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Sample GSM1169046 Query DataSets for GSM1169046
Status Public on Aug 21, 2013
Title Untreated-Proximal 89
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 ( 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 9.207884519
AFFX-BioB-5_at 9.182844391
AFFX-BioB-M_at 9.548752612
AFFX-BioC-3_at 11.45574666
AFFX-BioC-5_at 10.12792006
AFFX-BioDn-3_at 12.23965332
AFFX-BioDn-5_at 12.03539157
AFFX-CreX-3_at 15.20197317
AFFX-CreX-5_at 15.20241535
AFFX-DapX-3_at 8.021603547
AFFX-DapX-5_at 2.466756499
AFFX-DapX-M_at 6.18212019
AFFX-LysX-3_at 3.876196526
AFFX-LysX-5_at 2.340259518
AFFX-LysX-M_at 3.092298501
AFFX-PheX-3_at 3.817173082
AFFX-PheX-5_at 2.66611297
AFFX-PheX-M_at 3.120849466
AFFX-r2-Bs-dap-3_at 8.610017783
AFFX-r2-Bs-dap-5_at 2.693394187

Total number of rows: 24123

Table truncated, full table size 673 Kbytes.

Supplementary file Size Download File type/resource
GSM1169046_BL_180912_89_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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