RNA-seq in 4 tissues of 10 mammals

Experiment ID:ERP116168
Technology:RNA-Seq
Description:To study the tissue-specific evolution of regulatory elements and gene expression in the mammalian lineage, we created a comprehensive map of promoters and enhancers in 4 tissues of 10 mammalian species. To assay tissue-specific gene expression we performed RNA-seq experiments in adult liver, muscle, brain and testis of all 10 species. The species included in the study are: macaque, marmoset, mouse, rat, rabbit, pig, dog, cat, horse and opossum. To map in-vivo promoters and enhancers, we performed ChIP-seq experiments for H3K4me3, H3K27ac and H3K4me1 in all tissues and species and submitted these separately to ArrayExpress.
Source:ERP116168  SRA
Download:
Bulk RNA-Seq processed expression values in Oryctolagus cuniculusBulk RNA-Seq processed expression values in Rattus norvegicusBulk RNA-Seq processed expression values in Equus caballusBulk RNA-Seq processed expression values in Felis catusBulk RNA-Seq processed expression values in Macaca mulattaBulk RNA-Seq processed expression values in Mus musculusBulk RNA-Seq processed expression values in Callithrix jacchusBulk RNA-Seq processed expression values in Sus scrofaBulk RNA-Seq processed expression values in Canis lupus familiarisBulk RNA-Seq processed expression values in Monodelphis domestica

List of assays

Show

entries

Showing 1 to 20 of 120 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
ERX3441337UBERON:0000473 testisTestisMdomDv:0000016 12-month-old stage (opossum)1 year - adultmaleNANANAMonodelphis domesticaNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired119458995215604740079328309.5Browse results
ERX3441338UBERON:0000473 testisTestisRnorDv:0000016 10-week-old stage (rat)10 weeks - adultmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired14373018079575312002587829986.5Browse results
ERX3441339UBERON:0003663 hindlimb muscleskeletal muscle (from the upper hind leg)RnorDv:0000016 10-week-old stage (rat)10 weeks - adultmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired11640680864183681002090027268.5Browse results
ERX3441340UBERON:0000473 testisTestisMdomDv:0000016 12-month-old stage (opossum)1 year - adultmaleNANANAMonodelphis domesticaNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired132671927240964140079488311Browse results
ERX3441341UBERON:0003663 hindlimb muscleskeletal muscle (from the upper hind leg)RnorDv:0000016 10-week-old stage (rat)10 weeks - adultmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired6947022337175136002003926775.5Browse results
ERX3441342UBERON:0000473 testisTestisSscrDv:0000066 2-year-old stage (pig)2 years - adultmaleNANANASus scrofaNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired187142746111173964002870730627.5Browse results
ERX3441343UBERON:0000473 testisTestisMmusDv:0000155 9-week-old stage (mouse)9 weeks - adultmaleC57BL/6JNANAMus musculusNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired15125199795323171004211649764.5Browse results
ERX3441344UBERON:0000473 testisTestisRnorDv:0000016 10-week-old stage (rat)10 weeks - adultmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired187097528105099863002625130183.5Browse results
ERX3441345UBERON:0000955 brainBrainUBERON:0018241 prime adult stage1 year - adultmaleNANANAFelis catusNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired9026402934800046002449427327Browse results
ERX3441346UBERON:0000473 testisTestisMdomDv:0000016 12-month-old stage (opossum)1 year - adultmaleNANANAMonodelphis domesticaNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired155265340282807370079888327Browse results
ERX3441347UBERON:0000955 brainBrainUBERON:0018241 prime adult stage5 months - adultmaleNANANAOryctolagus cuniculusNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired9235689228857154002326726647.5Browse results
ERX3441348UBERON:0000955 brainBrainRnorDv:0000016 10-week-old stage (rat)10 weeks - adultmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired7322539429678373002293428362Browse results
ERX3441349UBERON:0000473 testisTestisUBERON:0000112 sexually immature stage2.5 years - adultmaleWelsh ponyNANAEquus caballusNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired418992801251985470002825329551.5Browse results
ERX3441350UBERON:0003663 hindlimb muscleskeletal muscle (from the upper hind leg)MmusDv:0000155 9-week-old stage (mouse)9 weeks - adultmaleC57BL/6JNANAMus musculusNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired5312011541824047002877342616.5Browse results
ERX3441351UBERON:0000955 brainBrainRnorDv:0000016 10-week-old stage (rat)10 weeks - adultmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired6657612326956432002262628215.5Browse results
ERX3441352UBERON:0003663 hindlimb muscleskeletal muscle (from the upper hind leg)UBERON:0018241 prime adult stage1.5 years - adultmaleNANANACallithrix jacchusNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired7542045041943476002629734668.5Browse results
ERX3441353UBERON:0000955 brainBrainUBERON:0018241 prime adult stage1.5 years - adultmaleNANANACallithrix jacchusNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired5868308516819078002954536450.5Browse results
ERX3441354UBERON:0000955 brainBrainSscrDv:0000066 2-year-old stage (pig)2 years - adultmaleNANANASus scrofaNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired16763123283637541002691529641Browse results
ERX3441355UBERON:0002107 liverLiverRnorDv:0000016 10-week-old stage (rat)10 weeks - adultmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired13266554179024580002047927035.5Browse results
ERX3441356UBERON:0002107 liverLiverSscrDv:0000066 2-year-old stage (pig)2 years - adultmaleNANANASus scrofaNAIlluminaIllumina NovaSeq 6000FULL_LENGTH150paired7149847443499791002492228700.5Browse results

Showing 1 to 20 of 120 entries