Odom_tRNA_evolution

Experiment ID:ERP000787
Technology:RNA-Seq
Description:Homologous vertebrate tissues express a highly conserved set of transcribed genes; paradoxically, expression of tRNAs that are required to translate mRNAs into proteins have been reported to be divergent. To resolve this paradox, we mapped the genome-wide occupancy of pol III in primary tissues isolated from six mammals. We confirmed that the specific tRNA genes bound by pol III, as well as the extent and stability of binding, can vary substantially among mammalian tissues, and we discovered that this divergence is far greater between species. We combined pol III occupancy from genomically discrete tRNA loci into collective binding into isoacceptor classes and then into amino acid-based isotype classes, and at each step we found increasing conservation. At the level of amino acid isotypes, pol III binding is almost invariant among all the tissues and species profiled. Thus, the basal transcriptional machinery is constrained collectively in its synthesis of functional tRNA isotypes, despite rapid divergence of polymerase binding to specific tRNA genes.
Source:ERP000787 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 familiarisBulk RNA-Seq processed expression values in Monodelphis domestica

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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
ERX016329UBERON:0002107 liverliverMdomDv:0000021 17-month-old stage (opossum)17 monthsmaleNANANAMonodelphis domesticaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH36single2306505310487094002017422107Browse results
ERX016332UBERON:0002107 liverliverUBERON:0000112 sexually immature stage14 monthsmaleNANANACanis lupus familiarisNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH45single72529803009850001433217585Browse results
ERX016333UBERON:0002107 liverliverMdomDv:0000021 17-month-old stage (opossum)17 monthsmaleNANANAMonodelphis domesticaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH35single214201539259460002024822125Browse results
ERX016335UBERON:0002107 liverliverUBERON:0018241 prime adult stage17-18 yearsmaleNANANAMacaca mulattaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH36single1828618012380058001823420743.5Browse results
ERX016336UBERON:0002107 liverliverMmusDv:0000062 2-month-old stage (mouse)2.5 monthsmaleC57BL/6JNANAMus musculusNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH41single96678296173366001464225125Browse results
ERX016337UBERON:0002107 liverliverMmusDv:0000062 2-month-old stage (mouse)2.5 monthsmaleC57BL/6JNANAMus musculusNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH41single81039645741442001451825047.5Browse results
ERX016338UBERON:0002107 liverliverUBERON:0000113 post-juvenileadultmaleNANANAHomo sapiensNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH100single1785129911300665002313731701.5Browse results
ERX016340UBERON:0002107 liverliverMmusDv:0000062 2-month-old stage (mouse)2.5 monthsmaleC57BL/6JNANAMus musculusNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH41single108508736041294001589125892Browse results
ERX016341UBERON:0002107 liverliverUBERON:0034919 juvenile stage9 weeksmaleNANANARattus norvegicusNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH42single208476326853711001788420296Browse results
ERX016343UBERON:0002107 liverliverUBERON:0018241 prime adult stage17-18 yearsmaleNANANAMacaca mulattaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH36single2562470611886842001986121540.5Browse results
ERX016348UBERON:0002107 liverliverUBERON:0034919 juvenile stage9 weeksmaleNANANARattus norvegicusNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH36single238280109963535001883820855Browse results
ERX016350UBERON:0002107 liverliverUBERON:0000112 sexually immature stage14 monthsmaleNANANACanis lupus familiarisNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH36single1701850610071515001577618411Browse results
ERX016352UBERON:0002107 liverliverMdomDv:0000021 17-month-old stage (opossum)17 monthsmaleNANANAMonodelphis domesticaNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH36single188641944917110001978921772.5Browse results
ERX016354UBERON:0002107 liverliverUBERON:0000113 post-juvenileadultmaleNANANAHomo sapiensNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH46single187811569306777002155430220Browse results
ERX016356UBERON:0002107 liverliverUBERON:0000112 sexually immature stage14 monthsmaleNANANACanis lupus familiarisNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH45single69128502748576001407217426Browse results
ERX016362UBERON:0002107 liverliverUBERON:0000113 post-juvenileadultmaleNANANAHomo sapiensNAIlluminaIllumina Genome Analyzer IIFULL_LENGTH100single151056277446741002246631322Browse results

Showing 1 to 16 of 16 entries

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