Habitat-specific gene expression in stickleback immune tissues from four parametric lake-river population pairs

Experiment ID:ERP009696
Technology:RNA-Seq
Description:The three-spined stickleback (Gasterosteus aculeatus) has repeatedly colonized and adapted to diverse freshwater habitats since the last glaciation. Among those freshwater habitats, adjacent lake and river populations harbour distinct parasite communities, a recurring ecological difference proposed to drive adaptive differentiation between lake and river stickleback ecotypes. To study the rapid adaptation of sticklebacks to lake and river habitats, we analysed gene expression profiles of 77 whole-transcriptome libraries of two immune-relevant tissues, the head kidney and the spleen, obtained from wild-caught sticklebacks of the two habitat types across multiple geographic locations. Differential expression analyses identified 189 genes showing statistically significant habitat-specific expression patterns among the three European locations. Among those genes, 15 genes are annotated with putative immune functions, and 50 have been experimentally associated with immune-responses in sticklebacks, reinforcing the hypothesis that parasites contribute to adaptive evolution of lake and river sticklebacks. Comparing expression profiles of European sticklebacks to populations in similar habitats in North America, five genes exhibited habitat-specific expression across continents.
Source:ERP009696 SRA
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Bulk RNA-Seq processed expression values in Gasterosteus aculeatus

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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.
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
ERX713931UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAfemaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002795222001635518475Browse results
ERX713932UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAfemaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired31668152198438001609718324.5Browse results
ERX713933UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAfemaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002538201001626418430.5Browse results
ERX713934UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAfemaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired19014931203581001528217916Browse results
ERX713935UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAmaleNorwayNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002772140001682118718Browse results
ERX713936UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAmaleNorwayNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired28314771954013001634518448Browse results
ERX713937UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAmaleCanadaNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002764136001712118863Browse results
ERX713938UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAmaleCanadaNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired19068511315288001623518387.5Browse results
ERX713939UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAfemaleCanadaNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002613487001620118375Browse results
ERX713940UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAfemaleCanadaNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired24993021623574001556318032Browse results
ERX713941UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAmaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002601124001639118479Browse results
ERX713942UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAmaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired29206991887891001602118285Browse results
ERX713943UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAmaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002941670001367817167.5Browse results
ERX713944UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAmaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired935168676570001030015419.5Browse results
ERX713945UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAfemaleNorwayNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002749373001682818704.5Browse results
ERX713946UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAfemaleNorwayNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired19231971318059001584018170Browse results
ERX713947UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAmaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002740941001678118691Browse results
ERX713948UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAmaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired22872271559713001608118317.5Browse results
ERX713949UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAfemaleNorwayNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002701741001612318363.5Browse results
ERX713950UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAfemaleNorwayNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired24545661648324001549518024.5Browse results

Showing 61 to 80 of 154 entries

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