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run_metadata

16 rows where devstage_curation = "Adult" and tissue_curation = "Scale"

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technology 2

experiment.library_source 2

experiment.library_selection 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Scale · 16 ✖

experiment.platform 1

experiment.library_strategy 1

devstage_curation_coarse 1

devstage_curation 1

  • Adult · 16 ✖
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
71632 71632 SRR21855290 SRX17843605 SRS15365430 SRP401856 PRJNA889065 A Tessellated Lymphoid Network Provides Whole Body Antigen Surveillance in Zebrafish GSE215189 Transcriptome Analysis T cells survey the host for cognate antigen in mammals by trafficking to and searching within lymph nodes distributed throughout the body. Non mammalian jawed vertebrates lack lymph nodes but still maintain highly diverse repertoires of T cells. How these T cells find antigen in hosts devoid of lymph nodes remains wholly unclear. In this study we exploit the in vivo imaging amenability of the zebrafish to investigate T cell organization trafficking and antigen surveillance in an animal completely lacking lymph nodes. We find that T cells organize into a previously undescribed whole body scale associated pattern that we have named the tessellated lymphoid network TLN. We find that the TLN harbors significantly more T cells than the gills gut kidney and spleen as well as populations of antigen presenting cells suggesting a central role in adaptive immune responses in fish. Within the TLN T cells perform a highly directional ballistic streaming mode of motility allowing them to traffic through the host in a coordinated ventral to dorsal loop. Local infection results in a dramatic shift in T cell motility from rapid streaming to a slower random walk in regions proximal to the infection. Here T cells sequentially interact with and ultimately form stable contacts with antigen presenting cells. Finally T cells within the TLN of infected fish show transcriptional changes consistent with TCR signaling and subsequent T cell activation. The TLN thus provides a mechanism for T cells to both traffic through the host and in the context of an infection effectively scan for and detect antigen mirroring the function of lymph nodes in mammals. Overall design: Adult zebrafish either without xxx or infected by L. monocytogenes through puncture wounding were euthanized and descaled to collect associated cells at 4 days post infection. Libraries were constructed from these cells using the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and sequenced using NovaSeq6000 Illumina with read lengths…   pubmed:37155881   Infected scRNAseq GSM6625507   tissue:Descaled cells|cell type:Descaled cells|treatment:infected Infected scRNAseq Raw FASTQ files were processed by cellranger 6.1.2 10x Genomics for demultiplexing barcoded processing and gene counting. Assembly: zv11 Supplementary files format and content: Tab separated values files and matrix files Descaled cells   Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal dorsal and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15 penicillin streptomycin and 2% FBS in a 15 mL falcon tube washed resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells and washed once more with cell isolation media. Library was performed according to the manufacter’s instructions Chromium Single Cell Gene Expression Solution 3’ v2 10x Genomics.   cell type:Descaled cells|treatment:infected GSM6625507 GSM6625507: Infected scRNAseq; Danio rerio; RNA Seq GSM6625507 r1 GSM6625507 1 Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal dorsal and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15 penicillin streptomycin and 2% FBS in a 15 mL falcon tube washed resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells and washed once more with cell isolation media. Library was performed according to the manufacter's instructions Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP401856   loader:fastq load.py Infected_S2_L001_R1_001.fastq.gz Infected_S2_L001_R2_001.fastq.gz fastq fastq 27971148231.0 239069643.0 GSM6625507 r1 0:28 1:89 A:8061885724;C:6040148313;G:6562354866;T:7306186742;N:572586 28 89     8061885724 6040148313 6562354866 7306186742 572586 SRX17843605 SRS15365430 SRA1517576 Ting Wang, Genetics, Washington University St Louis Anna Huttenlocher, Pediatrics, University of Wisconsin School of Medicine and Public Health 2 0.00829 0.90109 0.0031 0.16974 0.98742 0.79249 0.29098 0.56795 28 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United States 2022-10-10 Adult Adult Scale Surface Structure
71633 71633 SRR21855291 SRX17843605 SRS15365430 SRP401856 PRJNA889065 A Tessellated Lymphoid Network Provides Whole Body Antigen Surveillance in Zebrafish GSE215189 Transcriptome Analysis T cells survey the host for cognate antigen in mammals by trafficking to and searching within lymph nodes distributed throughout the body. Non mammalian jawed vertebrates lack lymph nodes but still maintain highly diverse repertoires of T cells. How these T cells find antigen in hosts devoid of lymph nodes remains wholly unclear. In this study we exploit the in vivo imaging amenability of the zebrafish to investigate T cell organization trafficking and antigen surveillance in an animal completely lacking lymph nodes. We find that T cells organize into a previously undescribed whole body scale associated pattern that we have named the tessellated lymphoid network TLN. We find that the TLN harbors significantly more T cells than the gills gut kidney and spleen as well as populations of antigen presenting cells suggesting a central role in adaptive immune responses in fish. Within the TLN T cells perform a highly directional ballistic streaming mode of motility allowing them to traffic through the host in a coordinated ventral to dorsal loop. Local infection results in a dramatic shift in T cell motility from rapid streaming to a slower random walk in regions proximal to the infection. Here T cells sequentially interact with and ultimately form stable contacts with antigen presenting cells. Finally T cells within the TLN of infected fish show transcriptional changes consistent with TCR signaling and subsequent T cell activation. The TLN thus provides a mechanism for T cells to both traffic through the host and in the context of an infection effectively scan for and detect antigen mirroring the function of lymph nodes in mammals. Overall design: Adult zebrafish either without xxx or infected by L. monocytogenes through puncture wounding were euthanized and descaled to collect associated cells at 4 days post infection. Libraries were constructed from these cells using the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and sequenced using NovaSeq6000 Illumina with read lengths…   pubmed:37155881   Infected scRNAseq GSM6625507   tissue:Descaled cells|cell type:Descaled cells|treatment:infected Infected scRNAseq Raw FASTQ files were processed by cellranger 6.1.2 10x Genomics for demultiplexing barcoded processing and gene counting. Assembly: zv11 Supplementary files format and content: Tab separated values files and matrix files Descaled cells   Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal dorsal and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15 penicillin streptomycin and 2% FBS in a 15 mL falcon tube washed resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells and washed once more with cell isolation media. Library was performed according to the manufacter’s instructions Chromium Single Cell Gene Expression Solution 3’ v2 10x Genomics.   cell type:Descaled cells|treatment:infected GSM6625507 GSM6625507: Infected scRNAseq; Danio rerio; RNA Seq GSM6625507 r1 GSM6625507 1 Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal dorsal and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15 penicillin streptomycin and 2% FBS in a 15 mL falcon tube washed resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells and washed once more with cell isolation media. Library was performed according to the manufacter's instructions Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP401856   loader:fastq load.py Infected_S2_L002_R1_001.fastq.gz Infected_S2_L002_R2_001.fastq.gz fastq fastq 28948392252.0 247422156.0 GSM6625507 r2 0:28 1:89 A:8329225374;C:6258698724;G:6802339342;T:7557690208;N:438604 28 89     8329225374 6258698724 6802339342 7557690208 438604 SRX17843605 SRS15365430 SRA1517576 Ting Wang, Genetics, Washington University St Louis Anna Huttenlocher, Pediatrics, University of Wisconsin School of Medicine and Public Health 2 0.00815 0.89934 0.00296 0.16878 0.98717 0.79032 0.32081 0.56999 28 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United States 2022-10-10 Adult Adult Scale Surface Structure
71634 71634 SRR21855292 SRX17843604 SRS15365429 SRP401856 PRJNA889065 A Tessellated Lymphoid Network Provides Whole Body Antigen Surveillance in Zebrafish GSE215189 Transcriptome Analysis T cells survey the host for cognate antigen in mammals by trafficking to and searching within lymph nodes distributed throughout the body. Non mammalian jawed vertebrates lack lymph nodes but still maintain highly diverse repertoires of T cells. How these T cells find antigen in hosts devoid of lymph nodes remains wholly unclear. In this study we exploit the in vivo imaging amenability of the zebrafish to investigate T cell organization trafficking and antigen surveillance in an animal completely lacking lymph nodes. We find that T cells organize into a previously undescribed whole body scale associated pattern that we have named the tessellated lymphoid network TLN. We find that the TLN harbors significantly more T cells than the gills gut kidney and spleen as well as populations of antigen presenting cells suggesting a central role in adaptive immune responses in fish. Within the TLN T cells perform a highly directional ballistic streaming mode of motility allowing them to traffic through the host in a coordinated ventral to dorsal loop. Local infection results in a dramatic shift in T cell motility from rapid streaming to a slower random walk in regions proximal to the infection. Here T cells sequentially interact with and ultimately form stable contacts with antigen presenting cells. Finally T cells within the TLN of infected fish show transcriptional changes consistent with TCR signaling and subsequent T cell activation. The TLN thus provides a mechanism for T cells to both traffic through the host and in the context of an infection effectively scan for and detect antigen mirroring the function of lymph nodes in mammals. Overall design: Adult zebrafish either without xxx or infected by L. monocytogenes through puncture wounding were euthanized and descaled to collect associated cells at 4 days post infection. Libraries were constructed from these cells using the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and sequenced using NovaSeq6000 Illumina with read lengths…   pubmed:37155881   Control scRNAseq GSM6625506   tissue:Descaled cells|cell type:Descaled cells|treatment:control Control scRNAseq Raw FASTQ files were processed by cellranger 6.1.2 10x Genomics for demultiplexing barcoded processing and gene counting. Assembly: zv11 Supplementary files format and content: Tab separated values files and matrix files Descaled cells   Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal dorsal and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15 penicillin streptomycin and 2% FBS in a 15 mL falcon tube washed resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells and washed once more with cell isolation media. Library was performed according to the manufacter’s instructions Chromium Single Cell Gene Expression Solution 3’ v2 10x Genomics.   cell type:Descaled cells|treatment:control GSM6625506 GSM6625506: Control scRNAseq; Danio rerio; RNA Seq GSM6625506 r1 GSM6625506 1 Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal dorsal and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15 penicillin streptomycin and 2% FBS in a 15 mL falcon tube washed resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells and washed once more with cell isolation media. Library was performed according to the manufacter's instructions Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP401856   loader:fastq load.py Control_S1_L001_R1_001.fastq.gz Control_S1_L001_R2_001.fastq.gz fastq fastq 22227506496.0 189978688.0 GSM6625506 r1 0:28 1:89 A:6692049340;C:4739918301;G:5329051962;T:5466033150;N:453743 28 89     6692049340 4739918301 5329051962 5466033150 453743 SRX17843604 SRS15365429 SRA1517576 Ting Wang, Genetics, Washington University St Louis Anna Huttenlocher, Pediatrics, University of Wisconsin School of Medicine and Public Health 2 0.01277 0.88905 0.00634 0.17657 0.98879 0.78119 0.33278 0.56433 28 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United States 2022-10-10 Adult Adult Scale Surface Structure
71635 71635 SRR21855293 SRX17843604 SRS15365429 SRP401856 PRJNA889065 A Tessellated Lymphoid Network Provides Whole Body Antigen Surveillance in Zebrafish GSE215189 Transcriptome Analysis T cells survey the host for cognate antigen in mammals by trafficking to and searching within lymph nodes distributed throughout the body. Non mammalian jawed vertebrates lack lymph nodes but still maintain highly diverse repertoires of T cells. How these T cells find antigen in hosts devoid of lymph nodes remains wholly unclear. In this study we exploit the in vivo imaging amenability of the zebrafish to investigate T cell organization trafficking and antigen surveillance in an animal completely lacking lymph nodes. We find that T cells organize into a previously undescribed whole body scale associated pattern that we have named the tessellated lymphoid network TLN. We find that the TLN harbors significantly more T cells than the gills gut kidney and spleen as well as populations of antigen presenting cells suggesting a central role in adaptive immune responses in fish. Within the TLN T cells perform a highly directional ballistic streaming mode of motility allowing them to traffic through the host in a coordinated ventral to dorsal loop. Local infection results in a dramatic shift in T cell motility from rapid streaming to a slower random walk in regions proximal to the infection. Here T cells sequentially interact with and ultimately form stable contacts with antigen presenting cells. Finally T cells within the TLN of infected fish show transcriptional changes consistent with TCR signaling and subsequent T cell activation. The TLN thus provides a mechanism for T cells to both traffic through the host and in the context of an infection effectively scan for and detect antigen mirroring the function of lymph nodes in mammals. Overall design: Adult zebrafish either without xxx or infected by L. monocytogenes through puncture wounding were euthanized and descaled to collect associated cells at 4 days post infection. Libraries were constructed from these cells using the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and sequenced using NovaSeq6000 Illumina with read lengths…   pubmed:37155881   Control scRNAseq GSM6625506   tissue:Descaled cells|cell type:Descaled cells|treatment:control Control scRNAseq Raw FASTQ files were processed by cellranger 6.1.2 10x Genomics for demultiplexing barcoded processing and gene counting. Assembly: zv11 Supplementary files format and content: Tab separated values files and matrix files Descaled cells   Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal dorsal and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15 penicillin streptomycin and 2% FBS in a 15 mL falcon tube washed resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells and washed once more with cell isolation media. Library was performed according to the manufacter’s instructions Chromium Single Cell Gene Expression Solution 3’ v2 10x Genomics.   cell type:Descaled cells|treatment:control GSM6625506 GSM6625506: Control scRNAseq; Danio rerio; RNA Seq GSM6625506 r1 GSM6625506 1 Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal dorsal and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15 penicillin streptomycin and 2% FBS in a 15 mL falcon tube washed resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells and washed once more with cell isolation media. Library was performed according to the manufacter's instructions Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP401856   loader:fastq load.py Control_S1_L002_R1_001.fastq.gz Control_S1_L002_R2_001.fastq.gz fastq fastq 22948305003.0 196139359.0 GSM6625506 r2 0:28 1:89 A:6891536928;C:4902194962;G:5508766043;T:5645479908;N:327162 28 89     6891536928 4902194962 5508766043 5645479908 327162 SRX17843604 SRS15365429 SRA1517576 Ting Wang, Genetics, Washington University St Louis Anna Huttenlocher, Pediatrics, University of Wisconsin School of Medicine and Public Health 2 0.01284 0.88937 0.00623 0.17647 0.98926 0.78315 0.32038 0.56842 28 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United States 2022-10-10 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");;