|
| 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 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 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) |
