metadata: run_metadata: 4 rows where experiment.library_selection = "size fractionation", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and tissue_curation

4 rows where experiment.library_selection = "size fractionation", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and tissue_curation_coarse = "Multi-system"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	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.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.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.mate2	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
10403	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	0.84449	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	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	0.84526	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	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	0.81065	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	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	0.81031	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

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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");;