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Sample GSM1169054 Query DataSets for GSM1169054
Status Public on Aug 21, 2013
Title Untreated-Distal 88
Sample type RNA
Source name Distal intestine, untreated
Organism Sus scrofa
Characteristics tissue: distal 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 8.759773218
AFFX-BioB-5_at 8.613146274
AFFX-BioB-M_at 9.201086949
AFFX-BioC-3_at 10.63944788
AFFX-BioC-5_at 9.538817691
AFFX-BioDn-3_at 12.15311116
AFFX-BioDn-5_at 11.93590356
AFFX-CreX-3_at 15.04658773
AFFX-CreX-5_at 15.0649425
AFFX-DapX-3_at 10.98816584
AFFX-DapX-5_at 4.920924178
AFFX-DapX-M_at 9.515010075
AFFX-LysX-3_at 7.435829644
AFFX-LysX-5_at 4.980813625
AFFX-LysX-M_at 4.462561251
AFFX-PheX-3_at 6.881758879
AFFX-PheX-5_at 4.943227657
AFFX-PheX-M_at 6.167751995
AFFX-r2-Bs-dap-3_at 11.41686449
AFFX-r2-Bs-dap-5_at 6.496728869

Total number of rows: 24123

Table truncated, full table size 674 Kbytes.

Supplementary file Size Download File type/resource
GSM1169054_IM_140812_88_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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