|
| Status |
Public on Nov 13, 2013 |
| Title |
brain-microglia-S9-1119008 (Expression Console) |
| Sample type |
RNA |
| |
|
| Source name |
brain-microglia
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain
cell type: microglia
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 |
brain microglia biological replicate 2
S9
|
| 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 |
|
| Relations |
| Alternative to |
GSM1134004 (exon-level analysis) |
