Transcriptome Profiling of Ten Porcine Tissues at the Gene, Isoform and TSS level

Experiment ID:ERP002055
Technology:RNA-Seq
Description:In this study we have employed RNA seq on ten different tissues including four brain tissues from two boars to gain a understanding of the differential variations in transcriptional profiles for these tissues consisting of occipital cortex, frontal cortex, hypothalamus and cerebellum along with such diverse tissues as heart, spleen, liver, kidney, lung and musculus longissimus dorsi. This has enabled us to perform comparative gene expression analysis of brain regions versus non-brain tissues along with inter-brain tissue comparisons. Hence, we have tested for differentially expressed genes and isoforms, differential splicing, transcription start sites (TSS), and differential promoter usage between all ten porcine tissues.
Source:ERP002055 SRA
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Bulk RNA-Seq processed expression values in Sus scrofa

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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
ERX183591UBERON:0002106 spleenspleenUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single35373062364148001568719572Browse results
ERX183592UBERON:0002037 cerebellumcerebellumUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single17314381146472001545119414Browse results
ERX183593UBERON:0000082 adult mammalian kidneykidneyUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single21997111554899001463218885Browse results
ERX183594UBERON:0002107 liverliverUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single32162592461047001380518438.5Browse results
ERX183595UBERON:0001870 frontal cortexfrontal cortexUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single836868580835001398018531.5Browse results
ERX183596UBERON:0002037 cerebellumcerebellumUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single1460159934923001490319062Browse results
ERX183597UBERON:0002106 spleenspleenUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single35481042491114001574219603Browse results
ERX183598UBERON:0001898 hypothalamushypothalamusUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single713840460773001353418271.5Browse results
ERX183599UBERON:0000948 heartheartUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single18517061322235001315818074Browse results
ERX183600UBERON:0002048 lunglungUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single22825661553563001561719462Browse results
ERX183601UBERON:0000082 adult mammalian kidneykidneyUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single22656671593462001443318765Browse results
ERX183602UBERON:0001898 hypothalamushypothalamusUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single433986279426001263517793Browse results
ERX183603UBERON:0002048 lunglungUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single41017762811128001638119894.5Browse results
ERX183604UBERON:0002106 spleenspleenUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single32382322235998001562919536.5Browse results
ERX183605UBERON:0001401 longissimus thoracis muscleLongissimus dorsiUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single19713141423595001283417899Browse results
ERX183606UBERON:0000082 adult mammalian kidneykidneyUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single1325386944926001391218465Browse results
ERX183607UBERON:0002048 lunglungUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single39312702721223001637919891Browse results
ERX183608UBERON:0000082 adult mammalian kidneykidneyUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single24465061663262001449118791.5Browse results
ERX183609UBERON:0001870 frontal cortexfrontal cortexUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single513926342047001330018167.5Browse results
ERX183610UBERON:0002106 spleenspleenUBERON:0018241 prime adult stageone year oldmaleLandraceNANASus scrofaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH50single28808612038255001591419733Browse results

Showing 1 to 20 of 100 entries

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