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Sample GSM5008100 Query DataSets for GSM5008100
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.
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 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.
Submission date Jan 06, 2021
Last update date Feb 04, 2021
Contact name Richard Eric Davis
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

Data table header descriptions
VALUE Cy3 fluorescence intensity
L2.Detection Pval

Data table
ID_REF VALUE L2.Detection Pval
ILMN_1250052 40.14617035 0.018162393
ILMN_2599935 673.2514032 0
ILMN_1249762 28.82123797 0.099358974
ILMN_1212991 293.647203 0
ILMN_1217583 39.05490855 0.018162393
ILMN_2728634 38.69434016 0.023504274
ILMN_1232875 28.82123797 0.147435897
ILMN_2736209 97.58624893 0
ILMN_1252690 42.93858755 0.009615385
ILMN_1255743 66.09977968 0
ILMN_2649955 112.9868159 0
ILMN_1257340 582.9830235 0
ILMN_2628708 198.4414418 0
ILMN_2588130 2547.201819 0
ILMN_2705628 204.5396165 0
ILMN_2689731 1332.895046 0
ILMN_2471359 208.6622015 0
ILMN_1234766 3702.664331 0
ILMN_1240451 41.93660149 0.009615385
ILMN_2614655 5144.339215 0

Total number of rows: 20346

Table truncated, full table size 596 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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