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Sample GSM3185826 Query DataSets for GSM3185826
Status Public on Jul 15, 2020
Title GXA_3011
Sample type RNA
Source name patient-derived tumor xenograft
Organism Homo sapiens
Characteristics passage: 3;6N4
Growth protocol PDX were passaged from mouse to mouse until RNA extraction
Extracted molecule total RNA
Extraction protocol RNA were extracted from four pieces of snap frozen tumor xenografts from four individual xenografts of the same tumors in the same or different passages using the mirVana kit (Ambion) according to the manufacturer’s instructions. A DNAse digest was performed. Each RNA preparation was subjected to quality control using NanoDrop 2000 to control for purity and Bioanalyzer (Agilent) to control for RNA integrity. Only the RNA samples with an integrity number (RIN) between 6.5 and 10 and a ratio between 28s and 18 sRNA between 1.0 and 2.0, and the RNA was pure (260/280 nm and 260/230 nm close to 2.0), were used for the microarray analysis.
Label biotin
Label protocol standard Affymetrix protocol
Hybridization protocol standard Affymetrix protocol
Scan protocol standard Affymetrix protocol
Data processing All analyses were carried out using the “R” statistical computing environment and associated modules from Biobase (affy, simpleaffy, affyPLM). Gene expression signal values were extracted directly from the CEL files using robust multiarray average analysis algorithm (‘gcrma’ R package from Bioconductor; justGCRMA function with default parameters)
Submission date Jun 11, 2018
Last update date Jul 15, 2020
Contact name Vincent Vuaroqueaux
Organization name 4HF Biotec
Department Bioinformatics
Street address Am Flughafen 14
City Freiburg
ZIP/Postal code 79108
Country Germany
Platform ID GPL570
Series (2)
GSE115637 Expression data from 27 Asian gastric patient-derived xenograft (PDX) models
GSE115755 Establishment of patient-derived tumor xenografts from Asian gastric adenocarcinoma is characterized by clonal selection and bias in molecular subtypes

Data table header descriptions
VALUE log2 GC-RMA signal

Data table
1007_s_at 10.20550489
1053_at 9.337451005
117_at 3.076628056
121_at 4.764391542
1255_g_at 2.310294121
1294_at 2.776766152
1316_at 5.818387259
1320_at 2.863806953
1405_i_at 5.428692173
1431_at 3.460658143
1438_at 2.879269886
1487_at 7.864768275
1494_f_at 2.208297923
1552256_a_at 7.5846308
1552257_a_at 9.742741999
1552258_at 2.473074974
1552261_at 2.726026969
1552263_at 7.251209694
1552264_a_at 7.804496917
1552266_at 2.871259864

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.

Supplementary file Size Download File type/resource
GSM3185826_AFG1125-4.CEL.gz 5.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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