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Sample GSM980750 Query DataSets for GSM980750
Status Public on Oct 30, 2013
Title apoE-RLN-78-weeks-1
Sample type RNA
 
Source name Lymph node renal
Organism Mus musculus
Characteristics tissue: Lymph node renal
strain: B6.129P2-Apoe<tm1Unc>/J
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 the associated renal lymph node were microdissected with a Palm MicroBeam laser system (P.A.L.M. Microlaser Technologies AG, Bernried, Germany) and pooled in Trizol (Invitrogen, Carlsbad, CA)(according to published procedures: Laser-Capture Microdissection of Hyperlipidemic/ApoE-/- Mouse Aorta Atherosclerosis. Methods Mol Biol. 2011;755:417-28).
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 structions. 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 Aug 06, 2012
Last update date Oct 31, 2013
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 (1)
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 1778.7 P 0.000052
AFFX-BioB-M_at 3136.6 P 0.000044
AFFX-BioB-3_at 1863.2 P 0.000044
AFFX-BioC-5_at 5707.4 P 0.000052
AFFX-BioC-3_at 6184.6 P 0.000044
AFFX-BioDn-5_at 10346.6 P 0.000044
AFFX-BioDn-3_at 17110.1 P 0.000044
AFFX-CreX-5_at 43811.5 P 0.000052
AFFX-CreX-3_at 46008.1 P 0.000044
AFFX-DapX-5_at 1714.3 P 0.00007
AFFX-DapX-M_at 2686.1 P 0.000095
AFFX-DapX-3_at 3345.1 P 0.000044
AFFX-LysX-5_at 218.4 P 0.000195
AFFX-LysX-M_at 324.8 P 0.010317
AFFX-LysX-3_at 855.3 P 0.00011
AFFX-PheX-5_at 290 P 0.000044
AFFX-PheX-M_at 451.9 P 0.000509
AFFX-PheX-3_at 421.3 P 0.000147
AFFX-ThrX-5_at 416.2 P 0.002023
AFFX-ThrX-M_at 593.7 P 0.000044

Total number of rows: 22690

Table truncated, full table size 620 Kbytes.




Supplementary file Size Download File type/resource
GSM980750_apoE_RLN_78_weeks_1.CEL.gz 1.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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