Digital gene expression and global mapping of polyadenylation sites with PolyA-Seq

Experiment ID:SRP007359
Technology:RNA-Seq
Description:We describe PolyA-Seq, a strand-specific method for high-throughput sequencing of the 3' ends of polyadenylated transcripts. PolyA-Seq is as accurate for digital gene expression as existing RNA sequencing approaches, and superior to microarrays. We used the approach to map polyadenylation (polyA) sites in 24 samples from normal tissues in human, rhesus, dog, mouse, and rat. Overall design: Detection of polyA sites in a mixture of 24 tissues in human, mouse, rat, dog and rhesus. Samples included two replicates each of MAQC Human Brain Reference and MAQC Universal Human Reference. Two additional human sets of reads are included that were used to distinguish true polyA sites from internal priming sites.
Source:SRP007359  SRA
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Bulk RNA-Seq processed expression values in Rattus norvegicusBulk RNA-Seq processed expression values in Homo sapiensBulk RNA-Seq processed expression values in Macaca mulattaBulk RNA-Seq processed expression values in Mus musculusBulk RNA-Seq processed expression values in Canis lupus familiaris

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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
SRX080216UBERON:0000955 brainbrainUBERON:0018241 prime adult stage4 yearmaleNANANACanis lupus familiarisNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single158083837195469001200116436.5Browse results
SRX080217UBERON:0000082 adult mammalian kidneykidneyUBERON:0018241 prime adult stage4 yearmaleNANANACanis lupus familiarisNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single157637177928341001158116238Browse results
SRX080218UBERON:0000473 testistestisUBERON:0018241 prime adult stage4 yearmaleNANANACanis lupus familiarisNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single155548947434381001376417662Browse results
SRX080219UBERON:0000955 brainbrainUBERON:0000104 life cycleNANANANANAHomo sapiensNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single1854066410109111002086429711.5Browse results
SRX080220UBERON:0002113 kidneykidneyUBERON:0000104 life cycleNANANANANAHomo sapiensNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single1823624112712059002122430406.5Browse results
SRX080221UBERON:0002107 liverliverUBERON:0000104 life cycleNANANANANAHomo sapiensNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single1787107313865698001970229337.5Browse results
SRX080222UBERON:0000955 brainbrain (MAQC)UBERON:0000113 post-juvenile23-86 yearsNANANANAHomo sapiensNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single1526224012746391002196231103.5Browse results
SRX080223UBERON:0000955 brainbrain (MAQC)UBERON:0000113 post-juvenile23-86 yearsNANANANAHomo sapiensNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single1487145012329239002169730889Browse results
SRX080224UBERON:0000468 multicellular organismUniversal Human Reference (MAQC)UBERON:0000104 life cycleNANANANANAHomo sapiensNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single1507791212524326002228631263Browse results
SRX080225UBERON:0000468 multicellular organismUniversal Human Reference (MAQC)UBERON:0000104 life cycleNANANANANAHomo sapiensNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single1488890612357215002249931436Browse results
SRX080226UBERON:0002385 muscle tissuemuscleUBERON:0000104 life cycleNANANANANAHomo sapiensNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single1921958214361278002182730755Browse results
SRX080227UBERON:0000468 multicellular organismUniversal Human Reference (MAQC)UBERON:0000104 life cycleNANANANANAHomo sapiensNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single167353419989956001805627754Browse results
SRX080228UBERON:0000473 testistestisUBERON:0000104 life cycleNAmaleNANANAHomo sapiensNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single1643333210925014002176330509.5Browse results
SRX080229UBERON:0000468 multicellular organismUniversal Human Reference (MAQC)UBERON:0000104 life cycleNANANANANAHomo sapiensNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single2297062617549849002227831058.5Browse results
SRX080230UBERON:0000955 brainbrainMmusDv:0000158 12-week-old stage (mouse)12 weeksfemaleNANANAMus musculusNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single135435453313421001516525448Browse results
SRX080231UBERON:0000082 adult mammalian kidneykidneyUBERON:0000112 sexually immature stage3-4 weeksfemaleNANANAMus musculusNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single123337469339163001635526113.5Browse results
SRX080232UBERON:0002107 liverliverMmusDv:0000154 8-week-old stage (mouse)8 weeksfemaleNANANAMus musculusNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single115844319294420001344824421Browse results
SRX080233UBERON:0002385 muscle tissuemuscleUBERON:0018241 prime adult stage6-8 weeksfemaleNANANAMus musculusNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single1768896113559213001870527703Browse results
SRX080234UBERON:0000473 testistestisUBERON:0018241 prime adult stage6-8 weeksmaleNANANAMus musculusNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single120680187729707001459425020.5Browse results
SRX080235UBERON:0000955 brainbrainUBERON:0000104 life cycleNANANANANARattus norvegicusNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH76single2001324910200167001406818242Browse results

Showing 1 to 20 of 26 entries