Rat_olfactory_transcriptome

Experiment ID:ERP002602
Technology:RNA-Seq
Description:The olfactory gene repertoire is largely species-specific, shaped by the nature and necessity of chemosensory information for survival in each species' niche. We are intrigued by this interspecific variation and aim to investigate the olfactory transcriptome across mammals. The rat is the best candidate species to start a comparative study because of its phylogenetic proximity to mice, because it has a similar biology, a similar but not identical olfactory receptor repertoire and a well annotated genome. Thus, analysing the olfactory transcriptome of the rat will serve both as the first step and as a proof of concept for the pan-mammalian comparative analysis we aim to do
Source:ERP002602 SRA

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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
ERX305303UBERON:0001997 olfactory epitheliumOlfactory epitheliumRnorDv:0000016 10-week-old stage (rat)10 weeksmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired3144643925111504002047123287.5Browse results
ERX305304UBERON:0001997 olfactory epitheliumOlfactory epitheliumRnorDv:0000016 10-week-old stage (rat)10 weeksmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired3264775725751337002059323460Browse results
ERX305305UBERON:0001997 olfactory epitheliumOlfactory epitheliumRnorDv:0000016 10-week-old stage (rat)10 weeksmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired2507223819888905002017223141Browse results
ERX305306UBERON:0002255 vomeronasal organVomeronasal organRnorDv:0000016 10-week-old stage (rat)10 weeksmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired3190347725820808001973922913.5Browse results
ERX305307UBERON:0002255 vomeronasal organVomeronasal organRnorDv:0000016 10-week-old stage (rat)10 weeksmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired2145972517175981001913422506.5Browse results
ERX305308UBERON:0002255 vomeronasal organVomeronasal organRnorDv:0000016 10-week-old stage (rat)10 weeksmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired1366521010965885001841421935.5Browse results
ERX305309UBERON:0001997 olfactory epitheliumOlfactory epitheliumRnorDv:0000016 10-week-old stage (rat)10 weeksmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired3169032625321301002048423335.5Browse results
ERX305310UBERON:0001997 olfactory epitheliumOlfactory epitheliumRnorDv:0000016 10-week-old stage (rat)10 weeksmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired3292280025978110002061423459Browse results
ERX305311UBERON:0001997 olfactory epitheliumOlfactory epitheliumRnorDv:0000016 10-week-old stage (rat)10 weeksmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired2524017420029949002020123160.5Browse results
ERX305312UBERON:0002255 vomeronasal organVomeronasal organRnorDv:0000016 10-week-old stage (rat)10 weeksmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired3216419226041449001977722902Browse results
ERX305313UBERON:0002255 vomeronasal organVomeronasal organRnorDv:0000016 10-week-old stage (rat)10 weeksmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired2162108617316712001912622529.5Browse results
ERX305314UBERON:0002255 vomeronasal organVomeronasal organRnorDv:0000016 10-week-old stage (rat)10 weeksmaleBrown NorwayNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH100paired1377324011061276001837621885.5Browse results