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
ERX713871UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAmaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002763986001685218706Browse results
ERX713872UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAmaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired31469922160451001653718559.5Browse results
ERX713873UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAfemaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002697048001626218411Browse results
ERX713874UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAfemaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired16685661117249001520117857.5Browse results
ERX713875UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAfemaleCanadaNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002634848001616818358.5Browse results
ERX713876UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAfemaleCanadaNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired29530021932215001588018222.5Browse results
ERX713877UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAfemaleCanadaNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002593999001724518909.5Browse results
ERX713878UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAfemaleCanadaNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired26968031738286001665218595.5Browse results
ERX713879UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAfemaleNorwayNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002706206001621418399Browse results
ERX713880UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAfemaleNorwayNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired33425662244741001601118286.5Browse results
ERX713881UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAfemaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002640457001675018665.5Browse results
ERX713882UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAfemaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired21648091428390001582218185Browse results
ERX713883UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAfemaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002654333001670118639Browse results
ERX713884UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAfemaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired29628841958490001625618396Browse results
ERX713885UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAmaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002703139001648818521.5Browse results
ERX713886UBERON:0002106 spleenspleenUBERON:0000104 life cycleNAmaleGermanyNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired20099951355527001563118069Browse results
ERX713887UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAfemaleNorwayNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002825466001612318354.5Browse results
ERX713888UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAfemaleNorwayNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired26423051858112001556718055.5Browse results
ERX713889UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAfemaleCanadaNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired40000002764127001644618532.5Browse results
ERX713890UBERON:0007132 head kidneyhead kidneyUBERON:0000104 life cycleNAfemaleCanadaNANAGasterosteus aculeatusNAIlluminaIllumina HiScanSQFULL_LENGTH101paired32794792251557001610318348Browse results

Showing 1 to 20 of 154 entries

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