|
| Status |
Public on Feb 22, 2017 |
| Title |
Sx subject at Day 3 [3266_246783_HG-U133A_2_39847_DU11-04S03315] |
| Sample type |
RNA |
| |
|
| Source name |
Whole peripheral blood at Day 3
|
| Organism |
Homo sapiens |
| Characteristics |
phenotype: symptomatic
time: Day 3
|
| Treatment protocol |
Subjects were orally administered ETEC strain H10407 in a bicarbonate solution, with random assignment to a dose of either 1 × 10^5 or 1 × 10^6 colony-forming units.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was completed using the PAXgene Blood miRNA Kit. PAXgene Blood RNA Tubes were first centrifuged to pellet the samples, then washed with water and resuspended. After digestion with Proteinase K, the samples were homogenized by centrifugation through PAXgene Shredder spin columns. Isopropanol was added to the samples to optimize binding conditions, and the samples were then centrifuged through PAXgene RNA spin columns, where total RNA >18 nucleotides (including miRNA) was bound to the silica-membrane. The bound RNA was treated with DNase to remove genomic DNA contamination and washed. Pure RNA was then eluted.
|
| Label |
biotin
|
| Label protocol |
Total RNA specimens were converted into double-stranded cDNA using an olgio dT-T7 primer. Double stranded cDNA was then used as a template for an invitro transcription reaction to produce a biotinylated cRNA target. The biotinylated cRNA was fragmented and hybridized to the appropriate GeneChip microarray
|
| |
|
| Hybridization protocol |
A hybridization cocktail is prepared, including the fragmented target, and probe array controls. It is then hybridized to the probe array during a 16-hour incubation
|
| Scan protocol |
Following hybridization, arrays are washed and stained using standard Affymetrix procedures before scanning on the Affymetrix GeneChip Scanner and data extraction using Affymetrix GCOS software.
|
| Description |
Gene expression at Day 3 for Sx subject
|
| Data processing |
The data were RMA normalized with the Bioconductor Affy package.
|
| |
|
| Submission date |
Feb 21, 2017 |
| Last update date |
Nov 30, 2020 |
| Contact name |
Sunil Suchindran |
| E-mail(s) |
ss240@duke.edu
|
| Organization name |
Duke University
|
| Department |
Center for Applied Genomics and Precision Medicine
|
| Street address |
101 Science Drive
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (1) |
| GSE95104 |
Transcriptomic Analysis of the Host Response and Innate Resilience to Enterotoxigenic Escherichia coli Infection in Humans |
|
| Relations |
| Reanalyzed by |
GSE162329 |
