|
| Status |
Public on Nov 11, 2017 |
| Title |
control-172 |
| Sample type |
RNA |
| |
|
| Source name |
Intestinal mucosa pinch biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: non-IBD control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pinch biopsies were obtained at colonoscopy using sterile cold biopsy forceps and snap-frozen for RNA extraction in Trizol reagent (Invitrogen). RNA was isolated using chloroform purification and isopropanol extraction and purified using QIAgen Rneasy Mini Kit.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed with Cy3 according to the manufacturer protoocl for one color microarray based gene expression analysis (Agilent)
|
| |
|
| Hybridization protocol |
Equal amount of Cy3 labeled target was hybridized to Sureprint G3 Human GE 8x60k array (Agilent) for 15 hours according to the manufacturers protocol
|
| Scan protocol |
Arrays were scanned using Agilent microarray scanner
|
| Data processing |
Raw signal intensities were extracted with feature extraction v11.5 software
Expression intensities were background corrected using the normal plus exponential convolutional method, followed by between-array quantile normalization in limma (version 3.26.9), resulting in log2-transformed intensity values.
|
| |
|
| Submission date |
Mar 24, 2017 |
| Last update date |
Nov 12, 2017 |
| Contact name |
Mei San Tang |
| Organization name |
Washington University in St Louis
|
| Department |
Pathology & Immunology
|
| Street address |
660 S Euclid, Campus Box 8118
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63108 |
| Country |
USA |
| |
|
| Platform ID |
GPL13607 |
| Series (2) |
| GSE97011 |
Genome wide transcriptional profiles of biopsies collected from non-IBD control subjects |
| GSE97012 |
Integrated Analysis Of Biopsies From Inflammatory Bowel Disease Patients Identifies SAA1 As A Link Between Mucosal Microbes With TH17 And TH22 Cells |
|
