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Sample GSM1134009 Query DataSets for GSM1134009
Status Public on Nov 13, 2013
Title brain-microglia-S6-1114545 (Aroma)
Sample type RNA
 
Source name brain-microglia
Organism Mus musculus
Characteristics tissue: brain
cell type: microglia
strain: C57BL/6
age: 6 weeks
gender: Female
Treatment protocol Tissue was dissociated, enriched by Percoll gradient, and cells were flow sorted.
Growth protocol not applicable
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from snap-frozen sorted cell pellets using TRIzol-chloroform extraction, resuspended in 10┬Ál Ambion Nuclease-free water (Life Technologies).
Label biotin
Label protocol Biotinylated cDNA were prepared according to the standard NuGen WT-Ovation Pico RNA Amplification system from 500pg-50 ng total RNA
 
Hybridization protocol Following fragmentation with NuGen Encore Biotin Module,5.0 ug of cDNA were hybridized into the GeneChip Hybridization Oven 640 for 18 hr at 45C on Exon 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip 7G 3000 Scanner
Description brain microglia biological replicate 1
S6
Data processing Data processed with RMA and quantile normalized using BioC aroma.affymetrix.
We used the Partek workflow as well as Aroma to analyze the Affymetrix Mouse Exon 1.0ST array to generate the DE gene list.
probe group file: MoEx-1_0-st-v1.r2.pgf
 
Submission date May 07, 2013
Last update date Nov 14, 2013
Contact name Winnie W Pong
Organization name Washington University School of Medicine
Department Department of Neurology
Lab David H Gutmann Laboratory
Street address 660 S. Euclid Avenue
City St Louis
State/province MO
ZIP/Postal code 63110
Country USA
 
Platform ID GPL6193
Series (2)
GSE46686 F11R is a novel monocyte prognostic biomarker for malignant glioma [Affymetrix]
GSE46690 F11R is a novel monocyte prognostic biomarker for malignant glioma
Relations
Alternative to GSM1134015 (gene-level analysis)

Data table header descriptions
ID_REF
VALUE Quantile normalized RMA signal estimates from Aroma

Data table
ID_REF VALUE
4534760 173.7068634
4348065 14.12924099
4324509 32.92024231
4693172 42.39063644
4385736 17.91331482
4349384 22.13824844
4323614 171.2226715
4379186 42.85206223
4468466 1189.668091
4439838 222.968399
4432757 461.8397217
4325964 46.10974121
4373064 40.76066971
4319591 99.91184235
4456357 32.29790497
5049146 67.01464081
4440162 122.2294159
4360521 320.8475037
4378287 279.2068481
4342474 35.66692734

Total number of rows: 21837

Table truncated, full table size 424 Kbytes.




Supplementary file Size Download File type/resource
GSM1134009_19905.CEL.gz 20.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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