|
| Status |
Public on Feb 04, 2021 |
| Title |
L1 Large tumor |
| Sample type |
RNA |
| |
|
| Source name |
B16 melanoma
|
| Organism |
Mus musculus |
| Characteristics |
cell line: B16 cell line
strain: C57BL/6
tumor size: large (70-80 mm2)
|
| Treatment protocol |
After 8 days, mice developed tumors that were either small (10-20 mm2) or large (70-80 mm2). Tumors were excised and dissected free of surrounding normal tissue.
|
| Growth protocol |
C57BL/6 mice were inoculated with 400,000 cells of the syngeneic B16 melanoma cell line.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of dissected tumors was extracted using the RNAqueous kit (Ambion). The RNA quality was checked by using a Bioanalyzer 2100 instrument (Agilent).
|
| Label |
biotin
|
| Label protocol |
100 nanograms of total RNA was amplified and biotin-labeled through a two-round Eberwine procedure using MessageAmp II and Illumina TotalPrep RNA amplification kits (Ambion).
|
| |
|
| Hybridization protocol |
Amplified cRNA was hybridized to Illumina mouse WG-6 version 2.0 mouse whole-genome arrays.
|
| Scan protocol |
As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.
|
| Description |
replicate 1
|
| Data processing |
The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value. After this, the only probe results that are kept for the normalized matrix are those in which the detection p value is <0.05, in at least 25% of the samples.
|
| |
|
| Submission date |
Jan 06, 2021 |
| Last update date |
Feb 04, 2021 |
| Contact name |
Richard Eric Davis |
| E-mail(s) |
redavis1@mdanderson.org
|
| Phone |
4437456831
|
| Organization name |
MD Anderson Cancer Center
|
| Street address |
7455 Fannin Street
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL6887 |
| Series (1) |
| GSE164357 |
Interleukin-1α mediates innate and acquired resistance to immunotherapy in melanoma |
|
