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
Download:
Bulk RNA-Seq processed expression values in Oryzias latipes

List of assays

Show

entries

Showing 21 to 40 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
ERX1246750UBERON:0002385 muscle tissueMuscleUBERON:0000104 life cycleNANACab-Male X HdR femaleNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired42154153479747001841521036Browse results
ERX1246751UBERON:0000948 heartHeartUBERON:0000104 life cycleNANAKaga X Hd-rRNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired45054043289027001783820735.5Browse results
ERX1246752UBERON:0000955 brainbrainUBERON:0000104 life cycleNANAKaga X Hd-rRNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired48828693328817002005921857Browse results
ERX1246753UBERON:0002385 muscle tissueMuscleUBERON:0000104 life cycleNANAKaga X Hd-rRNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired50862203902220001897721316Browse results
ERX1246754UBERON:0000948 heartHeartUBERON:0000104 life cycleNANAKaga X Hd-rRNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired56815564072977001801220824Browse results
ERX1246755UBERON:0000955 brainbrainUBERON:0000104 life cycleNANAKaga X Hd-rRNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired44617902834575001978221715.5Browse results
ERX1246756UBERON:0002385 muscle tissueMuscleUBERON:0000104 life cycleNANAKaga X Hd-rRNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired44749663548371001785620745Browse results
ERX1246757UBERON:0000948 heartHeartUBERON:0000104 life cycleNANACabNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired47906473722697001741320520.5Browse results
ERX1246758UBERON:0000955 brainbrainUBERON:0000104 life cycleNANACabNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired44703003187723001991021791.5Browse results
ERX1246759UBERON:0002385 muscle tissueMuscleUBERON:0000104 life cycleNANACabNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired46053163604668001825620954.5Browse results
ERX1246760UBERON:0000948 heartHeartUBERON:0000104 life cycleNANAHd-rRNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired46781563653790001731620468Browse results
ERX1246761UBERON:0000955 brainbrainUBERON:0000104 life cycleNANAHd-rRNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired53569163678247001961021642.5Browse results
ERX1246762UBERON:0002385 muscle tissueMuscleUBERON:0000104 life cycleNANAHd-rRNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired48778923771182001964821649Browse results
ERX1246763UBERON:0002107 liverliverUBERON:0000104 life cycleNANAHd-rRNANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired47016213935462001496019267.5Browse results
ERX1246764UBERON:0002107 liverliverUBERON:0000104 life cycleNANANANANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired48191164062567001630819982Browse results
ERX1246765UBERON:0002107 liverliverUBERON:0000104 life cycleNANANANANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired50349734229581001502219307.5Browse results
ERX1246766UBERON:0002107 liverliverUBERON:0000104 life cycleNANANANANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired51553284315580001546819524.5Browse results
ERX1246767UBERON:0002107 liverliverUBERON:0000104 life cycleNANANANANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired48892304170748001480419188.5Browse results
ERX1246768UBERON:0002107 liverliverUBERON:0000104 life cycleNANANANANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired50933273844776001578519691Browse results
ERX1246769UBERON:0002107 liverliverUBERON:0000104 life cycleNANANANANAOryzias latipesNAIlluminaIllumina HiSeq 2000FULL_LENGTH125paired56492904668184001521219420.5Browse results

Showing 21 to 40 of 176 entries

This website requires cookies, and limited processing of your personal data in order to function. By using the site you are agreeing to this as outlined in our privacy notice.
Do not show this banner again