|
Status |
Public on Feb 04, 2021 |
Title |
L2 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.
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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).
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|
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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 2
|
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.
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|
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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 |
|