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Sample GSM1134004 Query DataSets for GSM1134004
Status Public on Nov 13, 2013
Title brain-microglia-S9-1119008 (Aroma)
Sample type RNA
 
Source name brain-microglia
Organism Mus musculus
Characteristics tissue: brain
cell type: microglia
strain: C57BL/6
age: 6 weeks
gender: Male
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 2
S9
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 GSM1134010 (gene-level analysis)

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

Data table
ID_REF VALUE
4534760 201.7702637
4348065 9.921712875
4324509 37.73884583
4693172 35.36335373
4385736 14.75370216
4349384 20.92847443
4323614 205.6872559
4379186 50.72977448
4468466 992.3075562
4439838 258.0995483
4432757 405.4664612
4325964 32.72661591
4373064 31.82095909
4319591 74.44328308
4456357 29.74554062
5049146 44.59889221
4440162 105.2644196
4360521 359.7470703
4378287 305.7360535
4342474 29.45055389

Total number of rows: 21837

Table truncated, full table size 424 Kbytes.




Supplementary file Size Download File type/resource
GSM1134004_19900.CEL.gz 21.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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