RNA_seq_Salmonella_pig

Experiment ID:ERP004640
Technology:RNA-Seq
Description:Salmonella enterica serovar Typhimurium is a gram-negative bacterium that can colonize the gut of humans and several species of food producing farm animals to cause enteric or septicaemic salmonellosis. Besides compromising public health and food safety, sub-clinical salmonellosis is also believed to be a major problem affecting the profitability of the pig industry. Distinct responses to Salmonella infection have been observed in pigs, some recovering faster and shedding lower levels of Salmonella in faeces than others (low shedders, LS versus persistent shedders, PS). This trait variation could indicate the existence of a genetic component to Salmonella shedding and resistance that may be exploited in animal breeding and disease diagnostics. The study aimed to identify porcine genes and gene co-expression networks that differentiate distinct responses to Salmonella infection with respect to faecal Salmonella shedding.
Source:ERP004640 SRA
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Bulk RNA-Seq processed expression values in Sus scrofa

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Showing 1 to 16 of 16 entries

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.
Total UMI count
Total number of individual RNA molecules (UMI) for the annotated sample. Only applicable for libraries producing UMIs.
Mapped UMI count
Number of UMIs that could be mapped to the transcriptome. Only applicable for libraries producing UMIs.
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
ERX379620UBERON:0000178 bloodwhole bloodSscrDv:0000016 7-week-old stage (pig)7 weeksNAmixed-breedNANASus scrofaNAIlluminaIllumina HiScanSQFULL_LENGTH26single7488370956596970001643420439Browse results
ERX379625UBERON:0000178 bloodwhole bloodSscrDv:0000016 7-week-old stage (pig)7 weeksNAmixed-breedNANASus scrofaNAIlluminaIllumina HiScanSQFULL_LENGTH26single4214459032027344001706020573.5Browse results
ERX379626UBERON:0000178 bloodwhole bloodSscrDv:0000016 7-week-old stage (pig)7 weeksNAmixed-breedNANASus scrofaNAIlluminaIllumina HiScanSQFULL_LENGTH26single4524630330812400001583119853Browse results
ERX379627UBERON:0000178 bloodwhole bloodSscrDv:0000016 7-week-old stage (pig)7 weeksNAmixed-breedNANASus scrofaNAIlluminaIllumina HiScanSQFULL_LENGTH26single4415817928432057001642020170Browse results
ERX379629UBERON:0000178 bloodwhole bloodSscrDv:0000016 7-week-old stage (pig)7 weeksNAmixed-breedNANASus scrofaNAIlluminaIllumina HiScanSQFULL_LENGTH26single4089641431332582001368518984.5Browse results
ERX379630UBERON:0000178 bloodwhole bloodSscrDv:0000016 7-week-old stage (pig)7 weeksNAmixed-breedNANASus scrofaNAIlluminaIllumina HiScanSQFULL_LENGTH26single5276504334579266001536620043.5Browse results
ERX379631UBERON:0000178 bloodwhole bloodSscrDv:0000016 7-week-old stage (pig)7 weeksNAmixed-breedNANASus scrofaNAIlluminaIllumina HiScanSQFULL_LENGTH26single3397904020366368001598319863.5Browse results
ERX379633UBERON:0000178 bloodwhole bloodSscrDv:0000016 7-week-old stage (pig)7 weeksNAmixed-breedNANASus scrofaNAIlluminaIllumina HiScanSQFULL_LENGTH26single6936211945942017001556220391Browse results
ERX379638UBERON:0000178 bloodwhole bloodSscrDv:0000016 7-week-old stage (pig)7 weeksNAmixed-breedNANASus scrofaNAIlluminaIllumina HiScanSQFULL_LENGTH26single3820705924916108001662720284Browse results
ERX379639UBERON:0000178 bloodwhole bloodSscrDv:0000016 7-week-old stage (pig)7 weeksNAmixed-breedNANASus scrofaNAIlluminaIllumina HiScanSQFULL_LENGTH26single4404029027927090001533319654.5Browse results
ERX379640UBERON:0000178 bloodwhole bloodSscrDv:0000016 7-week-old stage (pig)7 weeksNAmixed-breedNANASus scrofaNAIlluminaIllumina HiScanSQFULL_LENGTH26single8502358048758798001708820730Browse results
ERX379642UBERON:0000178 bloodwhole bloodSscrDv:0000016 7-week-old stage (pig)7 weeksNAmixed-breedNANASus scrofaNAIlluminaIllumina HiScanSQFULL_LENGTH26single3345274219214725001566919725.5Browse results
ERX379643UBERON:0000178 bloodwhole bloodSscrDv:0000016 7-week-old stage (pig)7 weeksNAmixed-breedNANASus scrofaNAIlluminaIllumina HiScanSQFULL_LENGTH26single4949586226947653001687720421Browse results
ERX379644UBERON:0000178 bloodwhole bloodSscrDv:0000016 7-week-old stage (pig)7 weeksNAmixed-breedNANASus scrofaNAIlluminaIllumina HiScanSQFULL_LENGTH26single4607636222156435001690320356.5Browse results
ERX379646UBERON:0000178 bloodwhole bloodSscrDv:0000016 7-week-old stage (pig)7 weeksNAmixed-breedNANASus scrofaNAIlluminaIllumina HiScanSQFULL_LENGTH26single8744790447044488001724420797Browse results
ERX379647UBERON:0000178 bloodwhole bloodSscrDv:0000016 7-week-old stage (pig)7 weeksNAmixed-breedNANASus scrofaNAIlluminaIllumina HiScanSQFULL_LENGTH26single4284100226507900001689620315.5Browse results

Showing 1 to 16 of 16 entries

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