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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Showing 41 to 60 of 176 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
ERX1246770UBERON:0002107 liverliverUBERON:0000104 life cycleNANANANANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired54855004595052001590919768.5Browse results
ERX1246771UBERON:0002107 liverliverUBERON:0000104 life cycleNANANANANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired47500013774909001503419319Browse results
ERX1246772UBERON:0002107 liverliverUBERON:0000104 life cycleNANANANANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired47258103806525001526319419Browse results
ERX1246773UBERON:0002107 liverliverUBERON:0000104 life cycleNANANANANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired50352634183228001623019907Browse results
ERX1265920UBERON:0000948 heartHeartUBERON:0000104 life cycleNANAHd-rR X KagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired45450423514445001752520580.5Browse results
ERX1265921UBERON:0000955 brainbrainUBERON:0000104 life cycleNANAHd-rR X KagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired50671993482367001985221753Browse results
ERX1265922UBERON:0002385 muscle tissueMuscleUBERON:0000104 life cycleNANAHd-rR X KagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired52467324273646001818720918.5Browse results
ERX1265923UBERON:0000948 heartHeartUBERON:0000104 life cycleNANAHd-rR X KagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired53251394183267001805820873Browse results
ERX1265924UBERON:0000955 brainbrainUBERON:0000104 life cycleNANAHd-rR X KagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired53450443747224001996421829.5Browse results
ERX1265925UBERON:0002385 muscle tissueMuscleUBERON:0000104 life cycleNANAHd-rR X KagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired53857984339589001778620711.5Browse results
ERX1265926UBERON:0000948 heartHeartUBERON:0000104 life cycleNANAHdR-Male X Cab femaleNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired56547514149181001813220911.5Browse results
ERX1265927UBERON:0000955 brainbrainUBERON:0000104 life cycleNANAHdR-Male X Cab femaleNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired61605044218532002027021955.5Browse results
ERX1265928UBERON:0002385 muscle tissueMuscleUBERON:0000104 life cycleNANAHdR-Male X Cab femaleNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired58786964678366001875721220.5Browse results
ERX1265929UBERON:0000948 heartHeartUBERON:0000104 life cycleNANAHdR-Male X Cab femaleNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired59870324667603001846521061Browse results
ERX1265930UBERON:0000955 brainbrainUBERON:0000104 life cycleNANAHdR-Male X Cab femaleNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired51875063866899001982421727.5Browse results
ERX1265931UBERON:0002385 muscle tissueMuscleUBERON:0000104 life cycleNANAHdR-Male X Cab femaleNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired65156835393380001932921501.5Browse results
ERX1265932UBERON:0000948 heartHeartUBERON:0000104 life cycleNANAKagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired53586243849060001732620472.5Browse results
ERX1265933UBERON:0000955 brainbrainUBERON:0000104 life cycleNANAKagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired55852303695114001952321597.5Browse results
ERX1265934UBERON:0002385 muscle tissueMuscleUBERON:0000104 life cycleNANAKagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired56012624359203001809720866.5Browse results
ERX1265935UBERON:0000948 heartHeartUBERON:0000104 life cycleNANAKagaNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired63566304949492001774920699Browse results

Showing 41 to 60 of 176 entries

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