RNA-seq of porcine peripheral whole blood from pig divergently selected for residual feed intake and treated with lipopolysaccharide

Experiment ID:ERP022259

Technology:RNA-Seq

Description:Yorkshire pigs were divergently selected for residual feed intake (RFI) for 8 generations. Pigs with low RFI have reduced feed intake. Based on the resource allocation theory, we hypothesize that these low RFI pigs might have compromised immune response to immune stimulation. To test this hypothesis, twenty eight gilts of initial body weight (BW) of 63 +/- 4 kg from pigs selected for low RFI and high RFI were randomly selected for the ISU RFI selection project and utilized in two replicates (14 pigs/replicate) for this study. All pigs were housed in individual metabolism pens, had free access to water and were fed a corn-soy-based diet twice daily, and feed restricted (1.5 kg/day) as previously described. After a 9-day adaptation period pigs were randomly assigned within line to either a control (n = 6, three pigs per line) or lipopolysaccharide (LPS) challenge (n = 8, 4 pigs per line) group. Pigs in the challenge group were then repeatedly challenged with an intramuscular injection of 30, 36, 39, and 42 microg/kg BW of LPS from E. coli O5:B5 (sigma-Aldrich, St. Louis, MO) dissolved in saline solution at time points 0, 48, 96, and 144 hours post initial injection (hpi) to compensate for LPS tolerance after initial injection, respectively, while animals in the control group were injected with an equivalent volume of saline solution at the equivalent time points. Rectal temperatures of individual pigs were measured immediately before the initial injection (serving as baseline, called *0 hpi* for convenience), and 2, 4, 6, and 24 hpi, and 0, 4, 24 hours after each subsequent injection for all pigs. Blood samples were collected from the jugular vein into TempusTM Blood RNA tubes (Life Technologies, Grand Island, NY) for long-term storage at -80°C, EDTA tubes (BD, Franklin Lakes, NJ) for CBC tests and serum tubes for cytokine assays at 0, 2, 6, 24 and 168 hpi. At 168 hpi, all pigs were euthanized via barbiturate overdose, exsanguinated and tissue samples including the longissimus dorsi muscle, liver, spleen, and ileum were isolated, cleaned an frozen for later use. This study only focused on samples and data collected for the first 24 hours. Total RNA was extracted from the 32 blood samples of the treatment group in Replicate 2, collected at 0, 2, 6, and 24 hpi, by using preserved blood RNA purification kit I (Norgen Biotek Corp, Thorold, Ontario) per manufacturer's instruction. On-column DNA digestion was performed as described using DNase I (Qiagen, Valencia, CA). Globin transcripts (HBB and HBA) were depleted by following an RNase H-mediated method. The quantity and integrity of the RNA were monitored by using Nanodrop 2000 (Thermo Scientific, Waltham, MA) and Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) before and after globin depletion. The efficiency of globin depletion of each sample was checked by conventional RT-qPCR with beta-actin and GAPDH as the internal controls. Globin depletion efficiencies for all RNA samples were above 85%.

Source:ERP022259 SRA

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Bulk RNA-Seq processed expression values in Sus scrofa

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Library ID Identifier of the RNA-Seq library	Anat. entity ID ID of the anatomical localization of the sample	Anat. entity name Name of the anatomical localization of the sample	Anat. entity author annotation Free text annotation of anatomical localization of the sample as provided by authors	Stage ID ID of the developmental and life stage of the sample	Stage name Name of the developmental and life stage of the sample	Stage author annotation Free text annotation of the developmental and life stage of the sample as provided by authors	Sex Annotation of the sex of the sample	Strain Annotation of the strain of the sample	Time Free text annotation of the time of sampling as provided by authors	Time unit Unit for the time of sampling as provided by authors	Species	Physiological status Physiological status of the organism at time of sampling	Technology	Sequencing platform	Sequenced transcript part Possible values are: full length, all parts of the transcript are sequenced; 3': only the 3' end of the transcript is sequenced; 5': only the 5' end of the transcript is sequenced.	Fragmentation Size of the RNA fragmentation	Run sequencing type Paired-end or single-read run	Total read count Total number of reads for the library.	Mapped read count Number of reads that could be mapped to the transcriptome.	Distinct rank count When performing a fractional ranking of the genes in the annotated sample, based on their expression level, number of distinct ranks observed, to have a value of the power for distinguishing expression levels. Used as a weight to compute a weighted mean rank accross samples for each gene and compute expression scores in Bgee.	Max rank When performing a fractional ranking of the genes in the annotated sample, based on their expression level, maximum rank attained in the sample. Used to normalize ranks accross samples and compute expression scores in Bgee.	Link to processed expression values See the processed expression value results for this assay
ERX1958860	UBERON:0000178	blood	blood	UBERON:0034919	juvenile stage	body weight (BW) of 63 +/- 4 kg	female	Yorkshire	NA	NA	Sus scrofa	NA	Illumina	Illumina HiSeq 2000	FULL_LENGTH	98	paired	21726565	13772680	15404	19570	Browse results
ERX1958861	UBERON:0000178	blood	blood	UBERON:0034919	juvenile stage	body weight (BW) of 63 +/- 4 kg	female	Yorkshire	NA	NA	Sus scrofa	NA	Illumina	Illumina HiSeq 2000	FULL_LENGTH	98	paired	24286513	15929249	14597	19115.5	Browse results
ERX1958862	UBERON:0000178	blood	blood	UBERON:0034919	juvenile stage	body weight (BW) of 63 +/- 4 kg	female	Yorkshire	NA	NA	Sus scrofa	NA	Illumina	Illumina HiSeq 2000	FULL_LENGTH	98	paired	17632178	11144306	14773	19213	Browse results
ERX1958863	UBERON:0000178	blood	blood	UBERON:0034919	juvenile stage	body weight (BW) of 63 +/- 4 kg	female	Yorkshire	NA	NA	Sus scrofa	NA	Illumina	Illumina HiSeq 2000	FULL_LENGTH	98	paired	20661259	13014816	15225	19473.5	Browse results
ERX1958864	UBERON:0000178	blood	blood	UBERON:0034919	juvenile stage	body weight (BW) of 63 +/- 4 kg	female	Yorkshire	NA	NA	Sus scrofa	NA	Illumina	Illumina HiSeq 2000	FULL_LENGTH	98	paired	17130527	10712074	14999	19331.5	Browse results
ERX1958865	UBERON:0000178	blood	blood	UBERON:0034919	juvenile stage	body weight (BW) of 63 +/- 4 kg	female	Yorkshire	NA	NA	Sus scrofa	NA	Illumina	Illumina HiSeq 2000	FULL_LENGTH	98	paired	21029418	13215833	15396	19565.5	Browse results
ERX1958866	UBERON:0000178	blood	blood	UBERON:0034919	juvenile stage	body weight (BW) of 63 +/- 4 kg	female	Yorkshire	NA	NA	Sus scrofa	NA	Illumina	Illumina HiSeq 2000	FULL_LENGTH	98	paired	18933240	11718752	15222	19481.5	Browse results
ERX1958867	UBERON:0000178	blood	blood	UBERON:0034919	juvenile stage	body weight (BW) of 63 +/- 4 kg	female	Yorkshire	NA	NA	Sus scrofa	NA	Illumina	Illumina HiSeq 2000	FULL_LENGTH	98	paired	19039105	11769788	15387	19569.5	Browse results

Showing 1 to 8 of 8 entries