|
| Status |
Public on Jun 08, 2020 |
| Title |
Crohn's_Disease__patient11 |
| Sample type |
RNA |
| |
|
| Source name |
intestinal mucosa
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: intestinal mucosa
inflammation: Inflamed margin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA, including small RNA, from ileocolectomy samples was insolated using RNAeasy® Mini Kit extraction (QIAGEN Inc., CA, USA) following manufacturer's instructions. The samples were previously stabilizaded with RNAlater reagent during 24h. RNA quality and integrity were analyzed by Experion bioanalyzer (Bio-Rad, CA, USA).
|
| Label |
Biotin
|
| Label protocol |
Total RNA (1μg) was primed for reverse transcription with oligo-dT primer containing the T7 RNA polymerase promoter site. After second-strand cDNA synthesis, the dscDNA served as the template for an in vitro transcription (IVT) reaction to produce the target cRNA. IVT was performed by the linear amplification method in the presence of biotin-modified UTP to label the target cRNA. MessageAmp TM II-Biotin Enhanced kit was used (Ambion, Ma, USA).
|
| |
|
| Hybridization protocol |
Biotin labeled cRNA (10ug) was hybridized on CodeLink™ Human Whole Genome Bioarray overnight at 37°C (Applied Microarrays, AZ, USA). Labeling with Cy5-streptavidin was performed.
|
| Scan protocol |
Scanning was performed on InnoScan® 700 microarray scanner and Mapix Software (ArrayIt Corporation, CA, USA)
|
| Description |
RNA extracted from an instestinal biopsy of a CD patient
|
| Data processing |
Raw data include raw intensity values from all gene expression microarray probes (n=56,448 probes, Platform GPL2895). Non-normalized data include intensity values on the log2 scale for a total of 20,902 probes that passed the quality control analysis (Probes with RefSeq annotation -April 2015- and mapping to a single gene). Log2 transformation of GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray raw data, RefSeq probe annotation update (16th April, 2015), quantile normalization and batch effect adjustment using the preprocessCore and Combat R packages, respectively.
|
| |
|
| Submission date |
Jun 16, 2016 |
| Last update date |
Jun 08, 2020 |
| Contact name |
Adrià Aterido |
| E-mail(s) |
adria.aterido@vhir.org
|
| Phone |
+34 934029082
|
| Organization name |
Vall d'Hebron Hospital Research Institute
|
| Department |
Rheumatology Research Group
|
| Lab |
Rheumatology Research Group
|
| Street address |
c/ Baldiri Reixac nº15
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL18134 |
| Series (1) |
| GSE83448 |
Genome-wide transcriptional analysis in intestinal biopsies from Crohn's disease (CD) patients. |
|
