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run_metadata

25 rows where technology = "unknown" and tissue_curation = "Scale"

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experiment.library_selection 3

experiment.library_layout 2

devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

tissue_curation 1

  • Scale · 25 ✖

technology 1

  • unknown · 25 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

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
9970 9970 ERR5056255 ERX4862324 ERS4959151 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   9 days post harvest Zebrafish scale RNA seq total RNA SAMEA7198930 University of Bristol ENA first public:2021 04 20|ENA last update:2020 08 20|External Id:SAMEA7198930|INSDC center alias:BRISTOL|INSDC center name:University of Bristol|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 3|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 3|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 10 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_REG3_CTTGTA_L002_R1_001.fastq.gz fastq 435534645.0 8539895.0 ena RUN BRISTOL 08 01 2021 15:14:53:483 10 0:51 1:0 A:104994334;C:102642310;G:101303422;T:126578362;N:16217 51 0     104994334 102642310 101303422 126578362 16217 ERX4862324 ERS4959151 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.92322   0.08481   0.71997   0.45351   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9971 9971 ERR5056093 ERX4862162 ERS4959146 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   day x Zebrafish scale RNA seq total RNA SAMEA7198925 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198925|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 1|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 1|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 13:16:55:212 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_ONT1_CGATGT_L002_R1_001.fastq.gz fastq 613101549.0 12021599.0 ena RUN BRISTOL 08 01 2021 13:16:55:212 1 0:51 1:0 A:152016801;C:139221646;G:139332264;T:182506912;N:23926 51 0     152016801 139221646 139332264 182506912 23926 ERX4862162 ERS4959146 ERA3206646 University of Bristol|European Nucleotide Archive University of Bristol 1 0.90335   0.1072   0.71784   0.48228   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9972 9972 ERR5056077 ERX4862146 ERS4959146 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   day x Zebrafish scale RNA seq total RNA SAMEA7198925 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198925|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 1|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 1|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 12:07:14:527 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_ONT1_CGATGT_L001_R1_001.fastq.gz fastq 600285402.0 11770302.0 ena RUN BRISTOL 08 01 2021 12:07:14:527 1 0:51 1:0 A:148729943;C:136337224;G:136545524;T:178606078;N:66633 51 0     148729943 136337224 136545524 178606078 66633 ERX4862146 ERS4959146 ERA3206631 University of Bristol|European Nucleotide Archive University of Bristol 1 0.9026   0.10732   0.71683   0.47346   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9973 9973 ERR5056254 ERX4862323 ERS4959151 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   9 days post harvest Zebrafish scale RNA seq total RNA SAMEA7198930 University of Bristol ENA first public:2021 04 20|ENA last update:2020 08 20|External Id:SAMEA7198930|INSDC center alias:BRISTOL|INSDC center name:University of Bristol|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 3|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 3|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 9 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_REG3_CTTGTA_L001_R1_001.fastq.gz fastq 426117342.0 8355242.0 ena RUN BRISTOL 08 01 2021 15:14:53:483 9 0:51 1:0 A:102630499;C:100472291;G:99193964;T:123775368;N:45220 51 0     102630499 100472291 99193964 123775368 45220 ERX4862323 ERS4959151 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.92245   0.08463   0.71877   0.45377   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9974 9974 ERR5056253 ERX4862322 ERS4959150 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   9 days post harvest Zebrafish scale RNA seq total RNA SAMEA7198929 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198929|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 8 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_REG2_CAGATC_L002_R1_001.fastq.gz fastq 434571714.0 8521014.0 ena RUN BRISTOL 08 01 2021 15:14:53:483 8 0:51 1:0 A:106135147;C:102194661;G:100594136;T:125630448;N:17322 51 0     106135147 102194661 100594136 125630448 17322 ERX4862322 ERS4959150 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.91779   0.08112   0.7161   0.4437   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9975 9975 ERR5056252 ERX4862321 ERS4959150 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   9 days post harvest Zebrafish scale RNA seq total RNA SAMEA7198929 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198929|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 7 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_REG2_CAGATC_L001_R1_001.fastq.gz fastq 424788384.0 8329184.0 ena RUN BRISTOL 08 01 2021 15:14:53:483 7 0:51 1:0 A:103644078;C:99946940;G:98381633;T:122768121;N:47612 51 0     103644078 99946940 98381633 122768121 47612 ERX4862321 ERS4959150 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.91867   0.08097   0.71388   0.44882   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9976 9976 ERR5056251 ERX4862320 ERS4959149 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   9 days post harvest Zebrafish scale RNA seq total RNA SAMEA7198928 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198928|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 1|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 1|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 6 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_REG1_GCCAAT_L002_R1_001.fastq.gz fastq 481725498.0 9445598.0 ena RUN BRISTOL 08 01 2021 15:14:53:482 6 0:51 1:0 A:117075718;C:111922649;G:112057835;T:140651082;N:18214 51 0     117075718 111922649 112057835 140651082 18214 ERX4862320 ERS4959149 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.91312   0.08654   0.71747   0.46716   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9977 9977 ERR5056250 ERX4862319 ERS4959149 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   9 days post harvest Zebrafish scale RNA seq total RNA SAMEA7198928 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198928|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 1|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 1|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 5 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_REG1_GCCAAT_L001_R1_001.fastq.gz fastq 471197976.0 9239176.0 ena RUN BRISTOL 08 01 2021 15:14:53:482 5 0:51 1:0 A:114367789;C:109551764;G:109678406;T:137546387;N:53630 51 0     114367789 109551764 109678406 137546387 53630 ERX4862319 ERS4959149 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.91412   0.08674   0.71632   0.46601   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9978 9978 ERR5056249 ERX4862318 ERS4959148 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   day x Zebrafish scale SAMEA7198927 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198927|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 3|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 3|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 4 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_ONT3_ACAGTG_L002_R1_001.fastq.gz fastq 470142531.0 9218481.0 ena RUN BRISTOL 08 01 2021 15:14:53:482 4 0:51 1:0 A:116971308;C:106056823;G:107128214;T:139968487;N:17699 51 0     116971308 106056823 107128214 139968487 17699 ERX4862318 ERS4959148 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.90722   0.1158   0.72287   0.46674   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9979 9979 ERR5056248 ERX4862317 ERS4959148 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   day x Zebrafish scale SAMEA7198927 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198927|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 3|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 3|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 3 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_ONT3_ACAGTG_L001_R1_001.fastq.gz fastq 460312587.0 9025737.0 ena RUN BRISTOL 08 01 2021 15:14:53:482 3 0:51 1:0 A:114396758;C:103865119;G:105005018;T:136994559;N:51133 51 0     114396758 103865119 105005018 136994559 51133 ERX4862317 ERS4959148 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.90759   0.11359   0.7208   0.47232   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9980 9980 ERR5056247 ERX4862316 ERS4959147 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   day x Zebrafish scale RNA seq total RNA SAMEA7198926 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198926|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_ONT2_TGACCA_L002_R1_001.fastq.gz fastq 502898046.0 9860746.0 ena RUN BRISTOL 08 01 2021 15:14:53:482 2 0:51 1:0 A:123893447;C:111981365;G:116049412;T:150953220;N:20602 51 0     123893447 111981365 116049412 150953220 20602 ERX4862316 ERS4959147 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.90777   0.11921   0.7137   0.48182   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
9981 9981 ERR5056246 ERX4862315 ERS4959147 ERP123551 PRJEB39971 RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170 Other RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism. bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20   day x Zebrafish scale RNA seq total RNA SAMEA7198926 BRISTOL ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198926|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale                 Illumina HiSeq 2500 sequencing ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC DNase SINGLE ILLUMINA Illumina HiSeq 2500   ERP123551 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08 ZFG-15-01_ONT2_TGACCA_L001_R1_001.fastq.gz fastq 491866134.0 9644434.0 ena RUN BRISTOL 08 01 2021 15:14:53:482 1 0:51 1:0 A:121063841;C:109534722;G:113610951;T:147602721;N:53899 51 0     121063841 109534722 113610951 147602721 53899 ERX4862315 ERS4959147 ERA3206662 University of Bristol|European Nucleotide Archive University of Bristol 1 0.907   0.11935   0.71364   0.48543   51   B   usable mapping rate illumina hiseq_era unknown dnase trueseq bulk unknown unknown   United Kingdom 2020-08-20 Adult Adult Scale Surface Structure
28893 28893 SRR26821448 SRX22518177 SRS19529846 SRP471728 PRJNA1040136 Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs GSE247669 Transcriptome Analysis The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts osteoclasts and bone matrix providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study we have performed RNA seq analysis on intact scales fractured scales not exposed to ELF EMFs and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.   pubmed:38385024   10mT fractured 3 GSM7898626   source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs|geo loc name:missing|collection date:missing 10mT fractured 3 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. Whole scales   Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs GSM7898626 GSM7898626: 10mT fractured 3; Danio rerio; RNA Seq GSM7898626 r1 GSM7898626 1 Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     10mT_fractured_3_R2.fq.gz 10mT_fractured_3_R1.fq.gz fastq fastq 1301482800.0 4338276.0 GSM7898626 r1 0:150 1:150 A:335087662;C:232566321;G:385245929;T:348358361;N:224527 150 150     335087662 232566321 385245929 348358361 224527 SRX22518177 SRS19529846 SRA1750892 Kanazawa University Kanazawa University 2 0.67547 0.04621 0.23296 0.03359 0.78279 0.99648 0.54124 0.52153 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28894 28894 SRR26821449 SRX22518176 SRS19529845 SRP471728 PRJNA1040136 Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs GSE247669 Transcriptome Analysis The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts osteoclasts and bone matrix providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study we have performed RNA seq analysis on intact scales fractured scales not exposed to ELF EMFs and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.   pubmed:38385024   10mT fractured 2 GSM7898625   source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs|geo loc name:missing|collection date:missing 10mT fractured 2 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. Whole scales   Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs GSM7898625 GSM7898625: 10mT fractured 2; Danio rerio; RNA Seq GSM7898625 r1 GSM7898625 1 Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     10mT_fractured_2_R1.fq.gz 10mT_fractured_2_R2.fq.gz fastq fastq 1507967100.0 5026557.0 GSM7898625 r1 0:150 1:150 A:390969189;C:278659472;G:444481407;T:393553558;N:303474 150 150     390969189 278659472 444481407 393553558 303474 SRX22518176 SRS19529845 SRA1750892 Kanazawa University Kanazawa University 2 0.68061 0.08614 0.31496 0.0705 0.77001 0.99513 0.53747 0.57677 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28895 28895 SRR26821450 SRX22518175 SRS19529844 SRP471728 PRJNA1040136 Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs GSE247669 Transcriptome Analysis The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts osteoclasts and bone matrix providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study we have performed RNA seq analysis on intact scales fractured scales not exposed to ELF EMFs and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.   pubmed:38385024   10mT fractured 1 GSM7898624   source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs|geo loc name:missing|collection date:missing 10mT fractured 1 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. Whole scales   Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs GSM7898624 GSM7898624: 10mT fractured 1; Danio rerio; RNA Seq GSM7898624 r1 GSM7898624 1 Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     10mT_fractured_1_R2.fq.gz 10mT_fractured_1_R1.fq.gz fastq fastq 1718495100.0 5728317.0 GSM7898624 r1 0:150 1:150 A:452779669;C:319880075;G:491162181;T:454320323;N:352852 150 150     452779669 319880075 491162181 454320323 352852 SRX22518175 SRS19529844 SRA1750892 Kanazawa University Kanazawa University 2 0.67153 0.10745 0.32942 0.08781 0.76775 0.99427 0.53417 0.5895 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28896 28896 SRR26821451 SRX22518174 SRS19529843 SRP471728 PRJNA1040136 Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs GSE247669 Transcriptome Analysis The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts osteoclasts and bone matrix providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study we have performed RNA seq analysis on intact scales fractured scales not exposed to ELF EMFs and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.   pubmed:38385024   0mT fractured 3 GSM7898623   source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs|geo loc name:missing|collection date:missing 0mT fractured 3 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. Whole scales   Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs GSM7898623 GSM7898623: 0mT fractured 3; Danio rerio; RNA Seq GSM7898623 r1 GSM7898623 1 Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     0mT_fractured_3_R1.fq.gz 0mT_fractured_3_R2.fq.gz fastq fastq 1468748700.0 4895829.0 GSM7898623 r1 0:150 1:150 A:378980971;C:273130967;G:441424422;T:374917129;N:295211 150 150     378980971 273130967 441424422 374917129 295211 SRX22518174 SRS19529843 SRA1750892 Kanazawa University Kanazawa University 2 0.67867 0.10573 0.35963 0.0899 0.75982 0.99508 0.53209 0.48863 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28897 28897 SRR26821452 SRX22518173 SRS19529842 SRP471728 PRJNA1040136 Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs GSE247669 Transcriptome Analysis The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts osteoclasts and bone matrix providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study we have performed RNA seq analysis on intact scales fractured scales not exposed to ELF EMFs and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.   pubmed:38385024   0mT fractured 2 GSM7898622   source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs|geo loc name:missing|collection date:missing 0mT fractured 2 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. Whole scales   Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs GSM7898622 GSM7898622: 0mT fractured 2; Danio rerio; RNA Seq GSM7898622 r1 GSM7898622 1 Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     0mT_fractured_2_R1.fq.gz 0mT_fractured_2_R2.fq.gz fastq fastq 2406885600.0 8022952.0 GSM7898622 r1 0:150 1:150 A:646926387;C:366751040;G:726614721;T:666425874;N:167578 150 150     646926387 366751040 726614721 666425874 167578 SRX22518173 SRS19529842 SRA1750892 Kanazawa University Kanazawa University 2 0.67096 0.06177 0.27169 0.04875 0.77492 0.99805 0.55512 0.62711 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28898 28898 SRR26821453 SRX22518172 SRS19529841 SRP471728 PRJNA1040136 Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs GSE247669 Transcriptome Analysis The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts osteoclasts and bone matrix providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study we have performed RNA seq analysis on intact scales fractured scales not exposed to ELF EMFs and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.   pubmed:38385024   0mT fractured 1 GSM7898621   source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs|geo loc name:missing|collection date:missing 0mT fractured 1 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. Whole scales   Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs GSM7898621 GSM7898621: 0mT fractured 1; Danio rerio; RNA Seq GSM7898621 r1 GSM7898621 1 Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     0mT_fractured_1_R1.fq.gz 0mT_fractured_1_R2.fq.gz fastq fastq 2084550000.0 6948500.0 GSM7898621 r1 0:150 1:150 A:567504433;C:327104215;G:627285267;T:562454734;N:201351 150 150     567504433 327104215 627285267 562454734 201351 SRX22518172 SRS19529841 SRA1750892 Kanazawa University Kanazawa University 2 0.68491 0.14639 0.35327 0.12371 0.76459 0.99584 0.52889 0.52678 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28899 28899 SRR26821454 SRX22518171 SRS19529840 SRP471728 PRJNA1040136 Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs GSE247669 Transcriptome Analysis The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts osteoclasts and bone matrix providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study we have performed RNA seq analysis on intact scales fractured scales not exposed to ELF EMFs and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.   pubmed:38385024   Int 3 GSM7898620   source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Intact scales|geo loc name:missing|collection date:missing Int 3 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. Whole scales   Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   tissue:Whole scales|genotype:Wild type|treatment:Intact scales GSM7898620 GSM7898620: Int 3; Danio rerio; RNA Seq GSM7898620 r1 GSM7898620 1 Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     Int_3_R1.fq.gz Int_3_R2.fq.gz fastq fastq 2081211600.0 6937372.0 GSM7898620 r1 0:150 1:150 A:561341589;C:327618433;G:629445558;T:562620891;N:185129 150 150     561341589 327618433 629445558 562620891 185129 SRX22518171 SRS19529840 SRA1750892 Kanazawa University Kanazawa University 2 0.68553 0.11302 0.32184 0.0937 0.7654 0.99646 0.53135 0.50819 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28900 28900 SRR26821455 SRX22518170 SRS19529839 SRP471728 PRJNA1040136 Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs GSE247669 Transcriptome Analysis The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts osteoclasts and bone matrix providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study we have performed RNA seq analysis on intact scales fractured scales not exposed to ELF EMFs and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.   pubmed:38385024   Int 2 GSM7898619   source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Intact scales|geo loc name:missing|collection date:missing Int 2 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. Whole scales   Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   tissue:Whole scales|genotype:Wild type|treatment:Intact scales GSM7898619 GSM7898619: Int 2; Danio rerio; RNA Seq GSM7898619 r1 GSM7898619 1 Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     Int_2_R1.fq.gz Int_2_R2.fq.gz fastq fastq 1639167900.0 5463893.0 GSM7898619 r1 0:150 1:150 A:445245908;C:275437900;G:483637484;T:434649575;N:197033 150 150     445245908 275437900 483637484 434649575 197033 SRX22518170 SRS19529839 SRA1750892 Kanazawa University Kanazawa University 2 0.68102 0.1645 0.41429 0.1457 0.76641 0.9964 0.53665 0.50264 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28901 28901 SRR26821456 SRX22518169 SRS19529838 SRP471728 PRJNA1040136 Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs GSE247669 Transcriptome Analysis The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts osteoclasts and bone matrix providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study we have performed RNA seq analysis on intact scales fractured scales not exposed to ELF EMFs and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.   pubmed:38385024   Int 1 GSM7898618   source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Intact scales|geo loc name:missing|collection date:missing Int 1 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. Whole scales   Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   tissue:Whole scales|genotype:Wild type|treatment:Intact scales GSM7898618 GSM7898618: Int 1; Danio rerio; RNA Seq GSM7898618 r1 GSM7898618 1 Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     Int_1_R1.fq.gz Int_1_R2.fq.gz fastq fastq 2309186700.0 7697289.0 GSM7898618 r1 0:150 1:150 A:625174483;C:362587163;G:697384210;T:623845956;N:194888 150 150     625174483 362587163 697384210 623845956 194888 SRX22518169 SRS19529838 SRA1750892 Kanazawa University Kanazawa University 2 0.68814 0.09858 0.30026 0.08284 0.77315 0.99768 0.53387 0.50406 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
47613 47613 SRR6760977 SRX3733411 SRS2990508 SRP133266 PRJNA434353 Transcriptome assemblies 10 vertebrate species PRJNA434353 Other 2 types of content: a Raw RNA seq files from cell lines of 10 vertebrate species human mouse cow tasmanian devil chicken duck zebra finch xenopus medaka and zebrafish 4 replicates per species. b Refined transcriptomes post combining with paired proteomics data and data curation.     4 replicates   Zebrafish   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:missing|tissue:scale|cell line:BRF41|cell type:fibroblast|BioSampleModel:Model organism or animal                 Transcriptome assemblies 10 vertebrate species zebrafish replicate2 zebrafish replicate2 Zebrafish sample replicate 2     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP133266     Sample_imb_butter_2014_04_30_zebrafish_B_R2.fastq.gz Sample_imb_butter_2014_04_30_zebrafish_B_R1.fastq.gz fastq fastq 8021078014.0 39708307.0 Sample imb butter 2014 04 30 zebrafish B R2.fastq.gz 0:101 1:101 A:2198831905;C:1810184353;G:1779924959;T:2210094554;N:22042243 101 101     2198831905 1810184353 1779924959 2210094554 22042243 SRX3733411 SRS2990508 SRA660975 Institute of Molecular Biology|Quantitative Proteomics Institute of Molecular Biology 2 0.94194 0.93911 0.07724 0.08406 0.75724 0.75558 0.47712 0.49049 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Unknown 2019-02-15 Undetermined Undetermined Scale Surface Structure
47614 47614 SRR6760978 SRX3733410 SRS2990508 SRP133266 PRJNA434353 Transcriptome assemblies 10 vertebrate species PRJNA434353 Other 2 types of content: a Raw RNA seq files from cell lines of 10 vertebrate species human mouse cow tasmanian devil chicken duck zebra finch xenopus medaka and zebrafish 4 replicates per species. b Refined transcriptomes post combining with paired proteomics data and data curation.     4 replicates   Zebrafish   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:missing|tissue:scale|cell line:BRF41|cell type:fibroblast|BioSampleModel:Model organism or animal                 Transcriptome assemblies 10 vertebrate species zebrafish replicate1 zebrafish replicate1 Zebrafish sample replicate 1     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP133266     Sample_imb_butter_2014_04_29_zebrafish_A_R1.fastq.gz Sample_imb_butter_2014_04_29_zebrafish_A_R2.fastq.gz fastq fastq 7117920864.0 35237232.0 Sample imb butter 2014 04 29 zebrafish A R2.fastq.gz 0:101 1:101 A:1980152632;C:1580333689;G:1558362064;T:1979596193;N:19476286 101 101     1980152632 1580333689 1558362064 1979596193 19476286 SRX3733410 SRS2990508 SRA660975 Institute of Molecular Biology|Quantitative Proteomics Institute of Molecular Biology 2 0.9342 0.93044 0.08741 0.09642 0.75674 0.75497 0.49192 0.46492 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Unknown 2018-02-22 Undetermined Undetermined Scale Surface Structure
47615 47615 SRR6760981 SRX3733407 SRS2990508 SRP133266 PRJNA434353 Transcriptome assemblies 10 vertebrate species PRJNA434353 Other 2 types of content: a Raw RNA seq files from cell lines of 10 vertebrate species human mouse cow tasmanian devil chicken duck zebra finch xenopus medaka and zebrafish 4 replicates per species. b Refined transcriptomes post combining with paired proteomics data and data curation.     4 replicates   Zebrafish   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:missing|tissue:scale|cell line:BRF41|cell type:fibroblast|BioSampleModel:Model organism or animal                 Transcriptome assemblies 10 vertebrate species zebrafish replicate4 zebrafish replicate4 Zebrafish sample replicate 4     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP133266     Sample_imb_butter_2014_04_32_zebrafish_D_R1.fastq.gz Sample_imb_butter_2014_04_32_zebrafish_D_R2.fastq.gz fastq fastq 8570683654.0 42429127.0 Sample imb butter 2014 04 32 zebrafish D R1.fastq.gz 0:101 1:101 A:2343151377;C:1943560489;G:1909682494;T:2350658549;N:23630745 101 101     2343151377 1943560489 1909682494 2350658549 23630745 SRX3733407 SRS2990508 SRA660975 Institute of Molecular Biology|Quantitative Proteomics Institute of Molecular Biology 2 0.94036 0.94349 0.0838 0.0779 0.75538 0.75737 0.4881 0.48296 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Unknown 2019-02-15 Undetermined Undetermined Scale Surface Structure
47616 47616 SRR6760982 SRX3733406 SRS2990508 SRP133266 PRJNA434353 Transcriptome assemblies 10 vertebrate species PRJNA434353 Other 2 types of content: a Raw RNA seq files from cell lines of 10 vertebrate species human mouse cow tasmanian devil chicken duck zebra finch xenopus medaka and zebrafish 4 replicates per species. b Refined transcriptomes post combining with paired proteomics data and data curation.     4 replicates   Zebrafish   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:missing|tissue:scale|cell line:BRF41|cell type:fibroblast|BioSampleModel:Model organism or animal                 Transcriptome assemblies 10 vertebrate species zebrafish replicate3 zebrafish replicate3 Zebrafish sample replicate 3     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP133266     Sample_imb_butter_2014_04_31_zebrafish_C_R1.fastq.gz Sample_imb_butter_2014_04_31_zebrafish_C_R2.fastq.gz fastq fastq 5889796416.0 29157408.0 Sample imb butter 2014 04 31 zebrafish C R1.fastq.gz 0:101 1:101 A:1629550499;C:1313886355;G:1293890602;T:1636478119;N:15990841 101 101     1629550499 1313886355 1293890602 1636478119 15990841 SRX3733406 SRS2990508 SRA660975 Institute of Molecular Biology|Quantitative Proteomics Institute of Molecular Biology 2 0.93285 0.93628 0.09745 0.0871 0.7586 0.7611 0.47374 0.47763 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Unknown 2018-02-22 Undetermined Undetermined Scale Surface Structure

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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");;