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Sample GSM6172002 Query DataSets for GSM6172002
Status Public on Feb 28, 2024
Title Four weeks Fasted pigID=16
Sample type SRA
 
Source name jejunum small intestine scraping
Organism Sus scrofa
Characteristics Sex: female
strain: TN20; Large White x Norwegian Landrace, TopigsNorsvin, Vught, The Netherlands
diet: Sow's milk
age: Four weeks
treatment: Fasted
Treatment protocol Gene expression profiles from pig jejunum scrapings either fed or fasted at four and six weeks of age (n=16 per group). Piglets were kept at a commercial farm and did not receive any creep feed, and remained with the sow until four weeks of age, after which they were weighed and assigned to one of four groups: four-week-old fed piglets remained with the sow until time of slaugther, which occured on the farm at the same time as the four-week-old fasted piglets. Four-week-old fasted piglets were placeced in a seperate pen on the farm and were slaughtered 48h after the start of the intervention. Six-wweek-old piglets were transferred to the experimental research facility of Wageningen University at four weeks of age, and were pair-housed throughout the remainer of the study. They received a standard weaning diet for two-weeks, after which the fed piglets kept receiving feed for the 48h long intervention period, while the fasted piglets did not receive any feed starting 48h before slaughter. All piglets had ad libitum acces to water at all times.
Extracted molecule total RNA
Extraction protocol Piglets were anasthesized using a mixture of Zoletil+Xylazine (5:2 ratio, 1 mg/10 kg BW), and euthanized by lethal injection with pentobarbital (24 mg/kg BW), followed by exanguination. The intestine was isolated, and mid-jejunum was identified at 50% of the small intestinal length. Intestine was washed in cold PBS, dabbed dry and mucosa was scraped off using clean glass slides. Collected tissue was snap frozen in liquid nitrogen and stored at -80°C until further analysis. Total RNA was extracted by grinding frozen muscle tissue and dissolving approximately 5-10 mg in RLT buffer containing b-mercaptoethanol. Further RNA isolation was performed according to the RNAeasy mini kit instructions (Qiagen). RNA concentration was measured using NanoDrop spectrophotometer (Thermofisher). RNA integrity was measured using RNA Screentape on the 2200 Tapestation (Agilent).
RNA preparation, library construction and sequencing on BGISEQ-500 was performed at Beijing Genomics Institute.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-G400
 
Data processing RNA preparation, library construction and sequencing on BGISEQ-500 was performed at Beijing Genomics Institute.
Reads were aligned to the pig genome (Sus_scrofa.Sscrofa11.1.104) using STAR (-runThreadN 2 --genomeDir --readFilesIn --readFilesCommand gunzip -c --outFileNamePrefix --outSAMtype BAM SortedByCoordinate --outSAMunmapped None --outSAMattrIHstart 0 --outFilterType BySJout --sjdbGTFfile /Sus_scrofa.Sscrofa11.1.104.gtf --quantMode TranscriptomeSAM
Reads were quantified using Htseq
Assembly: Sus_scrofa.Sscrofa11.1.104
Supplementary files format and content: Raw counts using HTSeq
 
Submission date May 20, 2022
Last update date Feb 28, 2024
Contact name Evert M. van Schothorst
E-mail(s) evert.vanschothorst@wur.nl
Organization name Wageningen University
Lab Human and Animal Physiology
Street address De Elst 1
City Wageningen
ZIP/Postal code 6708 WD
Country Netherlands
 
Platform ID GPL29847
Series (1)
GSE203439 RNAseq of jejunal scrapings of pigs fed or fasted four- and six-week-old piglets
Relations
BioSample SAMN28561885
SRA SRX15391776

Supplementary file Size Download File type/resource
GSM6172002_16_counts.txt.gz 121.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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