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Sample GSM1134013 Query DataSets for GSM1134013
Status Public on Nov 13, 2013
Title bonemarrow-monocyte-S8-1119011 (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 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 GSM1134007 (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 3.837238
4305147 10.00764
4305425 7.011052
4305730 6.615027
4305790 5.012107
4305808 4.762583
4305936 6.534524
4306126 3.837952
4306193 5.527889
4306220 11.44353
4306323 3.513202
4306467 4.907793
4306475 5.356017
4306482 2.849809
4306490 9.035412
4306955 9.222145
4307112 5.67762
4307259 7.032486
4307291 8.946664
4307433 4.297991

Total number of rows: 23332

Table truncated, full table size 384 Kbytes.

Supplementary file Size Download File type/resource
GSM1134013_19903.CEL.gz 21.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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