Help Login Create account

Data released on September 01, 2014

Data looking at methylation changes of intestinal genes in the neonatal period of preterm neonate pigs.

Gao, F; Gong, D; Zhang, J (2014): Data looking at methylation changes of intestinal genes in the neonatal period of preterm neonate pigs. GigaScience Database. http://dx.doi.org/10.5524/100070 RIS BibTeX Text

For this study, six term pigs were delivered close to full term (115–116 days gestation, by cesarean section) from two pregnant sows (Large White × Duroc, Askelygaard, Denmark), serving as the 0d-term group. Within 6 hours of birth, these pigs were euthanized (sodium pentobarbitone, 200 mg/kg, intravenous), and mid small intestine was dissected out, snap frozen in liquid nitrogen and stored at -80°C.
Under anesthesia, six preterm pigs were obtained from five pregnant sows (Large White × Duroc; Askelygaard, Denmark) by cesarean delivery at 90- 92% (104–107 days) gestation. Six of these pigs were euthanized within 6 hours of birth without any feeding (0d-preterm group). The intestine was also dissected out and frozen at -80°C. The remaining 6 preterm pigs were reared individually in infant incubators (Air-Shields, Hatboro, PN) and fitted with orogastric catheters for PN and oro-gastric feeding tube. The pigs were given PN solution at a rate of 4 mL/(kg × h) on d1 and 6 mL/(kg × h) on d2 as well as minimal enteral nutrition: 24 mL/(kg × d) on d1 and 40 mL/(kg × d) on d2 with infant formula. The PN solution was based on a commercially available product (Kabiven, Fresenius Kabi) and adjusted in nutrient composition to meet the requirement of pigs. On d3, they were transferred to full enteral nutrition (EN) [120 mL/(kg × d)] for two more days before sacrifice. The mid intestine was also dissected out and frozen at -80°C.
Pigs were continuously monitored for clinical symptoms of Necrotizing enterocolitis (NEC) and at tissue collection the severity of NEC-like intestinal lesions was evaluated using scoring system. Six pigs remained healthy at the time of tissue collection on day 4 (4d-preterm) while six other pigs had significant NEC lesions identified in their intestines. Experimental and animal management procedures followed a high standard of veterinary care and were conducted in accordance with approval of institutional and national policies and guidelines.
For sanger sequencing, the processed sequence was aligned to the pig reference regions (all PCR regions) by the blast software. For HiSeq sequencing, the Illumina reads were post-processed and aligned to the pig reference regions (all PCR regions) using SOAP aligner (Version 2.01) with default parameters that excluded reads with more than five mismatched bases. Multiple reads mapping to the same position were counted only once to remove potential bias from PCR. Then we calculated the methylated level based on the effective data.

Contact Submitter

Related manuscripts:

doi:10.1186/1471-2164-15-716

Epigenomic

http://gigadb.org/images/data/cropped/100070_pig.png

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
mid-healthy9823PigpigSus scrofa Description:Six pigs remained healthy at the time of tissue collection on day 4.
Environment (feature):preterm neonates
Diet:enteral feeding 5 days
mid.int.104-106.day9823PigpigSus scrofa Description:six preterm pigs were obtained from five pregnant sows (Large White × Duroc Askelygaard, Denmark) by cesarean delivery at 90- 92% (104–106 days) gestation
Environment (feature):gestation age 104-106 days
mid.int-115.day9823PigpigSus scrofa Description:six term pigs were delivered close to full term (115–116 days gestation, by cesarean section) from two pregnant sows (Large White × Duroc, Askelygaard, Denmark)
Environment (feature):gestation age115 days
mid-NEC9823PigpigSus scrofa Description:six pigs had significant NEC(necrotizi...
Disease status:necrotizing enterocolitis
Environment (feature):preterm neonates
...
+
Displaying 1-4 of 4 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
mid.int.104-106.day, mid-NECMethylome dataUNKNOWN30.18 KB2013-12-11
mid.int.104-106.day, mid-NECMethylome dataUNKNOWN30.79 KB2013-12-11
mid.int.104-106.day, mid-NECMethylome dataUNKNOWN29.96 KB2013-12-11
mid.int.104-106.day, mid-NECMethylome dataUNKNOWN30.28 KB2013-12-11
mid-healthy, mid.int-115.dayMethylome dataUNKNOWN30.27 KB2013-12-11
mid-healthy, mid.int-115.dayMethylome dataUNKNOWN28.72 KB2013-12-11
mid-healthy, mid.int-115.dayMethylome dataUNKNOWN26.4 KB2013-12-11
mid-healthy, mid.int-115.dayMethylome dataUNKNOWN35.77 KB2013-12-11
mid-healthy, mid.int-115.dayMethylome dataUNKNOWN29.98 KB2013-12-11
mid-healthy, mid.int-115.dayMethylome dataUNKNOWN29.57 KB2013-12-11
Displaying 1-10 of 119 File(s).

Other datasets you might like: