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Sample GSM1134010 Query DataSets for GSM1134010
Status Public on Nov 13, 2013
Title brain-microglia-S9-1119008 (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: 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 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 2
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 GSM1134004 (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 4.49122
4305147 9.874874
4305425 6.578551
4305730 6.45717
4305790 4.256149
4305808 5.24851
4305936 6.855376
4306126 2.887836
4306193 5.065779
4306220 11.36477
4306323 2.779292
4306467 5.358383
4306475 5.683796
4306482 1.681051
4306490 8.471511
4306955 8.635141
4307112 5.996259
4307259 7.176518
4307291 9.110699
4307433 4.489775

Total number of rows: 23332

Table truncated, full table size 384 Kbytes.

Supplementary file Size Download File type/resource
GSM1134010_19900.CEL.gz 21.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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