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Sample GSM2200572 Query DataSets for GSM2200572
Status Public on Jun 30, 2017
Title Multi-Focal Atrophic Gastritis_sample16
Sample type RNA
 
Source name MAG_Gastric tissue RNA
Organism Homo sapiens
Characteristics ethnic group: Hispanic
stages of gastritis: Multi-Focal Atrophic Gastritis
tissue: Gastric tissue
Treatment protocol No treatment for patients was done. Six to 8 weeks old mice were infected with H. pylori for 4 to 6 months.
Growth protocol FFPE tissues of individuals with different stages of gastritis were used in this study; 6 week-old wild type and CD44-/- mice were maintained at specific pathogen free conditions.
Extracted molecule total RNA
Extraction protocol Total RNA from formalin-fixed paraffin-embedded (FFPE) tissues was extracted using the RecoverAll Total Nucleic Acid Isolation from Ambion (Austin, TX), in five 10-20µm-thick tissue sections, as recommended by the vendor. The RNA was resuspended in DEPC-water and quantified by NanoDrop (ThermoFisher Scientific, Waltham, MA). Fresh frozen gastric tissues from mice infected with H. pylori was extracted with Qiagen RNeasy kits
Label Cy3,Cy5
Label protocol Streptavidin labeled cDNA was obtained following protocols from Illumina for FFPE samples (Cancer Panel). Streptavidin-labeled cDNA was then ampified using Cy3 and Cy5 labeled primers
 
Hybridization protocol 60°C for 30 mins followed by 16h at 45°C
Scan protocol BeadArray Reader protocol for DASL Gene Expression and MouseWG-6 v2 from Illumina
Description SAMPLE 16
Data processing MAG, IM and Dysplasia gene expression in humans were determined using MAG as reference. For mouse data WT and DMBT1-/- analyses were done in separate using non-infected tissues as reference. For both analyses background was removed using the detection P value algorithm. Normalization was done with the cubic spline algorithm. Differential expression of genes was done using MAG (human) and non-infected (mice) values as reference.
 
Submission date Jun 15, 2016
Last update date Jun 30, 2017
Contact name Jovanny Zabaleta
E-mail(s) jzabal@lsuhsc.edu
Phone 5042102979
Organization name LSUHSC
Department Interdisciplinary Oncology
Street address 1700 Tulane Ave
City New Orleans
State/province LA
ZIP/Postal code 70112
Country USA
 
Platform ID GPL5826
Series (1)
GSE83389 Increased expression of Deleted in Malignant Brain Tumors (DMBT1) gene in advanced precancerous gastric lesions in three ethnic populations: effect of modulation on mouse mucous metaplasia in response to H. pylori infection

Data table header descriptions
ID_REF
VALUE Cubic spline normalized signals
Detection Pval

Data table
ID_REF VALUE Detection Pval
GI_10092618-S-3 680.3 0.89768
GI_10092618-S-1 1385.9 0.75884
GI_10092618-S-2 9619 0
GI_10337586-S-1 1829.8 0.63555
GI_10337586-S-3 2379.7 0.46239
GI_10337586-S-2 754.3 0.88668
GI_10834981-S-2 1522.6 0.7234
GI_10834981-S-1 1299.4 0.77993
GI_10834981-S-6 8763.4 0
GI_10834983-S-2 1349.7 0.7678
GI_10834983-S-4 835.7 0.87365
GI_10834983-S-1 1841.7 0.63197
GI_10835001-S-2 512.8 0.91966
GI_10835001-S-1 8091.1 0
GI_10835001-S-4 769.6 0.88431
GI_10835048-S-5 2945.6 0.29178
GI_10835048-S-6 694.9 0.89557
GI_10835048-S-1 1374.8 0.76161
GI_10835156-S-1 422.7 0.92989
GI_10835156-S-2 6497.5 0.00034

Total number of rows: 1506

Table truncated, full table size 43 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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