run_metadata
12 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "DNase" and tissue_curation_coarse = "Surface Structure"
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 |
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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");;