|
| Status |
Public on Mar 23, 2012 |
| Title |
EoE patient #4_before treatment |
| Sample type |
RNA |
| |
|
| Source name |
EoE patient_before treatment
|
| Organism |
Homo sapiens |
| Characteristics |
age range: Pediatric patient
clinical procedure: Biopsy
disease status: Before glucocorticoid steroid treatment
tissue: epithelium
histology procedure: Formalin-fixed paraffin-embedded
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue sections (10mm) were cut and mounted onto plain glass slides. If the biopsy section contained only epithelium, the sections were scraped from the slides and RNA was extracted using the RecoverAll Total Nucleic Acid Extraction kit for FFPE tissues (Ambion). If biopsy sections contained sub-epithelium, the sections were deparaffinized, stained, dehydrated through graded alcohols using the Paradise FFPE reagent System (Applied Biosystems, Foster City, CA) and subjected to LCM within 2 hr of deparaffinization. About 20000 epithelial cells were captured on LCM Macro CapSure caps (Applied Biosystems) using the Arcturus XT LCM instrument (Applied Biosystems). Total RNA was extracted from the caps also using the RecoverAll kit as above, and subjected to analysis by the Agilent Bioanalyzer using an RNA 6000 Nano or Pico LabChip (Agilent Technologies)
|
| Label |
biotin
|
| Label protocol |
Fifty nanograms of total RNA was amplified and transcribed into cDNA using the Ovation FFPE WTA system (Nugen Technologies, San Carlos, CA). Five to ten micrograms of amplified cDNA from the amplification above was fragmented and labeled for Affymetrix array analysis using the Encore Biotin Module (Nugen Technologies).
|
| |
|
| Hybridization protocol |
Hybridized for 17 hr at 45C and 60 rpm in an Affymetrix Hybridization Oven to Affymetrix Gene ST 1.0 Arrays. GeneChips were washed and stained using the Affymetrix Fluidics Station 450 and fluidics protocol FS450_0007.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
|
| Description |
Fresh bipspies were fixed right away and porcessed within the same day.
EE-4B
|
| Data processing |
The data were analyzed with Affymetrix Command Console and Expression Console using Affymetrix default analysis settings and global scaling as normalization method. Differential gene expression was analysed using Partek Genomics Suite software version 6.6 beta using RMA analysis mode and default settings.
|
| |
|
| Submission date |
Mar 22, 2012 |
| Last update date |
Mar 23, 2012 |
| Contact name |
Shaolei Lu |
| E-mail(s) |
slu@lifespan.org
|
| Phone |
401-444-5709
|
| Organization name |
Rhode Island Hospital
|
| Department |
Pathology
|
| Street address |
593 Eddy Steet
|
| City |
Providence |
| State/province |
Rhode Island |
| ZIP/Postal code |
02903 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE36725 |
Gene profiling in mucosal biopsies of Eosinophilic Esophagitis patients pre and post glucocorticoid steroid treatment |
| GSE36727 |
MicroRNA Profiling in Mucosal Biopsies of Eosinophilic Esophagitis Patients Pre and Post Glucocorticoid Steroid Treatment and Relationship with mRNA Target Expression |
|
