Medaka_Reciprocal_cross_RNAseq

Experiment ID:ERP010463
Technology:RNA-Seq
Description:Medaka fish is a long standing genetic model organism from the 1930s. Uniquely amongst vertebrates Medaka fish can be routinely inbred from the wild (laboratory mice are inbred, but this does not happen as a routine process from wild individuals), leading to a large number of fully inbred wild-derived strains. As part of a broader collaboration I am part of a project to inbred over 100 wild derived strains of Medaka and use them in a similar manner to Arabidopsis and Drosophila wild derived lines. To help explore the phenotyping possibilities in this context, we have taken already established wild Medaka lines and done reciprocal F1 crosses between 3 strains, and have 4 tissues, and a number of parental tissues, giving a total of 40 samples. By doing RNA-seq on these tissues we do a number of things: (a) assess the level of allele specific expression in Medaka (b) test whether there is any imprinting (parent of origin) in fish. This is thought to not be the case, but in fact has not been well tested (not least because getting truly inbred fish is hard) (c) assess the level of random allelic activation in brain (d) assess the feasibility for RNAseq based phenotyping in Medaka, providing preliminary data for future proposals.
Source:ERP010463 SRA
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Bulk RNA-Seq processed expression values in Oryzias latipes

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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
ERX1246730UBERON:0000948 heartHeartUBERON:0000104 life cycleNANAHd-rR X KagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired37973082938949001726720440.5Browse results
ERX1246731UBERON:0000955 brainbrainUBERON:0000104 life cycleNANAHd-rR X KagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired42186072905254001963521652.5Browse results
ERX1246732UBERON:0002385 muscle tissueMuscleUBERON:0000104 life cycleNANAHd-rR X KagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired44058333593027001792920781Browse results
ERX1246733UBERON:0000948 heartHeartUBERON:0000104 life cycleNANAHd-rR X KagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired44557353503349001775020706Browse results
ERX1246734UBERON:0000955 brainbrainUBERON:0000104 life cycleNANAHd-rR X KagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired44773663140842001967921666Browse results
ERX1246735UBERON:0002385 muscle tissueMuscleUBERON:0000104 life cycleNANAHd-rR X KagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired45196613644287001744420549Browse results
ERX1246736UBERON:0000948 heartHeartUBERON:0000104 life cycleNANAHdR-Male X Cab femaleNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired47379053476727001783820749.5Browse results
ERX1246737UBERON:0000955 brainbrainUBERON:0000104 life cycleNANAHdR-Male X Cab femaleNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired51319633520181002000121830Browse results
ERX1246738UBERON:0002385 muscle tissueMuscleUBERON:0000104 life cycleNANAHdR-Male X Cab femaleNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired49325973930999001841421051Browse results
ERX1246739UBERON:0000948 heartHeartUBERON:0000104 life cycleNANAHdR-Male X Cab femaleNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired50144283912064001815620913Browse results
ERX1246740UBERON:0000955 brainbrainUBERON:0000104 life cycleNANAHdR-Male X Cab femaleNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired43618003255677001964121660Browse results
ERX1246741UBERON:0002385 muscle tissueMuscleUBERON:0000104 life cycleNANAHdR-Male X Cab femaleNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired55010274558068001907421374Browse results
ERX1246742UBERON:0000948 heartHeartUBERON:0000104 life cycleNANAKagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired45259753255579001712120366.5Browse results
ERX1246743UBERON:0000955 brainbrainUBERON:0000104 life cycleNANAKagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired47288523135025001932521495.5Browse results
ERX1246744UBERON:0002385 muscle tissueMuscleUBERON:0000104 life cycleNANAKagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired46858553649336001777620714Browse results
ERX1246745UBERON:0000948 heartHeartUBERON:0000104 life cycleNANAKagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired53301254153853001747520547Browse results
ERX1246746UBERON:0000955 brainbrainUBERON:0000104 life cycleNANACab-Male X HdR femaleNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired53783363772013001984621748Browse results
ERX1246747UBERON:0002385 muscle tissueMuscleUBERON:0000104 life cycleNANACab-Male X HdR femaleNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired45301513618205001851921080Browse results
ERX1246748UBERON:0000948 heartHeartUBERON:0000104 life cycleNANACab-Male X HdR femaleNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired48675543846220001774920711Browse results
ERX1246749UBERON:0000955 brainbrainUBERON:0000104 life cycleNANACab-Male X HdR femaleNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired46067793291496001961721623.5Browse results

Showing 1 to 20 of 176 entries

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