RNA-seq of different tissues from Sus scrofa

Experiment ID:E-MTAB-5895
Technology:RNA-Seq
Description:RNA sequencing of pig tissues for transcriptome annotation and expression analysis. Tissue specific RNA-seq data was generated to support annotation of coding and non-coding genes and to measure tissue specific expression. This study is part of the FAANG project, promoting rapid prepublication of data to support the research community. These data are released under Fort Lauderdale principles, as confirmed in the Toronto Statement (Toronto International Data Release Workshop. Birney et al. 2009. Pre-publication data sharing. Nature 461:168-170). Any use of this dataset must abide by the FAANG data sharing principles. Data producers reserve the right to make the first publication of a global analysis of this data. If you are unsure if you are allowed to publish on this dataset, please contact alan.archibald@roslin.ed.ac.uk, lel.eory@roslin.ed.ac.uk and faang@iastate.edu to enquire. The full guidelines can be found at http://www.faang.org/data-share-principle.
DOI:10.3389/fgene.2019.01355
Source:E-MTAB-5895 ArrayExpress
Download:
Bulk RNA-Seq processed expression values in Sus scrofa

List of assays

Show

entries

Showing 1 to 20 of 56 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
ERX1886666UBERON:0000007 pituitary glandpituitary glandUBERON:0034919 juvenile stage4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH100paired6559819833240244002214723913.5Browse results
ERX1886667UBERON:0010533 metanephros cortexcortex of kidneyUBERON:0034919 juvenile stage4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH100paired6343038937662709002131923306Browse results
ERX1886668UBERON:0002084 heart left ventricleheart left ventricleUBERON:0034919 juvenile stage4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH100paired6771161845776473002048822860Browse results
ERX1886669UBERON:0001153 caecumcaecumUBERON:0034919 juvenile stage4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH150paired5597362432407021002086123021Browse results
ERX1886670UBERON:0001153 caecumcaecumUBERON:0034919 juvenile stage4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH100paired6897248941595134002143223348.5Browse results
ERX1886671UBERON:0002509 mesenteric lymph nodemesenteric lymph nodeUBERON:0034919 juvenile stage4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH150paired6391551329527670002076822968.5Browse results
ERX1886672UBERON:0002509 mesenteric lymph nodemesenteric lymph nodeUBERON:0034919 juvenile stage4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH100paired6971283235061354002177123554.5Browse results
ERX1886673UBERON:0001134 skeletal muscle tissueskeletal muscle tissueUBERON:0034919 juvenile stage4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH100paired6363269738359629002045622817Browse results
ERX1886674UBERON:0002106 spleenspleenUBERON:0034919 juvenile stage4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH100paired5725146025792805002171523514Browse results
ERX1886675UBERON:0000995 uterusuterusUBERON:0034919 juvenile stage4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH150paired4519099421059660002129223300.5Browse results
ERX1886677UBERON:0003688 omentumomentumUBERON:0034919 juvenile stage4 monthsfemaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH100paired4492049024076121002142623460.5Browse results
ERX1886678UBERON:0010533 metanephros cortexcortex of kidneyUBERON:0034919 juvenile stage4 monthsmaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH100paired6587782641465905002129023281Browse results
ERX1886679UBERON:0002084 heart left ventricleheart left ventricleUBERON:0034919 juvenile stage4 monthsmaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH100paired6482601640818586002081122999Browse results
ERX1886680UBERON:0001153 caecumcaecumUBERON:0034919 juvenile stage4 monthsmaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH100paired5180087130663615002115423125Browse results
ERX1886681UBERON:0002509 mesenteric lymph nodemesenteric lymph nodeUBERON:0034919 juvenile stage4 monthsmaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH150paired5524140227504045002110723151.5Browse results
ERX1886682UBERON:0002509 mesenteric lymph nodemesenteric lymph nodeUBERON:0034919 juvenile stage4 monthsmaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH100paired3557680517858628002092723011.5Browse results
ERX1886683UBERON:0002106 spleenspleenUBERON:0034919 juvenile stage4 monthsmaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH100paired4021064520308616002126423278Browse results
ERX1886684UBERON:0002372 tonsiltonsilUBERON:0034919 juvenile stage4 monthsmaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH150paired5978419231646292002145323368Browse results
ERX1886685UBERON:0002372 tonsiltonsilUBERON:0034919 juvenile stage4 monthsmaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH100paired10059902853240850002260624067Browse results
ERX1886686UBERON:0001301 epididymisepididymisUBERON:0034919 juvenile stage4 monthsmaleDurocNANASus scrofaNAIlluminaIllumina HiSeq 2500FULL_LENGTH150paired5259313026288908002154223465.5Browse results

Showing 1 to 20 of 56 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