run_metadata
9 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "PolyA" and tissue_curation = "Undetermined"
This data as json, CSV (advanced)
| Link | rowid ▼ | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 23 | 23 | DRR334968 | DRX323964 | DRS217304 | DRP008001 | PRJDB12578 | Allometric scaling of RNA abundance from genes to communities | DRP008001 | Other | The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes. | mRNA metatranscriptomic sequences from mock communities consist of five model species | mRNA mock community at 28 degrees rep 3 | SAMD00422588 | sample name:mRNA mock community 28 degrees rep 3|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:28|treatment:mRNA | NextSeq 2000 sequencing of SAMD00422588 | DRX323964 | m28 3 mRNA.fastq | 1 | NEBNext Kit for Illumina | RNA-Seq | METATRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | NextSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP008001 | NextSeq 2000 sequencing of SAMD00422588 | 3157078356.0 | 31416275.0 | DRR334968 | 0:100.49 1:0 | A:816263259;C:752748024;G:759884392;T:828182261;N:420 | 100 | 0 | 816263259 | 752748024 | 759884392 | 828182261 | 420 | DRX323964 | DRS217304 | DRA013226 | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | 1 | 0.64888 | 0.01832 | 0.73996 | 0.46811 | 99 | B | usable mapping rate | illumina | nextseq_v2 | unknown | poly_a | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 24 | 24 | DRR334967 | DRX323963 | DRS217303 | DRP008001 | PRJDB12578 | Allometric scaling of RNA abundance from genes to communities | DRP008001 | Other | The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes. | mRNA metatranscriptomic sequences from mock communities consist of five model species | mRNA mock community at 28 degrees rep 2 | SAMD00422587 | sample name:mRNA mock community 28 degrees rep 2|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:28|treatment:mRNA | NextSeq 2000 sequencing of SAMD00422587 | DRX323963 | m28 2 mRNA.fastq | 1 | NEBNext Kit for Illumina | RNA-Seq | METATRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | NextSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP008001 | NextSeq 2000 sequencing of SAMD00422587 | 3155807651.0 | 31404635.0 | DRR334967 | 0:100.49 1:0 | A:819014350;C:749873295;G:756284406;T:830635394;N:206 | 100 | 0 | 819014350 | 749873295 | 756284406 | 830635394 | 206 | DRX323963 | DRS217303 | DRA013226 | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | 1 | 0.76742 | 0.02238 | 0.72427 | 0.47376 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | poly_a | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 25 | 25 | DRR334966 | DRX323962 | DRS217302 | DRP008001 | PRJDB12578 | Allometric scaling of RNA abundance from genes to communities | DRP008001 | Other | The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes. | mRNA metatranscriptomic sequences from mock communities consist of five model species | mRNA mock community at 28 degrees rep 1 | SAMD00422586 | sample name:mRNA mock community 28 degrees rep 1|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:28|treatment:mRNA | NextSeq 2000 sequencing of SAMD00422586 | DRX323962 | m28 1 mRNA.fastq | 1 | NEBNext Kit for Illumina | RNA-Seq | METATRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | NextSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP008001 | NextSeq 2000 sequencing of SAMD00422586 | 2589772286.0 | 25765782.0 | DRR334966 | 0:100.51 1:0 | A:679223577;C:610675892;G:617869465;T:682003195;N:157 | 100 | 0 | 679223577 | 610675892 | 617869465 | 682003195 | 157 | DRX323962 | DRS217302 | DRA013226 | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | 1 | 0.42984 | 0.03367 | 0.73555 | 0.49223 | 100 | B | usable mapping rate | illumina | nextseq_v2 | unknown | poly_a | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 26 | 26 | DRR334965 | DRX323961 | DRS217318 | DRP008001 | PRJDB12578 | Allometric scaling of RNA abundance from genes to communities | DRP008001 | Other | The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes. | mRNA metatranscriptomic sequences from mock communities consist of five model species | mRNA mock community at 19 degrees rep 3 | SAMD00422602 | sample name:mRNA mock community 19 degrees rep 3|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:19|treatment:mRNA | NextSeq 2000 sequencing of SAMD00422602 | DRX323961 | m19 3 mRNA.fastq | 1 | NEBNext Kit for Illumina | RNA-Seq | METATRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | NextSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP008001 | NextSeq 2000 sequencing of SAMD00422602 | 3124746628.0 | 31095367.0 | DRR334965 | 0:100.49 1:0 | A:821891547;C:734660854;G:739230475;T:828963220;N:532 | 100 | 0 | 821891547 | 734660854 | 739230475 | 828963220 | 532 | DRX323961 | DRS217318 | DRA013226 | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | 1 | 0.72881 | 0.03264 | 0.69449 | 0.47416 | 99 | B | usable mapping rate | illumina | nextseq_v2 | unknown | poly_a | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 27 | 27 | DRR334964 | DRX323960 | DRS217317 | DRP008001 | PRJDB12578 | Allometric scaling of RNA abundance from genes to communities | DRP008001 | Other | The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes. | mRNA metatranscriptomic sequences from mock communities consist of five model species | mRNA mock community at 19 degrees rep 2 | SAMD00422601 | sample name:mRNA mock community 19 degrees rep 2|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:19|treatment:mRNA | NextSeq 2000 sequencing of SAMD00422601 | DRX323960 | m19 2 mRNA.fastq | 1 | NEBNext Kit for Illumina | RNA-Seq | METATRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | NextSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP008001 | NextSeq 2000 sequencing of SAMD00422601 | 3171661466.0 | 31561473.0 | DRR334964 | 0:100.49 1:0 | A:836793307;C:742872021;G:750053514;T:841942389;N:235 | 100 | 0 | 836793307 | 742872021 | 750053514 | 841942389 | 235 | DRX323960 | DRS217317 | DRA013226 | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | 1 | 0.63153 | 0.03639 | 0.69027 | 0.48494 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | poly_a | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 28 | 28 | DRR334963 | DRX323959 | DRS217316 | DRP008001 | PRJDB12578 | Allometric scaling of RNA abundance from genes to communities | DRP008001 | Other | The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes. | mRNA metatranscriptomic sequences from mock communities consist of five model species | mRNA mock community at 19 degrees rep 1 | SAMD00422600 | sample name:mRNA mock community 19 degrees rep 1|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:19|treatment:mRNA | NextSeq 2000 sequencing of SAMD00422600 | DRX323959 | m19 1 mRNA.fastq | 1 | NEBNext Kit for Illumina | RNA-Seq | METATRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | NextSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP008001 | NextSeq 2000 sequencing of SAMD00422600 | 2916453082.0 | 29023768.0 | DRR334963 | 0:100.48 1:0 | A:761416880;C:692014182;G:696272089;T:766749729;N:202 | 100 | 0 | 761416880 | 692014182 | 696272089 | 766749729 | 202 | DRX323959 | DRS217316 | DRA013226 | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | 1 | 0.71651 | 0.03406 | 0.68696 | 0.47496 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | poly_a | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 29 | 29 | DRR334962 | DRX323958 | DRS217315 | DRP008001 | PRJDB12578 | Allometric scaling of RNA abundance from genes to communities | DRP008001 | Other | The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes. | mRNA metatranscriptomic sequences from mock communities consist of five model species | mRNA mock community at 10 degrees rep 3 | SAMD00422599 | sample name:mRNA mock community 10 degrees rep 3|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:10|treatment:mRNA | NextSeq 2000 sequencing of SAMD00422599 | DRX323958 | m10 3 mRNA.fastq | 1 | NEBNext Kit for Illumina | RNA-Seq | METATRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | NextSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP008001 | NextSeq 2000 sequencing of SAMD00422599 | 2600103192.0 | 25872833.0 | DRR334962 | 0:100.50 1:0 | A:668944597;C:625686885;G:631010166;T:674461210;N:334 | 100 | 0 | 668944597 | 625686885 | 631010166 | 674461210 | 334 | DRX323958 | DRS217315 | DRA013226 | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | 1 | 0.57077 | 0.02949 | 0.71918 | 0.47633 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | poly_a | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 30 | 30 | DRR334961 | DRX323957 | DRS217314 | DRP008001 | PRJDB12578 | Allometric scaling of RNA abundance from genes to communities | DRP008001 | Other | The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes. | mRNA metatranscriptomic sequences from mock communities consist of five model species | mRNA mock community at 10 degrees rep 2 | SAMD00422598 | sample name:mRNA mock community 10 degrees rep 2|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:10|treatment:mRNA | NextSeq 2000 sequencing of SAMD00422598 | DRX323957 | m10 2 mRNA.fastq | 1 | NEBNext Kit for Illumina | RNA-Seq | METATRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | NextSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP008001 | NextSeq 2000 sequencing of SAMD00422598 | 2608660833.0 | 25958804.0 | DRR334961 | 0:100.49 1:0 | A:683370128;C:615324906;G:621209484;T:688756167;N:148 | 100 | 0 | 683370128 | 615324906 | 621209484 | 688756167 | 148 | DRX323957 | DRS217314 | DRA013226 | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | 1 | 0.63764 | 0.04316 | 0.69656 | 0.48579 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | poly_a | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 31 | 31 | DRR334960 | DRX323956 | DRS217301 | DRP008001 | PRJDB12578 | Allometric scaling of RNA abundance from genes to communities | DRP008001 | Other | The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes. | mRNA metatranscriptomic sequences from mock communities consist of five model species | mRNA mock community at 10 degrees rep 1 | SAMD00422585 | sample name:mRNA mock community 10 degrees rep 1|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:10|treatment:mRNA | NextSeq 2000 sequencing of SAMD00422585 | DRX323956 | m10 1 mRNA.fastq | 1 | NEBNext Kit for Illumina | RNA-Seq | METATRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | NextSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP008001 | NextSeq 2000 sequencing of SAMD00422585 | 2879915507.0 | 28651533.0 | DRR334960 | 0:100.52 1:0 | A:761972464;C:675761096;G:678969165;T:763212637;N:145 | 100 | 0 | 761972464 | 675761096 | 678969165 | 763212637 | 145 | DRX323956 | DRS217301 | DRA013226 | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | 1 | 0.47851 | 0.05671 | 0.72622 | 0.49269 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | poly_a | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;