|
| Status |
Public on Aug 21, 2013 |
| Title |
Untreated-Proximal 83 |
| Sample type |
RNA |
| |
|
| Source name |
Proximal intestine, untreated
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: proximal intestine
treatment: control saline were given twice daily from birth to tissue collection at d 5
|
| Treatment protocol |
Piglets from each litter were stratified according to birth weight and sex, and allocated into controls (CON, n=13) and an intervention group receiving oral and systemic broad-spectrum antibiotics (Ampicillin, Gentamycin, Metronidazol, ANTI, n=11). To assure high systemic and intra luminal MIC values antibiotics were given both orally and intramuscularly. All antibiotics were given directly after feeding with an oral bolus and control pigs were given corresponding amounts of saline. On day five, all piglets were euthanized, and small intestinal tissue collected.
|
| Growth protocol |
Twenty-four preterm piglets (Landrace x Large white x Duroc) were delivered by caesarean section on day 105 of gestation from two healthy sows. Piglets were housed in incubators with regulated temperature and oxygen supply. All piglets were initially provided with parenteral nutrition via a vascular catheter, combined with small amounts of minimal enteral nutrition. On day three, all parenteral nutrition was stopped and total enteral nutrition was given through an oro-gastric feeding tube until sacrifice and tissue collection on day five.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was lyzed in Trizol (Invitrogen). RNA was isolated using standard chloroform/isopropanol steps. Total RNA was further purified with the RNeasy Kit (Qiagen), including an RNase-free DNase I (Qiagen) digestion step.
|
| Label |
biotin
|
| Label protocol |
Fragmented and biotin-labelled aRNA was synthesized from total RNA using the 3' IVT Express Kit (Affymetrix) according to the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner.
|
| Description |
Caesarean-delivered preterm pigs were fed 3 d of parenteral nutrition followed by 2 d of enteral formula feeding. Antibiotics (n=11) or control saline (n=13) were given twice daily from birth to tissue collection at d 5. NEC-lesions and intestinal structure, function, microbiology and immunity markers were recorded.
|
| Data processing |
Initial data analysis was performed using Affymetrix GCOS 1.2 software. Data were further analyzed using Bioconductor (http://www.bioconductor.org) from the R Project for Statistical Computing (http://www.r-project.org). Normalization was performed with gcRMA. The moderated t-test provided by the Bioconductor package limma was used to test for differential expression. Data was considered significant when P<0.01, FC>2.
|
| |
|
| Submission date |
Jun 19, 2013 |
| Last update date |
Aug 21, 2013 |
| Contact name |
Denise Kelly |
| E-mail(s) |
[email protected]
|
| Phone |
+44 1224 716648
|
| Organization name |
University of Aberdeen
|
| Lab |
Gut Immunology Group
|
| Street address |
Institute of Medical Sciences
|
| City |
Aberdeen |
| ZIP/Postal code |
AB25 2ZD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL3533 |
| Series (1) |
| GSE48125 |
Neonatal antibotic prophylaxis modulates intestinal immunity and prevents necrotizing enterocolitis in preterm neonates |
|
