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Sample GSM1134008 Query DataSets for GSM1134008
Status Public on Nov 13, 2013
Title bonemarrow-monocyte-S3-1114542 (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: 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 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 1
S3
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 GSM1134014 (gene-level analysis)

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

Data table
ID_REF VALUE
4534760 401.8048096
4348065 9.315781593
4324509 270.5323181
4693172 28.83888054
4385736 28.36365891
4349384 21.94840431
4323614 142.3933868
4379186 53.70019913
4468466 877.1289063
4439838 152.06073
4432757 1406.688232
4325964 31.52113342
4373064 34.02532196
4319591 67.39402771
4456357 24.96950722
5049146 43.60168076
4440162 14.08016682
4360521 555.0966797
4378287 199.7340393
4342474 22.74375916

Total number of rows: 21837

Table truncated, full table size 424 Kbytes.




Supplementary file Size Download File type/resource
GSM1134008_19904.CEL.gz 21.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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