|
| Status |
Public on Apr 28, 2015 |
| Title |
TAM population A isolated from EG7 thymoma transplanted in WT recipient rep2 |
| Sample type |
RNA |
| |
|
| Source name |
CD11b+,Ly6C+,MHCII- tumor associated macrophage cells (TAMs) isolated from thymoma arising in WT mouse transplanted with EG7 lymphoma cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: TAM population A isolated from EG7 thymoma transplanted in WT recipient rep2
|
| Treatment protocol |
none
|
| Growth protocol |
none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer's protocol
|
| Label |
biotin
|
| Label protocol |
For samples analyzed on the Affymetrix HT_MG-430_PM array, biotinylated cRNA was prepared from 100 ng of toal RNA according to the standard Affymetrix 3’IVT Express protocol (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix). For samples analyzed on the Affymetrix Mouse Gene 2.0 ST array, sense target cDNA was prepared from 100ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671).
|
| |
|
| Hybridization protocol |
Following fragmentation, 5-6 micrograms of biotin-labeled targets were hybridized for 16 hr at 45C on an array. HT_MG-430_PM GeneChips were washed and stained in the Affymetrix GeneTitan system. Mouse Gene 2.0 ST GeneChips were washed and stained using in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
HT_MG-430_PM plate arrays were scanned using the Affymetrix GeneTitan system. Mouse Gene 2.0 ST GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
|
| Data processing |
Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console Software v1.1. Sample groups TMQ001-TMQ009, TAT101-TAT110, PJM001-PJM016 were summarized independently.
|
| |
|
| Submission date |
Jul 03, 2014 |
| Last update date |
Apr 28, 2015 |
| Contact name |
Geoffrey Neale |
| E-mail(s) |
[email protected]
|
| Organization name |
St Jude Childrens Research Hospital
|
| Department |
Hartwell Center
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL16570 |
| Series (1) |
| GSE59047 |
Regulation of tumor associated macrophages by cooperative inflammatory signaling |
|
