|
| Status |
Public on Mar 01, 2016 |
| Title |
stool_004A |
| Sample type |
RNA |
| |
|
| Source name |
fecal total RNA from study subject
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: stool
disease state: environmental enteric dysfunction
percent lactulose in urine: 0.556
gender: F
age (month): 40.15
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Stools were enriched by centrifugation for human content prior to RNA extraction. Fecal total RNA was extracted from human-enriched pellets and bacterial-enriched supernatants separately using “Specific A” protocol on the NucliSENS EasyMAG system (bioMérieux, Durham, NC).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA were prepared according to the vendor's standard protocol from a minimal 100 ng of total RNA using Life Technologies (Ambion) WT-plus RNA Amplification system.
|
| |
|
| Hybridization protocol |
Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Transcriptome Array 2.0 (HTA2.0) chips. The chips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
HTA2.0 arrays were scanned using the Affymetrix Scanner 7G.
|
| Description |
Gene expression data of stool RNAs from sick child
|
| Data processing |
The data were analyzed with Expression Console 1.4.1 software using Affymetrix default analysis settings. The Robust Mutlti-array Averaging (RMA) background correction, median polish probe summarization, and quantile normalization were applied as standard method.
|
| |
|
| Submission date |
Nov 04, 2015 |
| Last update date |
Mar 01, 2016 |
| Contact name |
Jinsheng Yu |
| E-mail(s) |
[email protected]
|
| Organization name |
Washington University School of Medicine
|
| Department |
Genetics
|
| Lab |
GTAC Lab
|
| Street address |
660 S. Euclid Ave.
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL17586 |
| Series (1) |
| GSE74681 |
Environmental enteric dysfunction includes a broad spectrum of inflammatory responses and epithelial repair processes. |
|
