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Status |
Public on Jun 30, 2017 |
Title |
Multi-Focal Atrophic Gastritis_sample18 |
Sample type |
RNA |
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Source name |
MAG_Gastric tissue RNA
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Organism |
Homo sapiens |
Characteristics |
ethnic group: Hispanic stages of gastritis: Multi-Focal Atrophic Gastritis tissue: Gastric tissue
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Treatment protocol |
No treatment for patients was done. Six to 8 weeks old mice were infected with H. pylori for 4 to 6 months.
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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.
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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
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Label |
Cy3,Cy5
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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
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Hybridization protocol |
60°C for 30 mins followed by 16h at 45°C
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Scan protocol |
BeadArray Reader protocol for DASL Gene Expression and MouseWG-6 v2 from Illumina
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Description |
SAMPLE 18
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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.
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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 |
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