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Sample GSM1134015 Query DataSets for GSM1134015
Status Public on Nov 13, 2013
Title brain-microglia-S6-1114545 (Expression Console)
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 10µl 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
Data processing The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were QC’d using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc). Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotations were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).
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
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.full.mps
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 GPL6096
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
Alternative to GSM1134009 (exon-level analysis)

Data table header descriptions
VALUE RMA signal estimates from Expression Console software with Affymetrix default RMA Gene analysis settings

Data table
4305140 3.648585
4305147 9.336941
4305425 6.845023
4305730 6.274148
4305790 4.582264
4305808 4.939207
4305936 4.709421
4306126 2.966626
4306193 5.531433
4306220 11.05397
4306323 3.202452
4306467 6.157089
4306475 4.757411
4306482 1.670533
4306490 8.283634
4306955 8.049084
4307112 5.52859
4307259 7.570439
4307291 9.001152
4307433 2.557513

Total number of rows: 23332

Table truncated, full table size 384 Kbytes.

Supplementary file Size Download File type/resource
GSM1134015_19905.CEL.gz 20.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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