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Sample GSM1169044 Query DataSets for GSM1169044
Status Public on Aug 21, 2013
Title Antibiotics-proximal 86
Sample type RNA
Source name Proximal intestine, antibiotics
Organism Sus scrofa
Characteristics tissue: proximal 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 7.718818026
AFFX-BioB-5_at 7.806647753
AFFX-BioB-M_at 8.280990115
AFFX-BioC-3_at 10.3155048
AFFX-BioC-5_at 9.120157491
AFFX-BioDn-3_at 11.46378429
AFFX-BioDn-5_at 11.22693834
AFFX-CreX-3_at 15.01882042
AFFX-CreX-5_at 14.95689762
AFFX-DapX-3_at 7.591611483
AFFX-DapX-5_at 2.466756499
AFFX-DapX-M_at 5.526255584
AFFX-LysX-3_at 3.284582676
AFFX-LysX-5_at 2.378566569
AFFX-LysX-M_at 2.794015126
AFFX-PheX-3_at 3.251195841
AFFX-PheX-5_at 2.256611907
AFFX-PheX-M_at 2.860944089
AFFX-r2-Bs-dap-3_at 8.322149128
AFFX-r2-Bs-dap-5_at 2.343731048

Total number of rows: 24123

Table truncated, full table size 673 Kbytes.

Supplementary file Size Download File type/resource
GSM1169044_BL_180912_86_Porcine_.CEL.gz 2.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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