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Sample GSM3185834 Query DataSets for GSM3185834
Status Public on Jul 15, 2020
Title GXA_3038
Sample type RNA
Source name patient-derived tumor xenograft
Organism Homo sapiens
Characteristics passage: 9
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 11.04797947
1053_at 8.245603947
117_at 3.271010969
121_at 3.570176204
1255_g_at 2.273193157
1294_at 2.728928707
1316_at 5.678648528
1320_at 2.757732874
1405_i_at 3.329072618
1431_at 2.727505057
1438_at 2.394022215
1487_at 7.921825638
1494_f_at 2.164803336
1552256_a_at 9.857534366
1552257_a_at 9.973901571
1552258_at 2.371721751
1552261_at 2.659104064
1552263_at 4.900064434
1552264_a_at 5.628650551
1552266_at 2.777738152

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.

Supplementary file Size Download File type/resource
GSM3185834_A1762-04.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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