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Sample GSM1169045 Query DataSets for GSM1169045
Status Public on Aug 21, 2013
Title Untreated-Proximal 88
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) D.Kelly@rri.sari.ac.uk
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
ID_REF
VALUE gcRMA normalized signal intensity, log2 scaled

Data table
ID_REF VALUE
AFFX-BioB-3_at 7.796759038
AFFX-BioB-5_at 8.190301036
AFFX-BioB-M_at 8.694925222
AFFX-BioC-3_at 10.73827274
AFFX-BioC-5_at 9.423873507
AFFX-BioDn-3_at 11.75892679
AFFX-BioDn-5_at 11.5168157
AFFX-CreX-3_at 14.96734134
AFFX-CreX-5_at 14.98766794
AFFX-DapX-3_at 7.556764277
AFFX-DapX-5_at 2.251119076
AFFX-DapX-M_at 5.35054032
AFFX-LysX-3_at 3.198428756
AFFX-LysX-5_at 2.381392524
AFFX-LysX-M_at 2.794015126
AFFX-PheX-3_at 3.258036684
AFFX-PheX-5_at 2.22259366
AFFX-PheX-M_at 2.853514518
AFFX-r2-Bs-dap-3_at 8.223179422
AFFX-r2-Bs-dap-5_at 2.730559003

Total number of rows: 24123

Table truncated, full table size 673 Kbytes.




Supplementary file Size Download File type/resource
GSM1169045_BL_180912_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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