFFX-CreX-5_at 30430.4 P 0.00006
AFFX-CreX-3_at 29318.5 P 0.000044
AFFX-DapX-5_at 765.1 P 0.00006
AFFX-DapX-M_at 1187.3 P 0.00011
AFFX-DapX-3_at 1466.8 P 0.000052
AFFX-LysX-5_at 89 P 0.00007
AFFX-LysX-M_at 122.4 A 0.108979
AFFX-LysX-3_at 324.8 P 0.000225
AFFX-PheX-5_at 146.2 P 0.000169
AFFX-PheX-M_at 173.7 P 0.000754
AFFX-PheX-3_at 174.4 P 0.00039
AFFX-ThrX-5_at 125.1 P 0.004484
AFFX-ThrX-M_at 285.9 P 0.00007

Total number of rows: 22690

Table truncated, full table size 618 Kbytes.




Supplementary file Size Download File type/resource
GSM252021.CEL.gz 1.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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