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
ERX713891UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAfemaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002599747001629918457.5Browse results
ERX713892UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAfemaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired26978331743543001576618172.5Browse results
ERX713893UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAmaleCanadaNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002737218001631518486Browse results
ERX713894UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAmaleCanadaNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired27225531856990001581218190Browse results
ERX713895UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAfemaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002810211001655318577Browse results
ERX713896UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAfemaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired29309672047195001609418336.5Browse results
ERX713897UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAmaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002768970001627518449.5Browse results
ERX713898UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAmaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired27075151866812001576518201.5Browse results
ERX713899UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAmaleCanadaNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002611086001713318874Browse results
ERX713900UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAmaleCanadaNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired17488691141681001601518275Browse results
ERX713901UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAfemaleNorwayNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002602688001588918232.5Browse results
ERX713902UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAfemaleNorwayNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired25566811661731001536917957.5Browse results
ERX713903UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAmaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002579190001646718513Browse results
ERX713904UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAmaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired17584491127364001543017979Browse results
ERX713905UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAmaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002627896001620318395.5Browse results
ERX713906UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAmaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired22608621484504001558918068Browse results
ERX713907UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAfemaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002766486001676218670Browse results
ERX713908UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAfemaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired27547081894677001627218427.5Browse results
ERX713909UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAfemaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002608043001647918514Browse results
ERX713910UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAfemaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired21717391414217001574218129.5Browse results

Showing 21 to 40 of 154 entries

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