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Sample GSM1169059 Query DataSets for GSM1169059
Status Public on Aug 21, 2013
Title Antibiotics-Distal 87
Sample type RNA
Source name Distal intestine, antibiotics
Organism Sus scrofa
Characteristics tissue: distal intestine
treatment: Antibiotics 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 ( from the R Project for Statistical Computing ( 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
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

Data table header descriptions
VALUE gcRMA normalized signal intensity, log2 scaled

Data table
AFFX-BioB-3_at 9.631311355
AFFX-BioB-5_at 9.552142947
AFFX-BioB-M_at 10.04775467
AFFX-BioC-3_at 11.48754498
AFFX-BioC-5_at 10.43550625
AFFX-BioDn-3_at 12.87212633
AFFX-BioDn-5_at 12.73775528
AFFX-CreX-3_at 15.58571009
AFFX-CreX-5_at 15.5901108
AFFX-DapX-3_at 10.90871496
AFFX-DapX-5_at 4.829630346
AFFX-DapX-M_at 9.207677247
AFFX-LysX-3_at 7.438200416
AFFX-LysX-5_at 5.420151762
AFFX-LysX-M_at 4.957016258
AFFX-PheX-3_at 7.20135659
AFFX-PheX-5_at 4.975401268
AFFX-PheX-M_at 6.17391124
AFFX-r2-Bs-dap-3_at 11.4053596
AFFX-r2-Bs-dap-5_at 6.434965655

Total number of rows: 24123

Table truncated, full table size 673 Kbytes.

Supplementary file Size Download File type/resource
GSM1169059_BL_180912_87_Porcine_.CEL.gz 1.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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