{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Multi-stage\" and technology = \"celseq\"", "rows": [[55365, "SRR10321288", "SRX7032108", "SRS5552214", "SRP226527", "PRJNA578764", "Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.", "GSE139218", "Transcriptome Analysis", "While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.", null, "pubmed:31868166", null, "FK2", "GSM4134187", null, "source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle", "FK2", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\"  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.", "Tgnppa:mCitrine ventricle 7dpi", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.", "Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016", null, "Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle", "GSM4134187", "GSM4134187: FK2; Danio rerio; RNA Seq", "GSM4134187", null, "1", "Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016", "GEO Accession:GSM4134187", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP226527", null, null, "Fk-2_H3MHFBGXY_S4_L001_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L001_R2_001.fastq.gz", "fastq fastq", 2747645940.0, 18195462.0, "GSM4134187 r1", "0:75.51 1:75.50", "A:761850296;C:390951746;G:422952266;T:1169751842;N:2139790", 75, 75, null, null, 761850296, 390951746, 422952266, 1169751842, 2139790, "SRX7032108", "SRS5552214", "SRA982819", "GEO", "Bakkers, Hubrecht Institute", 2, 0.23534, 0.89135, 0.19366, 0.15359, 0.99902, 0.86636, 0.40119, 0.71094, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2019-10-21", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [55366, "SRR10321289", "SRX7032108", "SRS5552214", "SRP226527", "PRJNA578764", "Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.", "GSE139218", "Transcriptome Analysis", "While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.", null, "pubmed:31868166", null, "FK2", "GSM4134187", null, "source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle", "FK2", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\"  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.", "Tgnppa:mCitrine ventricle 7dpi", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.", "Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016", null, "Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle", "GSM4134187", "GSM4134187: FK2; Danio rerio; RNA Seq", "GSM4134187", null, "1", "Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016", "GEO Accession:GSM4134187", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP226527", null, null, "Fk-2_H3MHFBGXY_S4_L002_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L002_R2_001.fastq.gz", "fastq fastq", 2719577388.0, 18010558.0, "GSM4134187 r2", "0:75.50 1:75.50", "A:750500832;C:383761329;G:435629268;T:1147504474;N:2181485", 75, 75, null, null, 750500832, 383761329, 435629268, 1147504474, 2181485, "SRX7032108", "SRS5552214", "SRA982819", "GEO", "Bakkers, Hubrecht Institute", 2, 0.21913, 0.88799, 0.16554, 0.15559, 0.99855, 0.8704, 0.48175, 0.71083, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2019-10-21", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [55367, "SRR10321290", "SRX7032108", "SRS5552214", "SRP226527", "PRJNA578764", "Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.", "GSE139218", "Transcriptome Analysis", "While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.", null, "pubmed:31868166", null, "FK2", "GSM4134187", null, "source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle", "FK2", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\"  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.", "Tgnppa:mCitrine ventricle 7dpi", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.", "Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016", null, "Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle", "GSM4134187", "GSM4134187: FK2; Danio rerio; RNA Seq", "GSM4134187", null, "1", "Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016", "GEO Accession:GSM4134187", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP226527", null, null, "Fk-2_H3MHFBGXY_S4_L003_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L003_R2_001.fastq.gz", "fastq fastq", 2396848795.0, 15867573.0, "GSM4134187 r3", "0:75.56 1:75.50", "A:649358056;C:340829352;G:366620430;T:1039511314;N:529643", 75, 75, null, null, 649358056, 340829352, 366620430, 1039511314, 529643, "SRX7032108", "SRS5552214", "SRA982819", "GEO", "Bakkers, Hubrecht Institute", 2, 0.22581, 0.89171, 0.18682, 0.15894, 0.99928, 0.87054, 0.41592, 0.70495, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2019-10-21", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [55368, "SRR10321291", "SRX7032108", "SRS5552214", "SRP226527", "PRJNA578764", "Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.", "GSE139218", "Transcriptome Analysis", "While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.", null, "pubmed:31868166", null, "FK2", "GSM4134187", null, "source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle", "FK2", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\"  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.", "Tgnppa:mCitrine ventricle 7dpi", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.", "Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016", null, "Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle", "GSM4134187", "GSM4134187: FK2; Danio rerio; RNA Seq", "GSM4134187", null, "1", "Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016", "GEO Accession:GSM4134187", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP226527", null, null, "Fk-2_H3MHFBGXY_S4_L004_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L004_R2_001.fastq.gz", "fastq fastq", 2610671390.0, 17282452.0, "GSM4134187 r4", "0:75.56 1:75.50", "A:691899084;C:368646569;G:415634004;T:1133907995;N:583738", 75, 75, null, null, 691899084, 368646569, 415634004, 1133907995, 583738, "SRX7032108", "SRS5552214", "SRA982819", "GEO", "Bakkers, Hubrecht Institute", 2, 0.24107, 0.8886, 0.19934, 0.15491, 0.99926, 0.8702, 0.31578, 0.66998, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2019-10-21", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [55369, "SRR10321284", "SRX7032107", "SRS5552213", "SRP226527", "PRJNA578764", "Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.", "GSE139218", "Transcriptome Analysis", "While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.", null, "pubmed:31868166", null, "FK1", "GSM4134186", null, "source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle", "FK1", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\"  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.", "Tgnppa:mCitrine ventricle 7dpi", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.", "Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016", null, "Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle", "GSM4134186", "GSM4134186: FK1; Danio rerio; RNA Seq", "GSM4134186", null, "1", "Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016", "GEO Accession:GSM4134186", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP226527", null, null, "FK-1_H3MHFBGXY_S3_L001_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L001_R2_001.fastq.gz", "fastq fastq", 2366670719.0, 15672127.0, "GSM4134186 r1", "0:75.50 1:75.51", "A:648000254;C:343663478;G:358343004;T:1014831853;N:1832130", 75, 75, null, null, 648000254, 343663478, 358343004, 1014831853, 1832130, "SRX7032107", "SRS5552213", "SRA982819", "GEO", "Bakkers, Hubrecht Institute", 2, 0.30353, 0.90485, 0.25842, 0.14878, 0.99912, 0.85857, 0.23863, 0.71645, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2019-10-21", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [55370, "SRR10321285", "SRX7032107", "SRS5552213", "SRP226527", "PRJNA578764", "Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.", "GSE139218", "Transcriptome Analysis", "While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.", null, "pubmed:31868166", null, "FK1", "GSM4134186", null, "source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle", "FK1", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\"  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.", "Tgnppa:mCitrine ventricle 7dpi", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.", "Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016", null, "Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle", "GSM4134186", "GSM4134186: FK1; Danio rerio; RNA Seq", "GSM4134186", null, "1", "Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016", "GEO Accession:GSM4134186", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP226527", null, null, "FK-1_H3MHFBGXY_S3_L002_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L002_R2_001.fastq.gz", "fastq fastq", 2360571906.0, 15632617.0, "GSM4134186 r2", "0:75.49 1:75.51", "A:643644738;C:339965378;G:371359828;T:1003716606;N:1885356", 75, 75, null, null, 643644738, 339965378, 371359828, 1003716606, 1885356, "SRX7032107", "SRS5552213", "SRA982819", "GEO", "Bakkers, Hubrecht Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2019-10-21", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [55371, "SRR10321286", "SRX7032107", "SRS5552213", "SRP226527", "PRJNA578764", "Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.", "GSE139218", "Transcriptome Analysis", "While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.", null, "pubmed:31868166", null, "FK1", "GSM4134186", null, "source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle", "FK1", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\"  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.", "Tgnppa:mCitrine ventricle 7dpi", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.", "Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016", null, "Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle", "GSM4134186", "GSM4134186: FK1; Danio rerio; RNA Seq", "GSM4134186", null, "1", "Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016", "GEO Accession:GSM4134186", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP226527", null, null, "FK-1_H3MHFBGXY_S3_L003_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L003_R2_001.fastq.gz", "fastq fastq", 2074411223.0, 13732357.0, "GSM4134186 r3", "0:75.55 1:75.51", "A:554276583;C:300804770;G:312025485;T:906833457;N:470928", 75, 75, null, null, 554276583, 300804770, 312025485, 906833457, 470928, "SRX7032107", "SRS5552213", "SRA982819", "GEO", "Bakkers, Hubrecht Institute", 2, 0.2996, 0.90397, 0.25521, 0.15245, 0.99933, 0.86314, 0.21969, 0.69653, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2019-10-21", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [55372, "SRR10321287", "SRX7032107", "SRS5552213", "SRP226527", "PRJNA578764", "Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.", "GSE139218", "Transcriptome Analysis", "While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.", null, "pubmed:31868166", null, "FK1", "GSM4134186", null, "source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle", "FK1", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\"  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.", "Tgnppa:mCitrine ventricle 7dpi", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.", "Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016", null, "Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle", "GSM4134186", "GSM4134186: FK1; Danio rerio; RNA Seq", "GSM4134186", null, "1", "Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016", "GEO Accession:GSM4134186", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP226527", null, null, "FK-1_H3MHFBGXY_S3_L004_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L004_R2_001.fastq.gz", "fastq fastq", 2267459781.0, 15009993.0, "GSM4134186 r4", "0:75.55 1:75.51", "A:592957170;C:326713096;G:354670327;T:992614149;N:505039", 75, 75, null, null, 592957170, 326713096, 354670327, 992614149, 505039, "SRX7032107", "SRS5552213", "SRA982819", "GEO", "Bakkers, Hubrecht Institute", 2, 0.3137, 0.9006, 0.26295, 0.14953, 0.99914, 0.8622, 0.19895, 0.70141, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2019-10-21", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [69930, "SRR22318718", "SRX18291979", "SRS15783401", "SRP374955", "PRJNA837586", "Labelling transcriptional response to dissociation using SLAMseq", "GSE202880", "Other", "Transcriptional response to dissociation is known to cause artefacts in single cell data sets. We used 4sU to label newly made transcripts during dissociation in order to to later remove them from the data set Overall design: 10mM 4sU was added to the dissociation buffer while the samples were enzymatically dissociated for 30 min. A 4sU injected control was added to the zebrafish samples to identify high turnover genes", "parent bioproject:PRJNA837863", "pubmed:36573354", null, "larvae  cold dissociated  rep 3", "GSM6735818", null, "tissue:whole larvae  48hpf|cell type:whole larvae  48hpf|genotype:WT|treatment:30 min 4sU during dissociation|time:48hpf", "larvae  cold dissociated  rep 3", "Demultiplexing bcl2fastq v2.19  CELseq barcodes demultiplexed using custom code https://github.com/anikaneuschulz/CELseq3 demultiplex mapping using STAR v2.7.3a aggregation of mutation information and calculation of labeling rates per gene / in bulk using custom code https://github.com/anikaneuschulz/MTglob pipeline genome build/assembly: dr11.95 processed data files format and content: Tab delimited mutation rates per gene", "whole larvae  48hpf", null, "10  anesthetized larvae were washed twice in ice cold HBSS Life Technologies GmbH #14175095 and resuspended in 200\u00b5l psychrophilic protease mix 1x Native Bacillus licheniformis Protease Creative Enzymes #NATE 0633 in HBSS  10 mM 4sU and incubated on ice for 30 min. Dissociation was aided by pipetting up and down with a 200 \u00b5l tip 25 times every 5 minutes. Enzymes were inactivated by adding 15 \u00b5l 10% BSA  Sigma Aldrich; #A4503 before spinning down and resuspending the cells in TRIzol RNA was extracted using TRIzol Chloroform Isopropanol according to the manufacturer\u2019s instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. Sequencing adapters were switched \u2013 Insert is in read 1!", null, "cell type:whole larvae  48hpf|genotype:WT|treatment:30 min 4sU during dissociation|time:48hpf", "GSM6735818", "GSM6735818: larvae  cold dissociated  rep 3; Danio rerio; RNA Seq", "GSM6735818 r1", "GSM6735818", "1", "10  anesthetized larvae were washed twice in ice cold HBSS Life Technologies GmbH #14175095 and resuspended in 200\u00b5l psychrophilic protease mix 1x Native Bacillus licheniformis Protease Creative Enzymes #NATE 0633 in HBSS  10 mM 4sU and incubated on ice for 30 min. Dissociation was aided by pipetting up and down with a 200 \u00b5l tip 25 times every 5 minutes. Enzymes were inactivated by adding 15 \u00b5l 10% BSA  Sigma Aldrich; #A4503 before spinning down and resuspending the cells in TRIzol RNA was extracted using TRIzol Chloroform Isopropanol according to the manufacturer's instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. Sequencing adapters were switched \u2013 Insert is in read 1!", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP374955", null, "assembly:dr11.95", "l_cold_dissociated_3_R1.fastq.gz l_cold_dissociated_3_R2.fastq.gz", "fastq fastq", 1990371450.0, 13269143.0, "GSM6735818 r1", "0:120 1:30", "A:566370443;C:348995823;G:430419075;T:644554767;N:31342", 120, 30, null, null, 566370443, 348995823, 430419075, 644554767, 31342, "SRX18291979", "SRS15783401", "SRA1542250", "Junker, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker, Max-Delbr\u00fcck-Center for Molecular Medicine", 2, 0.76687, 0.27949, 0.20883, 0.27941, 0.84124, 0.99989, 0.56374, 1.0, 120, 30, "B", "T", "mate2 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2022-11-17", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [69931, "SRR22318719", "SRX18291978", "SRS15783400", "SRP374955", "PRJNA837586", "Labelling transcriptional response to dissociation using SLAMseq", "GSE202880", "Other", "Transcriptional response to dissociation is known to cause artefacts in single cell data sets. We used 4sU to label newly made transcripts during dissociation in order to to later remove them from the data set Overall design: 10mM 4sU was added to the dissociation buffer while the samples were enzymatically dissociated for 30 min. 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Dissociation was aided by pipetting up and down with a 200 \u00b5l tip 25 times every 5 minutes. Enzymes were inactivated by adding 15 \u00b5l 10% BSA  Sigma Aldrich; #A4503 before spinning down and resuspending the cells in TRIzol RNA was extracted using TRIzol Chloroform Isopropanol according to the manufacturer\u2019s instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. 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Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. 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A 4sU injected control was added to the zebrafish samples to identify high turnover genes", "parent bioproject:PRJNA837863", "pubmed:36573354", null, "larvae  cold dissociated  rep 1", "GSM6735816", null, "tissue:whole larvae  48hpf|cell type:whole larvae  48hpf|genotype:WT|treatment:30 min 4sU during dissociation|time:48hpf", "larvae  cold dissociated  rep 1", "Demultiplexing bcl2fastq v2.19  CELseq barcodes demultiplexed using custom code https://github.com/anikaneuschulz/CELseq3 demultiplex mapping using STAR v2.7.3a aggregation of mutation information and calculation of labeling rates per gene / in bulk using custom code https://github.com/anikaneuschulz/MTglob pipeline genome build/assembly: dr11.95 processed data files format and content: Tab delimited mutation rates per gene", "whole larvae  48hpf", null, "10  anesthetized larvae were washed twice in ice cold HBSS Life Technologies GmbH #14175095 and resuspended in 200\u00b5l psychrophilic protease mix 1x Native Bacillus licheniformis Protease Creative Enzymes #NATE 0633 in HBSS  10 mM 4sU and incubated on ice for 30 min. Dissociation was aided by pipetting up and down with a 200 \u00b5l tip 25 times every 5 minutes. Enzymes were inactivated by adding 15 \u00b5l 10% BSA  Sigma Aldrich; #A4503 before spinning down and resuspending the cells in TRIzol RNA was extracted using TRIzol Chloroform Isopropanol according to the manufacturer\u2019s instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. 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Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. 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