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Sample GSM1134005 Query DataSets for GSM1134005
Status Public on Nov 13, 2013
Title bonemarrow-monocyte-S7-1119009 (Aroma)
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 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 bone marrow monocyte biological replicate 3
S7
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 GSM1134011 (gene-level analysis)

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

Data table
ID_REF VALUE
4534760 420.1878662
4348065 9.626074791
4324509 251.2743988
4693172 29.52140045
4385736 23.5907917
4349384 19.73991013
4323614 172.2244568
4379186 52.97826385
4468466 643.6447754
4439838 129.5002136
4432757 1696.259277
4325964 28.67848778
4373064 35.76066208
4319591 72.94882202
4456357 27.13138199
5049146 55.38551331
4440162 14.93089676
4360521 557.4611206
4378287 207.9715729
4342474 26.12655067

Total number of rows: 21837

Table truncated, full table size 424 Kbytes.




Supplementary file Size Download File type/resource
GSM1134005_19901.CEL.gz 22.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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