Evolutionary dynamics of gene and isoform regulation in mammalian tissues

Experiment ID:GSE41637
Technology:RNA-Seq
Description:Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear. To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth. We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific. Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators. Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling.
DOI:10.1126/science.1228186
Source:GSE41637  GEO
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Bulk RNA-Seq processed expression values in Rattus norvegicusBulk RNA-Seq processed expression values in Gallus gallusBulk RNA-Seq processed expression values in Macaca mulattaBulk RNA-Seq processed expression values in Bos taurusBulk RNA-Seq processed expression values in Mus musculus

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Showing 1 to 20 of 134 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
SRX196264UBERON:0000955 brainbrainUBERON:0000113 post-juvenilebreeding ageNADBA/2JNANAMus musculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50paired8726460472862807002887835189.5Browse results
SRX196265UBERON:0001155 coloncolonUBERON:0000113 post-juvenilebreeding ageNADBA/2JNANAMus musculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50paired10181649187953975002754533778Browse results
SRX196266UBERON:0000948 heartheartUBERON:0000113 post-juvenilebreeding ageNADBA/2JNANAMus musculusNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH36paired3517598224847247002045128751Browse results
SRX196267UBERON:0000082 adult mammalian kidneykidneyUBERON:0000113 post-juvenilebreeding ageNADBA/2JNANAMus musculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50paired119274786103871321002802934417.5Browse results
SRX196268UBERON:0002107 liverliverUBERON:0000113 post-juvenilebreeding ageNADBA/2JNANAMus musculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50paired116292478103173931002413631778Browse results
SRX196269UBERON:0002048 lunglungUBERON:0000113 post-juvenilebreeding ageNADBA/2JNANAMus musculusNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH36paired3405062622524048002222629655Browse results
SRX196270UBERON:0001134 skeletal muscle tissueskeletal muscleUBERON:0000113 post-juvenilebreeding ageNADBA/2JNANAMus musculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50paired113111277104982985002483732112.5Browse results
SRX196271UBERON:0002106 spleenspleenUBERON:0000113 post-juvenilebreeding ageNADBA/2JNANAMus musculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50paired11407225788781141002783533886.5Browse results
SRX196272UBERON:0000473 testistestesUBERON:0000113 post-juvenilebreeding agemaleDBA/2JNANAMus musculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50paired10919993892062351003305237659Browse results
SRX196273UBERON:0000955 brainbrainUBERON:0000113 post-juvenilebreeding ageNAC57BL/6JNANAMus musculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH80paired11882435397061708002939835698Browse results
SRX196274UBERON:0001155 coloncolonUBERON:0000113 post-juvenilebreeding ageNAC57BL/6JNANAMus musculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH80paired8744733477295989002653733074.5Browse results
SRX196275UBERON:0000082 adult mammalian kidneykidneyUBERON:0000113 post-juvenilebreeding ageNAC57BL/6JNANAMus musculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH77paired118885190105495485002735333975.5Browse results
SRX196276UBERON:0002107 liverliverUBERON:0000113 post-juvenilebreeding ageNAC57BL/6JNANAMus musculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH80paired134045721120338300002424132021.5Browse results
SRX196277UBERON:0002048 lunglungUBERON:0000113 post-juvenilebreeding ageNAC57BL/6JNANAMus musculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH80paired6236290151758197002718733743Browse results
SRX196278UBERON:0001134 skeletal muscle tissueskeletal muscleUBERON:0000113 post-juvenilebreeding ageNAC57BL/6JNANAMus musculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH80paired117171737106701334002581532943Browse results
SRX196279UBERON:0002106 spleenspleenUBERON:0000113 post-juvenilebreeding ageNAC57BL/6JNANAMus musculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH80paired11481414292043742002732233717Browse results
SRX196280UBERON:0000473 testistestesUBERON:0000113 post-juvenilebreeding agemaleC57BL/6JNANAMus musculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH80paired11652514798299384003146936652.5Browse results
SRX196281UBERON:0000955 brainbrainUBERON:0000113 post-juvenilebreeding ageNACD-1NANAMus musculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH40paired3251123418308439002114929084Browse results
SRX196282UBERON:0001155 coloncolonUBERON:0000113 post-juvenilebreeding ageNACD-1NANAMus musculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH40paired3424844420013823002018128258.5Browse results
SRX196283UBERON:0000948 heartheartUBERON:0000113 post-juvenilebreeding ageNACD-1NANAMus musculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH40paired159686058456717001839527393.5Browse results

Showing 1 to 20 of 134 entries