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
10403,ERR8527374,ERX8137561,ERS10539829,ERP135430,PRJEB50826,scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,E-MTAB-11079_2,Transcriptome Analysis,Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted  from pooled kidneys of ren+/+ or ren /  zebrafish  which carried ren:RFP and acta2:EGFP reporter genes  allowing the isolation of renin expressing cells and smooth muscle cells.,ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10,,Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA  specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.,ZF2,SAMEA12941033,University Of Edinburgh,ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941033|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF2|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP; ren / |individual:9 12 kidneys pooled|inferred cell type:recruited RLC|organism part:kidney|phenotype:ren knockout|sample name:E MTAB 11079 2:ZF2|sex:mixed|strain:WIK,,,,,,,,,NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,E MTAB 11079 2:ZF2 p,ZF2 p,scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively.  Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA   specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.,Experimental Factor: phenotype:ren knockout,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,NextSeq 500,,ERP135430,NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10,ZF2_S2_L002_I1_001.fastq.gz ZF2_S2_L002_R1_001.fastq.gz ZF2_S2_L002_R2_001.fastq.gz,fastq fastq fastq,38557081640.0,125185330.0,E MTAB 11079 2:ZF2 S2 L002,0:8 1:150 2:150,A:13781315856;C:6436030786;G:6578059630;T:10759631611;N:561117,8,150,150,,13781315856,6436030786,6578059630,10759631611,561117,ERX8137561,ERS10539829,ERA9016154,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.0,0.84449,0.0,0.09657,1.0,0.8242,,0.52635,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,size_fractionation,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-06-10,Adult,Adult,Multi-tissue,Multi-system
10404,ERR8527377,ERX8137561,ERS10539829,ERP135430,PRJEB50826,scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,E-MTAB-11079_2,Transcriptome Analysis,Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted  from pooled kidneys of ren+/+ or ren /  zebrafish  which carried ren:RFP and acta2:EGFP reporter genes  allowing the isolation of renin expressing cells and smooth muscle cells.,ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10,,Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA  specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.,ZF2,SAMEA12941033,University Of Edinburgh,ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941033|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF2|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP; ren / |individual:9 12 kidneys pooled|inferred cell type:recruited RLC|organism part:kidney|phenotype:ren knockout|sample name:E MTAB 11079 2:ZF2|sex:mixed|strain:WIK,,,,,,,,,NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,E MTAB 11079 2:ZF2 p,ZF2 p,scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively.  Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA   specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.,Experimental Factor: phenotype:ren knockout,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,NextSeq 500,,ERP135430,NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10,ZF2_S2_L001_I1_001.fastq.gz ZF2_S2_L001_R1_001.fastq.gz ZF2_S2_L001_R2_001.fastq.gz,fastq fastq fastq,38872269128.0,126208666.0,E MTAB 11079 2:ZF2 S2 L001,0:8 1:150 2:150,A:15151865400;C:6355030057;G:6591732598;T:9763441371;N:530374,8,150,150,,15151865400,6355030057,6591732598,9763441371,530374,ERX8137561,ERS10539829,ERA9016154,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.0,0.84526,0.0,0.09779,1.0,0.82609,,0.54388,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,size_fractionation,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-06-10,Adult,Adult,Multi-tissue,Multi-system
10405,ERR8527376,ERX8137560,ERS10539828,ERP135430,PRJEB50826,scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,E-MTAB-11079_2,Transcriptome Analysis,Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted  from pooled kidneys of ren+/+ or ren /  zebrafish  which carried ren:RFP and acta2:EGFP reporter genes  allowing the isolation of renin expressing cells and smooth muscle cells.,ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10,,Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA  specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.,ZF1,SAMEA12941032,University Of Edinburgh,ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941032|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF1|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP|individual:9 12 kidneys pooled|inferred cell type:juxtaglomerular cell|organism part:kidney|phenotype:wild type|sample name:E MTAB 11079 2:ZF1|sex:mixed|strain:WIK,,,,,,,,,NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,E MTAB 11079 2:ZF1 p,ZF1 p,scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively.  Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA   specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.,Experimental Factor: phenotype:wild type,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,NextSeq 500,,ERP135430,NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10,ZF1_S1_L002_I1_001.fastq.gz ZF1_S1_L002_R1_001.fastq.gz ZF1_S1_L002_R2_001.fastq.gz,fastq fastq fastq,39415722500.0,127973125.0,E MTAB 11079 2:ZF1 S1 L002,0:8 1:150 2:150,A:14261012964;C:6339158428;G:6467430919;T:11323758989;N:576200,8,150,150,,14261012964,6339158428,6467430919,11323758989,576200,ERX8137560,ERS10539828,ERA9016154,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.0,0.81065,0.0,0.08289,1.0,0.82434,,0.52903,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,size_fractionation,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-06-10,Adult,Adult,Multi-tissue,Multi-system
10406,ERR8527375,ERX8137560,ERS10539828,ERP135430,PRJEB50826,scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,E-MTAB-11079_2,Transcriptome Analysis,Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted  from pooled kidneys of ren+/+ or ren /  zebrafish  which carried ren:RFP and acta2:EGFP reporter genes  allowing the isolation of renin expressing cells and smooth muscle cells.,ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10,,Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA  specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.,ZF1,SAMEA12941032,University Of Edinburgh,ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941032|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF1|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP|individual:9 12 kidneys pooled|inferred cell type:juxtaglomerular cell|organism part:kidney|phenotype:wild type|sample name:E MTAB 11079 2:ZF1|sex:mixed|strain:WIK,,,,,,,,,NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,E MTAB 11079 2:ZF1 p,ZF1 p,scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively.  Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA   specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.,Experimental Factor: phenotype:wild type,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,NextSeq 500,,ERP135430,NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10,ZF1_S1_L001_I1_001.fastq.gz ZF1_S1_L001_R1_001.fastq.gz ZF1_S1_L001_R2_001.fastq.gz,fastq fastq fastq,39744721324.0,129041303.0,E MTAB 11079 2:ZF1 S1 L001,0:8 1:150 2:150,A:15670316830;C:6278039908;G:6505806971;T:10257683184;N:544007,8,150,150,,15670316830,6278039908,6505806971,10257683184,544007,ERX8137560,ERS10539828,ERA9016154,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.0,0.81031,0.0,0.08495,1.0,0.82169,,0.51724,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,size_fractionation,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-06-10,Adult,Adult,Multi-tissue,Multi-system
36271,SRR298568,SRX079846,SRS212652,SRP007331,PRJNA141525,Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.,GSE29418,Transcriptome Analysis,RNA libraries from immunoprecipitates of Tdrd1  Ziwi and Zili  total testis RNA  total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.,,pubmed:21743441,,ZiwiIPTes,GSM727525,,tissue:RNA obtained from immunoprecipitation with Ziwi antibody from zebrafish testis extract|strain:TL,ZiwiIPTes,three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9.,RNA obtained from immunoprecipitation with Ziwi antibody from zebrafish testis extract,,Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 µl Dynabeads Invitrogen  3 or 6 testes  and Ziwi antibody in a total volume of 500 µl.  RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis  adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H  reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.,,strain:TL,GSM727525,GSM727525: ZiwiIPTes,GSM727525: ZiwiIPTes,GSM727525: ZiwiIPTes,1,,GEO Accession:GSM727525,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP007331,,read name barcode proc directive:ignore,ZiwiIPTes.fastq,fastq,976120596.0,27114461.0,GSM727525 1,0:36,,36,,,,,,,,,SRX079846,SRS212652,SRA039167,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.10415,,0.03658,,0.96173,,0.30033,,36,,B,,usable mapping rate,illumina,early_illumina,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2011-05-20,Undetermined,Undetermined,Multi-tissue,Multi-system
36276,SRR298563,SRX079841,SRS212647,SRP007331,PRJNA141525,Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.,GSE29418,Transcriptome Analysis,RNA libraries from immunoprecipitates of Tdrd1  Ziwi and Zili  total testis RNA  total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.,,pubmed:21743441,,TDRD1IPshort,GSM727520,,tissue:RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract|strain:TL,TDRD1IPshort,three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9.,RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract,,Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 µl Dynabeads Invitrogen  3 or 6 testes  and Tdrd1 antibody 1:100 in a total volume of 500 µl.  RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis  adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H  reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.,,strain:TL,GSM727520,GSM727520: TDRD1IPshort,GSM727520: TDRD1IPshort,GSM727520: TDRD1IPshort,1,,GEO Accession:GSM727520,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP007331,,read name barcode proc directive:ignore,TDRD1IPshort.fastq,fastq,957724884.0,26603469.0,GSM727520 1,0:36,,36,,,,,,,,,SRX079841,SRS212647,SRA039167,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.10539,,0.05124,,0.93935,,0.34909,,36,,B,,usable mapping rate,illumina,early_illumina,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2011-05-20,Undetermined,Undetermined,Multi-tissue,Multi-system
36277,SRR298562,SRX079840,SRS212646,SRP007331,PRJNA141525,Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.,GSE29418,Transcriptome Analysis,RNA libraries from immunoprecipitates of Tdrd1  Ziwi and Zili  total testis RNA  total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.,,pubmed:21743441,,TDRD1IPlong,GSM727519,,tissue:RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract|strain:TL,TDRD1IPlong,three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9.,RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract,,Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 µl Dynabeads Invitrogen  3 or 6 testes  and Tdrd1 antibody 1:100 in a total volume of 500 µl.  For cDNA synthesis  the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H  reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.,,strain:TL,GSM727519,GSM727519: TDRD1IPlong,GSM727519: TDRD1IPlong,GSM727519: TDRD1IPlong,1,,GEO Accession:GSM727519,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>46</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP007331,,read name barcode proc directive:ignore,TDRD1IPlong.fastq,fastq,1098157770.0,23872995.0,GSM727519 1,0:46,,46,,,,,,,,,SRX079840,SRS212646,SRA039167,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.63282,,0.29001,,0.80095,,0.51046,,46,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2011-05-20,Undetermined,Undetermined,Multi-tissue,Multi-system
41348,SRR4302022,SRX2194190,SRS1716514,SRP090540,PRJNA344550,Danio rerio strain:AB Raw sequence reads,PRJNA344550,Whole Genome Sequencing,Identification of circular RNAs in zebrafish,,pubmed:27878987,,,Zebrafish circRNA,,strain:AB|age:Adult|sex:pooled male and female|tissue:brain  eyes  heart  liver  spleen  kidney  intestines  skin  muscle  gill  ovary  testis|BioSampleModel:Model organism or animal,,,,,,,,,Identification of circular RNAs in zebrafish,Zebrafish circRNAs,Key Lab of Agricultural Animal Genetics,1,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP090540,,,MIX_R1.fastq.gz MIX_R2.fastq.gz,fastq fastq,21319208400.0,71064028.0,Zebrafish circRNAs,0:150 1:150,A:4973737880;C:5734846860;G:5920594296;T:4689011877;N:1017487,150,150,,,4973737880,5734846860,5920594296,4689011877,1017487,SRX2194190,SRS1716514,SRA480645,Huazhong Agricultural University|Key Lab of Agricultural Animal Genetics,Huazhong Agricultural University,2,0.89959,0.92292,0.28429,0.27588,0.87207,0.86866,0.65238,0.78485,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,China,2016-11-28,Adult,Adult,Multi-tissue,Multi-system