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Sample GSM1134011 Query DataSets for GSM1134011
Status Public on Nov 13, 2013
Title bonemarrow-monocyte-S7-1119009 (Expression Console)
Sample type RNA
Source name bonemarrow-monocyte
Organism Mus musculus
Characteristics tissue: bone marrow
cell type: monocyte
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 bone marrow monocyte biological replicate 3
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 GSM1134005 (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 4.54345
4305147 9.987137
4305425 6.784979
4305730 5.968719
4305790 3.948895
4305808 3.558566
4305936 5.625583
4306126 3.36264
4306193 5.249366
4306220 11.58393
4306323 2.737086
4306467 5.558679
4306475 5.014247
4306482 1.63174
4306490 8.712133
4306955 9.173843
4307112 5.514147
4307259 7.473892
4307291 9.17651
4307433 4.170414

Total number of rows: 23332

Table truncated, full table size 384 Kbytes.

Supplementary file Size Download File type/resource
GSM1134011_19901.CEL.gz 22.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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