{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Hatching\" and technology = \"celseq\"", "rows": [[41006, "SRR3996110", "SRX1997147", "SRS1598490", "SRP075286", "PRJNA321866", "Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars", "GSE81533", "Other", "A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches  analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace  a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.", null, null, null, "dynamics RNA", "GSM2258257", null, "tissue:Single embryos|developmental stage:48h", "dynamics RNA", "Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction  for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv  and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars  we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment  combined with the 3\u2019 location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library  and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library", "Single embryos", "Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/\u03bcl in combination with an sgRNA targeting GFP final concentration 25 ng/\u03bcl  sequence: GGTGTTCTGCTGGTAGTGGT.", "TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP  including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads \u2013 Beckman Coulter. Finally  sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina\u2019s TruSeq Small RNA Sample Prep Kit.", null, "developmental stage:48h", "GSM2258257", "GSM2258257: dynamics RNA; Danio rerio; RNA Seq", "GSM2258257", null, "1", "TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP  including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads \u2013 Beckman Coulter. Finally  sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina\u2019s TruSeq Small RNA Sample Prep Kit.", "GEO Accession:GSM2258257", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP075286", null, null, "Philipp-dynamics-RNA_HKLJYBGXX_S8_L001_R1_001.fastq.gz Philipp-dynamics-RNA_HKLJYBGXX_S8_L001_R2_001.fastq.gz", "fastq fastq", 80515624.0, 530034.0, "GSM2258257 r1", "0:75.99 1:75.92", "A:14695730;C:23934258;G:29464421;T:12392506;N:28709", 75, 75, null, null, 14695730, 23934258, 29464421, 12392506, 28709, "SRX1997147", "SRS1598490", "SRA426643", "GEO", "Max Delbr\u00fcck Center", 2, 0.0, 1e-05, 0.0, 0.0, 1.0, 0.99997, null, 0.0, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-08-03", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41007, "SRR3996111", "SRX1997147", "SRS1598490", "SRP075286", "PRJNA321866", "Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars", "GSE81533", "Other", "A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches  analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace  a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.", null, null, null, "dynamics RNA", "GSM2258257", null, "tissue:Single embryos|developmental stage:48h", "dynamics RNA", "Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction  for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv  and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars  we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment  combined with the 3\u2019 location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library  and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library", "Single embryos", "Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/\u03bcl in combination with an sgRNA targeting GFP final concentration 25 ng/\u03bcl  sequence: GGTGTTCTGCTGGTAGTGGT.", "TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP  including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads \u2013 Beckman Coulter. Finally  sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina\u2019s TruSeq Small RNA Sample Prep Kit.", null, "developmental stage:48h", "GSM2258257", "GSM2258257: dynamics RNA; Danio rerio; RNA Seq", "GSM2258257", null, "1", "TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP  including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads \u2013 Beckman Coulter. Finally  sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina\u2019s TruSeq Small RNA Sample Prep Kit.", "GEO Accession:GSM2258257", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP075286", null, null, "Philipp-dynamics-RNA_HKLJYBGXX_S8_L002_R1_001.fastq.gz Philipp-dynamics-RNA_HKLJYBGXX_S8_L002_R2_001.fastq.gz", "fastq fastq", 80995216.0, 533194.0, "GSM2258257 r2", "0:75.99 1:75.92", "A:14785958;C:24008314;G:29766059;T:12409358;N:25527", 75, 75, null, null, 14785958, 24008314, 29766059, 12409358, 25527, "SRX1997147", "SRS1598490", "SRA426643", "GEO", "Max Delbr\u00fcck Center", 2, 1e-05, 1e-05, 0.0, 0.0, 0.99997, 1.0, 0.0, null, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-08-03", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41008, "SRR3996112", "SRX1997147", "SRS1598490", "SRP075286", "PRJNA321866", "Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars", "GSE81533", "Other", "A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches  analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace  a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.", null, null, null, "dynamics RNA", "GSM2258257", null, "tissue:Single embryos|developmental stage:48h", "dynamics RNA", "Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction  for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv  and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars  we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment  combined with the 3\u2019 location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library  and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library", "Single embryos", "Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/\u03bcl in combination with an sgRNA targeting GFP final concentration 25 ng/\u03bcl  sequence: GGTGTTCTGCTGGTAGTGGT.", "TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP  including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads \u2013 Beckman Coulter. Finally  sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina\u2019s TruSeq Small RNA Sample Prep Kit.", null, "developmental stage:48h", "GSM2258257", "GSM2258257: dynamics RNA; Danio rerio; RNA Seq", "GSM2258257", null, "1", "TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP  including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads \u2013 Beckman Coulter. Finally  sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina\u2019s TruSeq Small RNA Sample Prep Kit.", "GEO Accession:GSM2258257", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP075286", null, null, "Philipp-dynamics-RNA_HKLJYBGXX_S8_L003_R1_001.fastq.gz Philipp-dynamics-RNA_HKLJYBGXX_S8_L003_R2_001.fastq.gz", "fastq fastq", 73436227.0, 483449.0, "GSM2258257 r3", "0:75.98 1:75.92", "A:13427325;C:21824372;G:26876634;T:11306254;N:1642", 75, 75, null, null, 13427325, 21824372, 26876634, 11306254, 1642, "SRX1997147", "SRS1598490", "SRA426643", "GEO", "Max Delbr\u00fcck Center", 2, 2e-05, 1e-05, 0.0, 0.0, 0.99997, 1.0, 0.0, null, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-08-03", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41009, "SRR3996113", "SRX1997147", "SRS1598490", "SRP075286", "PRJNA321866", "Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars", "GSE81533", "Other", "A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches  analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace  a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.", null, null, null, "dynamics RNA", "GSM2258257", null, "tissue:Single embryos|developmental stage:48h", "dynamics RNA", "Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction  for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv  and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars  we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment  combined with the 3\u2019 location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library  and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library", "Single embryos", "Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/\u03bcl in combination with an sgRNA targeting GFP final concentration 25 ng/\u03bcl  sequence: GGTGTTCTGCTGGTAGTGGT.", "TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP  including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads \u2013 Beckman Coulter. Finally  sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina\u2019s TruSeq Small RNA Sample Prep Kit.", null, "developmental stage:48h", "GSM2258257", "GSM2258257: dynamics RNA; Danio rerio; RNA Seq", "GSM2258257", null, "1", "TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP  including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads \u2013 Beckman Coulter. Finally  sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina\u2019s TruSeq Small RNA Sample Prep Kit.", "GEO Accession:GSM2258257", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP075286", null, null, "Philipp-dynamics-RNA_HKLJYBGXX_S8_L004_R1_001.fastq.gz Philipp-dynamics-RNA_HKLJYBGXX_S8_L004_R2_001.fastq.gz", "fastq fastq", 78694337.0, 518048.0, "GSM2258257 r4", "0:75.98 1:75.92", "A:14385406;C:23351418;G:28887789;T:12068521;N:1203", 75, 75, null, null, 14385406, 23351418, 28887789, 12068521, 1203, "SRX1997147", "SRS1598490", "SRA426643", "GEO", "Max Delbr\u00fcck Center", 2, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, null, null, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-08-03", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43755, "SRR6054093", "SRX3201032", "SRS2528004", "SRP118319", "PRJNA408129", "Spatially resolved RNA sequencing of the embryonic zebrafish heart", "GSE104057", "Transcriptome Analysis", "Development of specialized cell types and structures in the vertebrate heart is regulated by spatially restricted molecular pathways. Disruptions in these pathways can cause severe congenital cardiac malformations or functional defects. To better understand these pathways and how they regulate cardiac development and function we used tomo seq  combining high throughput RNA sequencing with tissue sectioning  to establish a genome wide expression dataset with high spatial resolution for the developing zebrafish heart. Analysis of the dataset revealed over 1100 genes differentially expressed in sub compartments. Pacemaker cells in the sinoatrial region induce heart contractions  but little is known about the mechanisms underlying their development and function. Using our transcriptome map  we identified spatially restricted Wnt/\u00df catenin signaling activity in pacemaker cells  which was controlled by Islet 1 activity. Moreover  Wnt/\u00df catenin signaling at a specific developmental stage in the myocardium controls heart rate by regulating pacemaker cellular response to parasympathetic stimuli. Thus  this high resolution transcriptome map incorporating all cell types in the embryonic heart can expose spatially restricted molecular pathways critical for specific cardiac functions. Overall design: To generate spatially resolved RNA seq data for the developing zebrafish hearts 2 dpf  we cryosectioned 3 hearts  extracted RNA from the individual sections  amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina NextSeq using 75bp paired end sequencing. Sample Heart #1 is the primary sample. Heart #2 and #3 are biological replicates used for comparison.", null, "pubmed:29400650", null, "heart3 2dpf wt", "GSM2788520", null, "source name:isolated embryonic heart|tissue:embryonic heart|developmental stage:48 hpf direction:posterior/inflow tract to anterior/outflow tract; located in sections #11   #39|section thickness:10\u00b5m sections", "heart3 2dpf wt", "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. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: csv file containing transcript counts per gene rows and section columns", "isolated embryonic heart", "Unfixed embryonic hearts were dissected and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012  see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell", null, "tissue:embryonic heart|developmental stage:48 hpf direction:posterior/inflow tract to anterior/outflow tract; located in sections #11   #39|section thickness:10\u00b5m sections", "GSM2788520", "GSM2788520: heart3 2dpf wt; Danio rerio; RNA Seq", "GSM2788520", null, "1", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012  see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell", "GEO Accession:GSM2788520", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP118319", null, null, "heart_03_SB032dpfwt_R1.fastq.gz heart_03_SB032dpfwt_R2.fastq.gz", "fastq fastq", 2662906147.0, 17670214.0, "GSM2788520 r1", "0:75.39 1:75.31", "A:828280216;C:376671462;G:437493213;T:1019745554;N:715702", 75, 75, null, null, 828280216, 376671462, 437493213, 1019745554, 715702, "SRX3201032", "SRS2528004", "SRA610777", "GEO", "Jeroen Bakkers lab, Cardiac Development and Genetics, Hubrecht Institute", 2, 0.04145, 0.36579, 0.03839, 0.09603, 0.99912, 0.89623, 0.41379, 0.5674, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2017-09-20", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [43756, "SRR6054092", "SRX3201031", "SRS2528003", "SRP118319", "PRJNA408129", "Spatially resolved RNA sequencing of the embryonic zebrafish heart", "GSE104057", "Transcriptome Analysis", "Development of specialized cell types and structures in the vertebrate heart is regulated by spatially restricted molecular pathways. Disruptions in these pathways can cause severe congenital cardiac malformations or functional defects. To better understand these pathways and how they regulate cardiac development and function we used tomo seq  combining high throughput RNA sequencing with tissue sectioning  to establish a genome wide expression dataset with high spatial resolution for the developing zebrafish heart. Analysis of the dataset revealed over 1100 genes differentially expressed in sub compartments. Pacemaker cells in the sinoatrial region induce heart contractions  but little is known about the mechanisms underlying their development and function. Using our transcriptome map  we identified spatially restricted Wnt/\u00df catenin signaling activity in pacemaker cells  which was controlled by Islet 1 activity. Moreover  Wnt/\u00df catenin signaling at a specific developmental stage in the myocardium controls heart rate by regulating pacemaker cellular response to parasympathetic stimuli. Thus  this high resolution transcriptome map incorporating all cell types in the embryonic heart can expose spatially restricted molecular pathways critical for specific cardiac functions. Overall design: To generate spatially resolved RNA seq data for the developing zebrafish hearts 2 dpf  we cryosectioned 3 hearts  extracted RNA from the individual sections  amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina NextSeq using 75bp paired end sequencing. Sample Heart #1 is the primary sample. Heart #2 and #3 are biological replicates used for comparison.", null, "pubmed:29400650", null, "heart2 2dpf wt", "GSM2788519", null, "source name:isolated embryonic heart|tissue:embryonic heart|developmental stage:48 hpf direction:posterior/inflow tract to anterior/outflow tract; located in sections #49   #96|section thickness:10\u00b5m sections", "heart2 2dpf wt", "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. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: csv file containing transcript counts per gene rows and section columns", "isolated embryonic heart", "Unfixed embryonic hearts were dissected and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012  see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell", null, "tissue:embryonic heart|developmental stage:48 hpf direction:posterior/inflow tract to anterior/outflow tract; located in sections #49   #96|section thickness:10\u00b5m sections", "GSM2788519", "GSM2788519: heart2 2dpf wt; Danio rerio; RNA Seq", "GSM2788519", null, "1", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012  see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell", "GEO Accession:GSM2788519", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP118319", null, null, "heart_02_SB-150707_R1.fastq.gz heart_02_SB-150707_R2.fastq.gz", "fastq fastq", 5482437730.0, 36337096.0, "GSM2788519 r1", "0:75.41 1:75.47", "A:1859596349;C:686627791;G:950285046;T:1980208127;N:5720417", 75, 75, null, null, 1859596349, 686627791, 950285046, 1980208127, 5720417, "SRX3201031", "SRS2528003", "SRA610777", "GEO", "Jeroen Bakkers lab, Cardiac Development and Genetics, Hubrecht Institute", 2, 0.14301, 0.55835, 0.12504, 0.16935, 0.99285, 0.86334, 0.46837, 0.58661, 76, 74, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2017-09-20", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [43757, "SRR6054091", "SRX3201030", "SRS2528002", "SRP118319", "PRJNA408129", "Spatially resolved RNA sequencing of the embryonic zebrafish heart", "GSE104057", "Transcriptome Analysis", "Development of specialized cell types and structures in the vertebrate heart is regulated by spatially restricted molecular pathways. Disruptions in these pathways can cause severe congenital cardiac malformations or functional defects. To better understand these pathways and how they regulate cardiac development and function we used tomo seq  combining high throughput RNA sequencing with tissue sectioning  to establish a genome wide expression dataset with high spatial resolution for the developing zebrafish heart. Analysis of the dataset revealed over 1100 genes differentially expressed in sub compartments. Pacemaker cells in the sinoatrial region induce heart contractions  but little is known about the mechanisms underlying their development and function. Using our transcriptome map  we identified spatially restricted Wnt/\u00df catenin signaling activity in pacemaker cells  which was controlled by Islet 1 activity. Moreover  Wnt/\u00df catenin signaling at a specific developmental stage in the myocardium controls heart rate by regulating pacemaker cellular response to parasympathetic stimuli. Thus  this high resolution transcriptome map incorporating all cell types in the embryonic heart can expose spatially restricted molecular pathways critical for specific cardiac functions. Overall design: To generate spatially resolved RNA seq data for the developing zebrafish hearts 2 dpf  we cryosectioned 3 hearts  extracted RNA from the individual sections  amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina NextSeq using 75bp paired end sequencing. Sample Heart #1 is the primary sample. Heart #2 and #3 are biological replicates used for comparison.", null, "pubmed:29400650", null, "heart1 2dpf wt", "GSM2788518", null, "source name:isolated embryonic heart|tissue:embryonic heart|developmental stage:48 hpf direction:anterior/outflow tract to posterior/inflow tract; located in sections #2   #41|section thickness:10\u00b5m sections", "heart1 2dpf wt", "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. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: csv file containing transcript counts per gene rows and section columns", "isolated embryonic heart", "Unfixed embryonic hearts were dissected and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012  see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell", null, "tissue:embryonic heart|developmental stage:48 hpf direction:anterior/outflow tract to posterior/inflow tract; located in sections #2   #41|section thickness:10\u00b5m sections", "GSM2788518", "GSM2788518: heart1 2dpf wt; Danio rerio; RNA Seq", "GSM2788518", null, "1", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012  see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell", "GEO Accession:GSM2788518", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP118319", null, null, "heart_01_SB-06-2dpf_wt_R2.fastq.gz heart_01_SB-06-2dpf_wt_R1.fastq.gz", "fastq fastq", 8152229052.0, 54104958.0, "GSM2788518 r1", "0:75.41 1:75.27", "A:2955268830;C:1118145970;G:1152323290;T:2924136690;N:2354272", 75, 75, null, null, 2955268830, 1118145970, 1152323290, 2924136690, 2354272, "SRX3201030", "SRS2528002", "SRA610777", "GEO", "Jeroen Bakkers lab, Cardiac Development and Genetics, Hubrecht Institute", 2, 0.02706, 0.26955, 0.01984, 0.05871, 0.99675, 0.93194, 0.37979, 0.63172, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2017-09-20", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48199, "SRR7119866", "SRX4041509", "SRS3258988", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf mut 35", "GSM3131257", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ", "Danio rerio RNAseq singleHeart 2dpf mut 35", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ", "GSM3131257", "GSM3131257: Danio rerio RNAseq singleHeart 2dpf mut 35; Danio rerio; RNA Seq", "GSM3131257", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131257", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_35_NDCII_sample_0035.fastq.gz", "fastq", 137582100.0, 1834428.0, "GSM3131257 r1", "0:75", "A:42420010;C:23366189;G:30187957;T:41528798;N:79146", 75, null, null, null, 42420010, 23366189, 30187957, 41528798, 79146, "SRX4041509", "SRS3258988", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.69634, null, 0.15154, null, 0.85827, null, 0.50259, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48200, "SRR7119865", "SRX4041508", "SRS3258987", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf mut 34", "GSM3131256", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ", "Danio rerio RNAseq singleHeart 2dpf mut 34", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ", "GSM3131256", "GSM3131256: Danio rerio RNAseq singleHeart 2dpf mut 34; Danio rerio; RNA Seq", "GSM3131256", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131256", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_34_NDCII_sample_0034.fastq.gz", "fastq", 115231725.0, 1536423.0, "GSM3131256 r1", "0:75", "A:36189151;C:19748534;G:25280516;T:33944039;N:69485", 75, null, null, null, 36189151, 19748534, 25280516, 33944039, 69485, "SRX4041508", "SRS3258987", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.65755, null, 0.14147, null, 0.8635, null, 0.53314, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48201, "SRR7119864", "SRX4041507", "SRS3258986", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf mut 33", "GSM3131255", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ", "Danio rerio RNAseq singleHeart 2dpf mut 33", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ", "GSM3131255", "GSM3131255: Danio rerio RNAseq singleHeart 2dpf mut 33; Danio rerio; RNA Seq", "GSM3131255", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131255", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_33_NDCII_sample_0033.fastq.gz", "fastq", 86985525.0, 1159807.0, "GSM3131255 r1", "0:75", "A:27397325;C:14512545;G:19080050;T:25941403;N:54202", 75, null, null, null, 27397325, 14512545, 19080050, 25941403, 54202, "SRX4041507", "SRS3258986", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.63426, null, 0.16676, null, 0.87568, null, 0.5457, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48202, "SRR7119863", "SRX4041506", "SRS3258985", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf mut 32", "GSM3131254", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ", "Danio rerio RNAseq singleHeart 2dpf mut 32", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ", "GSM3131254", "GSM3131254: Danio rerio RNAseq singleHeart 2dpf mut 32; Danio rerio; RNA Seq", "GSM3131254", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131254", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_32_NDCII_sample_0032.fastq.gz", "fastq", 64224375.0, 856325.0, "GSM3131254 r1", "0:75", "A:20154725;C:11180349;G:13983116;T:18869397;N:36788", 75, null, null, null, 20154725, 11180349, 13983116, 18869397, 36788, "SRX4041506", "SRS3258985", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.65978, null, 0.16164, null, 0.8775, null, 0.54741, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48203, "SRR7119862", "SRX4041505", "SRS3258984", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf mut 31", "GSM3131253", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ", "Danio rerio RNAseq singleHeart 2dpf mut 31", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ", "GSM3131253", "GSM3131253: Danio rerio RNAseq singleHeart 2dpf mut 31; Danio rerio; RNA Seq", "GSM3131253", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131253", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_31_NDCII_sample_0031.fastq.gz", "fastq", 159901350.0, 2132018.0, "GSM3131253 r1", "0:75", "A:50993443;C:26156045;G:34865968;T:47792042;N:93852", 75, null, null, null, 50993443, 26156045, 34865968, 47792042, 93852, "SRX4041505", "SRS3258984", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.6343, null, 0.22382, null, 0.84707, null, 0.44037, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48204, "SRR7119861", "SRX4041504", "SRS3258983", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf mut 29", "GSM3131252", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ", "Danio rerio RNAseq singleHeart 2dpf mut 29", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ", "GSM3131252", "GSM3131252: Danio rerio RNAseq singleHeart 2dpf mut 29; Danio rerio; RNA Seq", "GSM3131252", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131252", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_29_NDCII_sample_0029.fastq.gz", "fastq", 205405950.0, 2738746.0, "GSM3131252 r1", "0:75", "A:64163069;C:34538013;G:45210194;T:61373525;N:121149", 75, null, null, null, 64163069, 34538013, 45210194, 61373525, 121149, "SRX4041504", "SRS3258983", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.65436, null, 0.20449, null, 0.84831, null, 0.52226, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48205, "SRR7119860", "SRX4041503", "SRS3258982", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf mut 28", "GSM3131251", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ", "Danio rerio RNAseq singleHeart 2dpf mut 28", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ", "GSM3131251", "GSM3131251: Danio rerio RNAseq singleHeart 2dpf mut 28; Danio rerio; RNA Seq", "GSM3131251", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131251", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_28_NDCII_sample_0028.fastq.gz", "fastq", 88773525.0, 1183647.0, "GSM3131251 r1", "0:75", "A:27560501;C:15646178;G:19351624;T:26163900;N:51322", 75, null, null, null, 27560501, 15646178, 19351624, 26163900, 51322, "SRX4041503", "SRS3258982", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.67182, null, 0.16278, null, 0.86527, null, 0.53604, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48206, "SRR7119859", "SRX4041502", "SRS3258981", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf mut 27", "GSM3131250", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ", "Danio rerio RNAseq singleHeart 2dpf mut 27", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ", "GSM3131250", "GSM3131250: Danio rerio RNAseq singleHeart 2dpf mut 27; Danio rerio; RNA Seq", "GSM3131250", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131250", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_27_NDCII_sample_0027.fastq.gz", "fastq", 135825300.0, 1811004.0, "GSM3131250 r1", "0:75", "A:42874929;C:23016416;G:29588893;T:40267147;N:77915", 75, null, null, null, 42874929, 23016416, 29588893, 40267147, 77915, "SRX4041502", "SRS3258981", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.64606, null, 0.13997, null, 0.86401, null, 0.53196, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48207, "SRR7119858", "SRX4041501", "SRS3258980", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf mut 26", "GSM3131249", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ", "Danio rerio RNAseq singleHeart 2dpf mut 26", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ", "GSM3131249", "GSM3131249: Danio rerio RNAseq singleHeart 2dpf mut 26; Danio rerio; RNA Seq", "GSM3131249", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131249", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_26_NDCII_sample_0026.fastq.gz", "fastq", 70861500.0, 944820.0, "GSM3131249 r1", "0:75", "A:22209781;C:12313683;G:15411508;T:20885853;N:40675", 75, null, null, null, 22209781, 12313683, 15411508, 20885853, 40675, "SRX4041501", "SRS3258980", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.65979, null, 0.17285, null, 0.8687, null, 0.51907, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48218, "SRR7119847", "SRX4041490", "SRS3258968", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf wt 14", "GSM3131238", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 2dpf wt 14", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "GSM3131238", "GSM3131238: Danio rerio RNAseq singleHeart 2dpf wt 14; Danio rerio; RNA Seq", "GSM3131238", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131238", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_14_NDCII_sample_0014.fastq.gz", "fastq", 81736125.0, 1089815.0, "GSM3131238 r1", "0:75", "A:25374411;C:14225355;G:17601172;T:24489651;N:45536", 75, null, null, null, 25374411, 14225355, 17601172, 24489651, 45536, "SRX4041490", "SRS3258968", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.68142, null, 0.17857, null, 0.86965, null, 0.53118, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48219, "SRR7119846", "SRX4041489", "SRS3258967", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf wt 13", "GSM3131237", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 2dpf wt 13", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "GSM3131237", "GSM3131237: Danio rerio RNAseq singleHeart 2dpf wt 13; Danio rerio; RNA Seq", "GSM3131237", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131237", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_13_NDCII_sample_0013.fastq.gz", "fastq", 62250900.0, 830012.0, "GSM3131237 r1", "0:75", "A:19221325;C:10606446;G:13851770;T:18535596;N:35763", 75, null, null, null, 19221325, 10606446, 13851770, 18535596, 35763, "SRX4041489", "SRS3258967", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.67033, null, 0.16463, null, 0.88669, null, 0.52197, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48220, "SRR7119845", "SRX4041488", "SRS3258966", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf wt 12", "GSM3131236", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 2dpf wt 12", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "GSM3131236", "GSM3131236: Danio rerio RNAseq singleHeart 2dpf wt 12; Danio rerio; RNA Seq", "GSM3131236", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131236", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_12_NDCII_sample_0012.fastq.gz", "fastq", 65079975.0, 867733.0, "GSM3131236 r1", "0:75", "A:20574087;C:11008240;G:14305699;T:19155761;N:36188", 75, null, null, null, 20574087, 11008240, 14305699, 19155761, 36188, "SRX4041488", "SRS3258966", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.65516, null, 0.23525, null, 0.87227, null, 0.55436, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48221, "SRR7119844", "SRX4041487", "SRS3258965", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf wt 11", "GSM3131235", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 2dpf wt 11", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "GSM3131235", "GSM3131235: Danio rerio RNAseq singleHeart 2dpf wt 11; Danio rerio; RNA Seq", "GSM3131235", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131235", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_11_NDCII_sample_0011.fastq.gz", "fastq", 56312400.0, 750832.0, "GSM3131235 r1", "0:75", "A:17682751;C:9499488;G:12398396;T:16701718;N:30047", 75, null, null, null, 17682751, 9499488, 12398396, 16701718, 30047, "SRX4041487", "SRS3258965", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.66642, null, 0.21243, null, 0.87868, null, 0.52403, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48222, "SRR7119843", "SRX4041486", "SRS3258964", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf wt 10", "GSM3131234", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 2dpf wt 10", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "GSM3131234", "GSM3131234: Danio rerio RNAseq singleHeart 2dpf wt 10; Danio rerio; RNA Seq", "GSM3131234", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131234", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_10_NDCII_sample_0010.fastq.gz", "fastq", 51364950.0, 684866.0, "GSM3131234 r1", "0:75", "A:16163832;C:8838505;G:11290003;T:15043422;N:29188", 75, null, null, null, 16163832, 8838505, 11290003, 15043422, 29188, "SRX4041486", "SRS3258964", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.65278, null, 0.18749, null, 0.87722, null, 0.53824, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48223, "SRR7119842", "SRX4041485", "SRS3258963", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf wt 9", "GSM3131233", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 2dpf wt 9", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "GSM3131233", "GSM3131233: Danio rerio RNAseq singleHeart 2dpf wt 9; Danio rerio; RNA Seq", "GSM3131233", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131233", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_9_NDCII_sample_0009.fastq.gz", "fastq", 149036325.0, 1987151.0, "GSM3131233 r1", "0:75", "A:47706695;C:23942760;G:33072602;T:44228491;N:85777", 75, null, null, null, 47706695, 23942760, 33072602, 44228491, 85777, "SRX4041485", "SRS3258963", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.56223, null, 0.19674, null, 0.87079, null, 0.52559, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48224, "SRR7119841", "SRX4041484", "SRS3258962", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf wt 8", "GSM3131232", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 2dpf wt 8", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "GSM3131232", "GSM3131232: Danio rerio RNAseq singleHeart 2dpf wt 8; Danio rerio; RNA Seq", "GSM3131232", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131232", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_8_NDCII_sample_0008.fastq.gz", "fastq", 61857375.0, 824765.0, "GSM3131232 r1", "0:75", "A:19180813;C:10701206;G:13569705;T:18368818;N:36833", 75, null, null, null, 19180813, 10701206, 13569705, 18368818, 36833, "SRX4041484", "SRS3258962", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.68869, null, 0.14177, null, 0.86722, null, 0.50808, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48225, "SRR7119840", "SRX4041483", "SRS3258960", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf wt 7", "GSM3131231", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 2dpf wt 7", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "GSM3131231", "GSM3131231: Danio rerio RNAseq singleHeart 2dpf wt 7; Danio rerio; RNA Seq", "GSM3131231", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131231", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_7_NDCII_sample_0007.fastq.gz", "fastq", 34999125.0, 466655.0, "GSM3131231 r1", "0:75", "A:10839927;C:6031095;G:7710789;T:10397147;N:20167", 75, null, null, null, 10839927, 6031095, 7710789, 10397147, 20167, "SRX4041483", "SRS3258960", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.67853, null, 0.1345, null, 0.89727, null, 0.42905, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48226, "SRR7119839", "SRX4041482", "SRS3258959", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf wt 6", "GSM3131230", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 2dpf wt 6", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "GSM3131230", "GSM3131230: Danio rerio RNAseq singleHeart 2dpf wt 6; Danio rerio; RNA Seq", "GSM3131230", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131230", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_6_NDCII_sample_0006.fastq.gz", "fastq", 53258025.0, 710107.0, "GSM3131230 r1", "0:75", "A:16706696;C:9150576;G:11345601;T:16024331;N:30821", 75, null, null, null, 16706696, 9150576, 11345601, 16024331, 30821, "SRX4041482", "SRS3258959", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.6829, null, 0.14834, null, 0.87799, null, 0.49352, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48227, "SRR7119838", "SRX4041481", "SRS3258958", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf wt 5", "GSM3131229", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 2dpf wt 5", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "GSM3131229", "GSM3131229: Danio rerio RNAseq singleHeart 2dpf wt 5; Danio rerio; RNA Seq", "GSM3131229", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131229", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_5_NDCII_sample_0005.fastq.gz", "fastq", 46391850.0, 618558.0, "GSM3131229 r1", "0:75", "A:14186549;C:7964105;G:10302794;T:13910329;N:28073", 75, null, null, null, 14186549, 7964105, 10302794, 13910329, 28073, "SRX4041481", "SRS3258958", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.67937, null, 0.14832, null, 0.88274, null, 0.51203, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48228, "SRR7119837", "SRX4041480", "SRS3258957", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf wt 4", "GSM3131228", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 2dpf wt 4", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "GSM3131228", "GSM3131228: Danio rerio RNAseq singleHeart 2dpf wt 4; Danio rerio; RNA Seq", "GSM3131228", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131228", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_4_NDCII_sample_0004.fastq.gz", "fastq", 119548650.0, 1593982.0, "GSM3131228 r1", "0:75", "A:37089578;C:20710248;G:25820048;T:35861658;N:67118", 75, null, null, null, 37089578, 20710248, 25820048, 35861658, 67118, "SRX4041480", "SRS3258957", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.67925, null, 0.18634, null, 0.84431, null, 0.49844, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48229, "SRR7119836", "SRX4041479", "SRS3258956", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf wt 3", "GSM3131227", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 2dpf wt 3", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "GSM3131227", "GSM3131227: Danio rerio RNAseq singleHeart 2dpf wt 3; Danio rerio; RNA Seq", "GSM3131227", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131227", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_3_NDCII_sample_0003.fastq.gz", "fastq", 52534500.0, 700460.0, "GSM3131227 r1", "0:75", "A:16258360;C:8995544;G:11338397;T:15914972;N:27227", 75, null, null, null, 16258360, 8995544, 11338397, 15914972, 27227, "SRX4041479", "SRS3258956", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.68677, null, 0.14664, null, 0.87541, null, 0.49296, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [48230, "SRR7119835", "SRX4041478", "SRS3258955", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 2dpf wt 2", "GSM3131226", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 2dpf wt 2", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+", "GSM3131226", "GSM3131226: Danio rerio RNAseq singleHeart 2dpf wt 2; Danio rerio; RNA Seq", "GSM3131226", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131226", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_2_NDCII_sample_0002.fastq.gz", "fastq", 27282075.0, 363761.0, "GSM3131226 r1", "0:75", "A:8540828;C:4756416;G:5793210;T:8176534;N:15087", 75, null, null, null, 8540828, 4756416, 5793210, 8176534, 15087, "SRX4041478", "SRS3258955", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.689, null, 0.16716, null, 0.89512, null, 0.51016, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [55357, "SRR10321296", "SRX7032110", "SRS5552216", "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, "LG B", "GSM4134189", null, "source name:Tgmyl7:GFP 2dpf embryo|Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo", "LG B", "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.", "Tgmyl7:GFP 2dpf embryo", "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:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo", "GSM4134189", "GSM4134189: LG B; Danio rerio; RNA Seq", "GSM4134189", 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:GSM4134189", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP226527", null, null, "LG-B_HF2K3BGXC_S8_L001_R1_001.fastq.gz LG-B_HF2K3BGXC_S8_L001_R2_001.fastq.gz", "fastq fastq", 1267797208.0, 14741828.0, "GSM4134189 r1", "0:26 1:60", "A:311335670;C:234211034;G:233670769;T:488236082;N:343653", 26, 60, null, null, 311335670, 234211034, 233670769, 488236082, 343653, "SRX7032110", "SRS5552216", "SRA982819", "GEO", "Bakkers, Hubrecht Institute", 2, 0.11947, 0.86802, 0.10602, 0.33834, 0.97402, 0.77475, 0.53341, 0.48502, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2019-10-21", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [55358, "SRR10321297", "SRX7032110", "SRS5552216", "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, "LG B", "GSM4134189", null, "source name:Tgmyl7:GFP 2dpf embryo|Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo", "LG B", "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.", "Tgmyl7:GFP 2dpf embryo", "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:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo", "GSM4134189", "GSM4134189: LG B; Danio rerio; RNA Seq", "GSM4134189", 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:GSM4134189", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP226527", null, null, "LG-B_HF2K3BGXC_S8_L002_R1_001.fastq.gz LG-B_HF2K3BGXC_S8_L002_R2_001.fastq.gz", "fastq fastq", 1243626134.0, 14460769.0, "GSM4134189 r2", "0:26 1:60", "A:303377313;C:228128597;G:235179890;T:476626682;N:313652", 26, 60, null, null, 303377313, 228128597, 235179890, 476626682, 313652, "SRX7032110", "SRS5552216", "SRA982819", "GEO", "Bakkers, Hubrecht Institute", 2, 0.11708, 0.86416, 0.10403, 0.33647, 0.9751, 0.77494, 0.53712, 0.49135, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2019-10-21", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [55359, "SRR10321298", "SRX7032110", "SRS5552216", "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, "LG B", "GSM4134189", null, "source name:Tgmyl7:GFP 2dpf embryo|Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo", "LG B", "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.", "Tgmyl7:GFP 2dpf embryo", "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:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo", "GSM4134189", "GSM4134189: LG B; Danio rerio; RNA Seq", "GSM4134189", 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:GSM4134189", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP226527", null, null, "LG-B_HF2K3BGXC_S8_L003_R1_001.fastq.gz LG-B_HF2K3BGXC_S8_L003_R2_001.fastq.gz", "fastq fastq", 1279414002.0, 14876907.0, "GSM4134189 r3", "0:26 1:60", "A:313771869;C:236451307;G:236190971;T:492760785;N:239070", 26, 60, null, null, 313771869, 236451307, 236190971, 492760785, 239070, "SRX7032110", "SRS5552216", "SRA982819", "GEO", "Bakkers, Hubrecht Institute", 2, 0.11797, 0.86817, 0.10442, 0.33882, 0.97394, 0.7713, 0.54719, 0.48818, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2019-10-21", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [55360, "SRR10321299", "SRX7032110", "SRS5552216", "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, "LG B", "GSM4134189", null, "source name:Tgmyl7:GFP 2dpf embryo|Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo", "LG B", "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.", "Tgmyl7:GFP 2dpf embryo", "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:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo", "GSM4134189", "GSM4134189: LG B; Danio rerio; RNA Seq", "GSM4134189", 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:GSM4134189", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP226527", null, null, "LG-B_HF2K3BGXC_S8_L004_R1_001.fastq.gz LG-B_HF2K3BGXC_S8_L004_R2_001.fastq.gz", "fastq fastq", 1253047262.0, 14570317.0, "GSM4134189 r4", "0:26 1:60", "A:305572355;C:230224915;G:236268214;T:480774305;N:207473", 26, 60, null, null, 305572355, 230224915, 236268214, 480774305, 207473, "SRX7032110", "SRS5552216", "SRA982819", "GEO", "Bakkers, Hubrecht Institute", 2, 0.11724, 0.86376, 0.10408, 0.336, 0.97522, 0.77273, 0.53004, 0.4873, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2019-10-21", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [55361, "SRR10321292", "SRX7032109", "SRS5552215", "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, "LG A", "GSM4134188", null, "source name:Tgmyl7:GFP 2dpf embryo|Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo", "LG A", "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.", "Tgmyl7:GFP 2dpf embryo", "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:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo", "GSM4134188", "GSM4134188: LG A; Danio rerio; RNA Seq", "GSM4134188", 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:GSM4134188", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP226527", null, null, "LG-A_HF2K3BGXC_S7_L001_R1_001.fastq.gz LG-A_HF2K3BGXC_S7_L001_R2_001.fastq.gz", "fastq fastq", 718764350.0, 8357725.0, "GSM4134188 r1", "0:26 1:60", "A:175945701;C:132625850;G:132781182;T:277212457;N:199160", 26, 60, null, null, 175945701, 132625850, 132781182, 277212457, 199160, "SRX7032109", "SRS5552215", "SRA982819", "GEO", "Bakkers, Hubrecht Institute", 2, 0.11716, 0.82752, 0.10489, 0.34715, 0.97686, 0.77423, 0.57648, 0.4889, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2019-10-21", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [55362, "SRR10321293", "SRX7032109", "SRS5552215", "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, "LG A", "GSM4134188", null, "source name:Tgmyl7:GFP 2dpf embryo|Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo", "LG A", "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.", "Tgmyl7:GFP 2dpf embryo", "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:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo", "GSM4134188", "GSM4134188: LG A; Danio rerio; RNA Seq", "GSM4134188", 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:GSM4134188", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP226527", null, null, "LG-A_HF2K3BGXC_S7_L002_R1_001.fastq.gz LG-A_HF2K3BGXC_S7_L002_R2_001.fastq.gz", "fastq fastq", 706043402.0, 8209807.0, "GSM4134188 r2", "0:26 1:60", "A:171617783;C:129365895;G:133886696;T:270994479;N:178549", 26, 60, null, null, 171617783, 129365895, 133886696, 270994479, 178549, "SRX7032109", "SRS5552215", "SRA982819", "GEO", "Bakkers, Hubrecht Institute", 2, 0.11469, 0.82025, 0.10321, 0.34365, 0.97853, 0.77358, 0.5514, 0.49163, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2019-10-21", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [55363, "SRR10321294", "SRX7032109", "SRS5552215", "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, "LG A", "GSM4134188", null, "source name:Tgmyl7:GFP 2dpf embryo|Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo", "LG A", "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.", "Tgmyl7:GFP 2dpf embryo", "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:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo", "GSM4134188", "GSM4134188: LG A; Danio rerio; RNA Seq", "GSM4134188", 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:GSM4134188", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP226527", null, null, "LG-A_HF2K3BGXC_S7_L003_R1_001.fastq.gz LG-A_HF2K3BGXC_S7_L003_R2_001.fastq.gz", "fastq fastq", 724780910.0, 8427685.0, "GSM4134188 r3", "0:26 1:60", "A:177259308;C:133737279;G:134127261;T:279526553;N:130509", 26, 60, null, null, 177259308, 133737279, 134127261, 279526553, 130509, "SRX7032109", "SRS5552215", "SRA982819", "GEO", "Bakkers, Hubrecht Institute", 2, 0.11681, 0.82709, 0.10477, 0.3456, 0.97743, 0.77555, 0.5658, 0.47721, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2019-10-21", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [55364, "SRR10321295", "SRX7032109", "SRS5552215", "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, "LG A", "GSM4134188", null, "source name:Tgmyl7:GFP 2dpf embryo|Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo", "LG A", "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.", "Tgmyl7:GFP 2dpf embryo", "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:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo", "GSM4134188", "GSM4134188: LG A; Danio rerio; RNA Seq", "GSM4134188", 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:GSM4134188", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP226527", null, null, "LG-A_HF2K3BGXC_S7_L004_R1_001.fastq.gz LG-A_HF2K3BGXC_S7_L004_R2_001.fastq.gz", "fastq fastq", 710625138.0, 8263083.0, "GSM4134188 r4", "0:26 1:60", "A:172737690;C:130422622;G:134392616;T:272953106;N:119104", 26, 60, null, null, 172737690, 130422622, 134392616, 272953106, 119104, "SRX7032109", "SRS5552215", "SRA982819", "GEO", "Bakkers, Hubrecht Institute", 2, 0.11478, 0.82425, 0.10243, 0.34317, 0.97796, 0.77425, 0.53983, 0.48743, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2019-10-21", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [61999, "SRR13115089", "SRX9557302", "SRS7769186", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZNI160317 P1 8", "GSM4930061", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZNI160317 P1 8", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930061", "GSM4930061: ZNI160317 P1 8; Danio rerio; RNA Seq", "GSM4930061", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930061", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZNI160317_P1_8_R1.fastq.gz ZNI160317_P1_8_R2.fastq.gz", "fastq fastq", 1337385100.0, 13373851.0, "GSM4930061 r1", "0:30 1:70", "A:347006359;C:234653057;G:234033243;T:521283652;N:408789", 30, 70, null, null, 347006359, 234653057, 234033243, 521283652, 408789, "SRX9557302", "SRS7769186", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.43417, 0.78388, 0.40203, 0.40818, 0.99299, 0.77843, 0.50945, 0.55316, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62000, "SRR13115088", "SRX9557301", "SRS7763907", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZNI160317 P1 7", "GSM4930060", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZNI160317 P1 7", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930060", "GSM4930060: ZNI160317 P1 7; Danio rerio; RNA Seq", "GSM4930060", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930060", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZNI160317_P1_7_R1.fastq.gz ZNI160317_P1_7_R2.fastq.gz", "fastq fastq", 1279888600.0, 12798886.0, "GSM4930060 r1", "0:30 1:70", "A:326535111;C:229909698;G:228370251;T:494684312;N:389228", 30, 70, null, null, 326535111, 229909698, 228370251, 494684312, 389228, "SRX9557301", "SRS7763907", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.48745, 0.80016, 0.46063, 0.38614, 0.99097, 0.78147, 0.46969, 0.58779, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62001, "SRR13115087", "SRX9557300", "SRS7770578", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZNI160317 P1 6", "GSM4930059", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZNI160317 P1 6", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930059", "GSM4930059: ZNI160317 P1 6; Danio rerio; RNA Seq", "GSM4930059", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930059", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZNI160317_P1_6_R1.fastq.gz ZNI160317_P1_6_R2.fastq.gz", "fastq fastq", 1356342900.0, 13563429.0, "GSM4930059 r1", "0:30 1:70", "A:379084008;C:226360122;G:228552139;T:521934821;N:411810", 30, 70, null, null, 379084008, 226360122, 228552139, 521934821, 411810, "SRX9557300", "SRS7770578", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.44737, 0.74966, 0.42078, 0.34194, 0.9934, 0.79091, 0.84735, 0.42938, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62002, "SRR13115086", "SRX9557299", "SRS7758037", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZNI160317 P1 5", "GSM4930058", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZNI160317 P1 5", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930058", "GSM4930058: ZNI160317 P1 5; Danio rerio; RNA Seq", "GSM4930058", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930058", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZNI160317_P1_5_R1.fastq.gz ZNI160317_P1_5_R2.fastq.gz", "fastq fastq", 1167185600.0, 11671856.0, "GSM4930058 r1", "0:30 1:70", "A:281862692;C:225836593;G:215293596;T:443836278;N:356441", 30, 70, null, null, 281862692, 225836593, 215293596, 443836278, 356441, "SRX9557299", "SRS7758037", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.40867, 0.83648, 0.37699, 0.32708, 0.99048, 0.78938, 0.83594, 0.51462, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62007, "SRR13115081", "SRX9557294", "SRS7758850", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZNC181016 12", "GSM4930053", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZNC181016 12", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930053", "GSM4930053: ZNC181016 12; Danio rerio; RNA Seq", "GSM4930053", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930053", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZNC181016_12_R1.fastq.gz ZNC181016_12_R2.fastq.gz", "fastq fastq", 476005400.0, 4760054.0, "GSM4930053 r1", "0:30 1:70", "A:124538753;C:84143341;G:82570226;T:184169560;N:583520", 30, 70, null, null, 124538753, 84143341, 82570226, 184169560, 583520, "SRX9557294", "SRS7758850", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.42712, 0.77974, 0.39704, 0.48771, 0.99389, 0.86135, 0.73235, 0.64741, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62008, "SRR13115080", "SRX9557293", "SRS7765456", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZNC181016 11", "GSM4930052", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZNC181016 11", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930052", "GSM4930052: ZNC181016 11; Danio rerio; RNA Seq", "GSM4930052", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930052", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZNC181016_11_R1.fastq.gz ZNC181016_11_R2.fastq.gz", "fastq fastq", 786776600.0, 7867766.0, "GSM4930052 r1", "0:30 1:70", "A:213121780;C:142546342;G:132623188;T:297537196;N:948094", 30, 70, null, null, 213121780, 142546342, 132623188, 297537196, 948094, "SRX9557293", "SRS7765456", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.41249, 0.76451, 0.39753, 0.55115, 0.99086, 0.84307, 0.62648, 0.41771, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62009, "SRR13115079", "SRX9557292", "SRS7762461", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZNC181016 10", "GSM4930051", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZNC181016 10", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930051", "GSM4930051: ZNC181016 10; Danio rerio; RNA Seq", "GSM4930051", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930051", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZNC181016_10_R1.fastq.gz ZNC181016_10_R2.fastq.gz", "fastq fastq", 497840900.0, 4978409.0, "GSM4930051 r1", "0:30 1:70", "A:137854508;C:86121616;G:83106652;T:190153177;N:604947", 30, 70, null, null, 137854508, 86121616, 83106652, 190153177, 604947, "SRX9557292", "SRS7762461", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.43691, 0.74632, 0.41151, 0.5336, 0.99324, 0.84906, 0.82241, 0.65847, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62010, "SRR13115078", "SRX9557291", "SRS7771620", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZNC181016 9", "GSM4930050", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZNC181016 9", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930050", "GSM4930050: ZNC181016 9; Danio rerio; RNA Seq", "GSM4930050", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930050", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZNC181016_9_R1.fastq.gz ZNC181016_9_R2.fastq.gz", "fastq fastq", 932985500.0, 9329855.0, "GSM4930050 r1", "0:30 1:70", "A:250634435;C:162916909;G:167128292;T:351161628;N:1144236", 30, 70, null, null, 250634435, 162916909, 167128292, 351161628, 1144236, "SRX9557291", "SRS7771620", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.54048, 0.54987, 0.52828, 0.36431, 0.99362, 0.86535, 0.61298, 0.67072, 30, 70, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62011, "SRR13115077", "SRX9557290", "SRS7763268", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZNC160317 P1 4", "GSM4930049", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZNC160317 P1 4", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930049", "GSM4930049: ZNC160317 P1 4; Danio rerio; RNA Seq", "GSM4930049", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930049", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZNC160317_P1_4_R1.fastq.gz ZNC160317_P1_4_R2.fastq.gz", "fastq fastq", 1307869800.0, 13078698.0, "GSM4930049 r1", "0:30 1:70", "A:317290751;C:239429367;G:234943406;T:515801063;N:405213", 30, 70, null, null, 317290751, 239429367, 234943406, 515801063, 405213, "SRX9557290", "SRS7763268", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.33232, 0.8203, 0.31733, 0.37763, 0.98985, 0.77374, 0.71932, 0.58771, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62012, "SRR13115076", "SRX9557289", "SRS7768293", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZNC160317 P1 3", "GSM4930048", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZNC160317 P1 3", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930048", "GSM4930048: ZNC160317 P1 3; Danio rerio; RNA Seq", "GSM4930048", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930048", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZNC160317_P1_3_R1.fastq.gz ZNC160317_P1_3_R2.fastq.gz", "fastq fastq", 457462200.0, 4574622.0, "GSM4930048 r1", "0:30 1:70", "A:108644216;C:83870596;G:86397141;T:178408097;N:142150", 30, 70, null, null, 108644216, 83870596, 86397141, 178408097, 142150, "SRX9557289", "SRS7768293", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.50502, 0.8447, 0.46926, 0.30821, 0.98748, 0.78955, 0.52537, 0.59534, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62013, "SRR13115075", "SRX9557288", "SRS7776259", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZNC160317 P1 2", "GSM4930047", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZNC160317 P1 2", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930047", "GSM4930047: ZNC160317 P1 2; Danio rerio; RNA Seq", "GSM4930047", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930047", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZNC160317_P1_2_R1.fastq.gz ZNC160317_P1_2_R2.fastq.gz", "fastq fastq", 1340603100.0, 13406031.0, "GSM4930047 r1", "0:30 1:70", "A:322845512;C:246499562;G:249678813;T:521170210;N:409003", 30, 70, null, null, 322845512, 246499562, 249678813, 521170210, 409003, "SRX9557288", "SRS7776259", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.35361, 0.84311, 0.33033, 0.35892, 0.98725, 0.7723, 0.63118, 0.58869, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62014, "SRR13115074", "SRX9557287", "SRS7772244", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZNC160317 P1 1", "GSM4930046", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZNC160317 P1 1", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930046", "GSM4930046: ZNC160317 P1 1; Danio rerio; RNA Seq", "GSM4930046", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930046", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZNC160317_P1_1_R1.fastq.gz ZNC160317_P1_1_R2.fastq.gz", "fastq fastq", 532291500.0, 5322915.0, "GSM4930046 r1", "0:30 1:70", "A:127478940;C:97180307;G:100496111;T:206975403;N:160739", 30, 70, null, null, 127478940, 97180307, 100496111, 206975403, 160739, "SRX9557287", "SRS7772244", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.50083, 0.83039, 0.4776, 0.33992, 0.98589, 0.78255, 0.59541, 0.59566, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62015, "SRR13115073", "SRX9557286", "SRS7771774", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZNC151116 12", "GSM4930045", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZNC151116 12", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930045", "GSM4930045: ZNC151116 12; Danio rerio; RNA Seq", "GSM4930045", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930045", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZNC151116_12_R1.fastq.gz ZNC151116_12_R2.fastq.gz", "fastq fastq", 1207658000.0, 12076580.0, "GSM4930045 r1", "0:30 1:70", "A:297106318;C:212194469;G:224350366;T:473097329;N:909518", 30, 70, null, null, 297106318, 212194469, 224350366, 473097329, 909518, "SRX9557286", "SRS7771774", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.42243, 0.66493, 0.4018, 0.15026, 0.9949, 0.85701, 0.69732, 0.72078, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62016, "SRR13115072", "SRX9557285", "SRS7762982", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZNC151116 11", "GSM4930044", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZNC151116 11", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930044", "GSM4930044: ZNC151116 11; Danio rerio; RNA Seq", "GSM4930044", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930044", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZNC151116_11_R1.fastq.gz ZNC151116_11_R2.fastq.gz", "fastq fastq", 1264736000.0, 12647360.0, "GSM4930044 r1", "0:30 1:70", "A:305172802;C:225250825;G:234261405;T:499104109;N:946859", 30, 70, null, null, 305172802, 225250825, 234261405, 499104109, 946859, "SRX9557285", "SRS7762982", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.58354, 0.87807, 0.56642, 0.15401, 0.99364, 0.8412, 0.63236, 0.70146, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62017, "SRR13115071", "SRX9557284", "SRS7764916", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZNC151116 10", "GSM4930043", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZNC151116 10", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930043", "GSM4930043: ZNC151116 10; Danio rerio; RNA Seq", "GSM4930043", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930043", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZNC151116_10_R1.fastq.gz ZNC151116_10_R2.fastq.gz", "fastq fastq", 1177857100.0, 11778571.0, "GSM4930043 r1", "0:30 1:70", "A:285930811;C:206559699;G:218627577;T:465859304;N:879709", 30, 70, null, null, 285930811, 206559699, 218627577, 465859304, 879709, "SRX9557284", "SRS7764916", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.45186, 0.88321, 0.43175, 0.19229, 0.9946, 0.83169, 0.80603, 0.72758, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62018, "SRR13115070", "SRX9557283", "SRS7764847", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZNC151116 9", "GSM4930042", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZNC151116 9", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930042", "GSM4930042: ZNC151116 9; Danio rerio; RNA Seq", "GSM4930042", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930042", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZNC151116_9_R1.fastq.gz ZNC151116_9_R2.fastq.gz", "fastq fastq", 1261452300.0, 12614523.0, "GSM4930042 r1", "0:30 1:70", "A:305810580;C:222719536;G:231761383;T:500202963;N:957838", 30, 70, null, null, 305810580, 222719536, 231761383, 500202963, 957838, "SRX9557283", "SRS7764847", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.62185, 0.88423, 0.58866, 0.19394, 0.99318, 0.81602, 0.59672, 0.71811, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62047, "SRR13115041", "SRX9557254", "SRS7770301", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZN MAX P2 4", "GSM4930013", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZN MAX P2 4", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930013", "GSM4930013: ZN MAX P2 4; Danio rerio; RNA Seq", "GSM4930013", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930013", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZN_MAX_P2_4_R1.fastq.gz ZN_MAX_P2_4_R2.fastq.gz", "fastq fastq", 964632400.0, 9646324.0, "GSM4930013 r1", "0:30 1:70", "A:258078490;C:168445099;G:158779289;T:376011663;N:3317859", 30, 70, null, null, 258078490, 168445099, 158779289, 376011663, 3317859, "SRX9557254", "SRS7770301", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.33482, 0.75255, 0.31578, 0.60748, 0.99072, 0.85036, 0.35024, 0.65362, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62048, "SRR13115040", "SRX9557253", "SRS7767387", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZN MAX P2 3", "GSM4930012", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZN MAX P2 3", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930012", "GSM4930012: ZN MAX P2 3; Danio rerio; RNA Seq", "GSM4930012", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930012", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZN_MAX_P2_3_R1.fastq.gz ZN_MAX_P2_3_R2.fastq.gz", "fastq fastq", 1503797500.0, 15037975.0, "GSM4930012 r1", "0:30 1:70", "A:410761938;C:260031957;G:248254746;T:579534898;N:5213961", 30, 70, null, null, 410761938, 260031957, 248254746, 579534898, 5213961, "SRX9557253", "SRS7767387", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.37598, 0.74182, 0.35119, 0.63203, 0.98967, 0.83086, 0.89035, 0.57769, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62049, "SRR13115039", "SRX9557252", "SRS7762034", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZN MAX P2 2", "GSM4930011", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZN MAX P2 2", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930011", "GSM4930011: ZN MAX P2 2; Danio rerio; RNA Seq", "GSM4930011", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930011", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZN_MAX_P2_2_R1.fastq.gz ZN_MAX_P2_2_R2.fastq.gz", "fastq fastq", 2218481900.0, 22184819.0, "GSM4930011 r1", "0:30 1:70", "A:595460410;C:376545718;G:367310829;T:871462154;N:7702789", 30, 70, null, null, 595460410, 376545718, 367310829, 871462154, 7702789, "SRX9557252", "SRS7762034", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.39633, 0.75355, 0.36402, 0.59398, 0.99093, 0.83075, 0.92352, 0.68029, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62050, "SRR13115038", "SRX9557251", "SRS7759028", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZN MAX P2 1", "GSM4930010", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZN MAX P2 1", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930010", "GSM4930010: ZN MAX P2 1; Danio rerio; RNA Seq", "GSM4930010", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930010", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZN_MAX_P2_1_R1.fastq.gz ZN_MAX_P2_1_R2.fastq.gz", "fastq fastq", 2018316100.0, 20183161.0, "GSM4930010 r1", "0:30 1:70", "A:538643226;C:348832695;G:348026653;T:775767393;N:7046133", 30, 70, null, null, 538643226, 348832695, 348026653, 775767393, 7046133, "SRX9557251", "SRS7759028", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.41931, 0.78504, 0.39101, 0.49917, 0.9934, 0.85328, 0.50449, 0.78391, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62051, "SRR13115037", "SRX9557250", "SRS7765592", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZN MAX P1 12", "GSM4930009", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZN MAX P1 12", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930009", "GSM4930009: ZN MAX P1 12; Danio rerio; RNA Seq", "GSM4930009", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930009", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZN_MAX_P1_12_R1.fastq.gz ZN_MAX_P1_12_R2.fastq.gz", "fastq fastq", 1856484400.0, 18564844.0, "GSM4930009 r1", "0:30 1:70", "A:492818908;C:346137294;G:317211835;T:694001591;N:6314772", 30, 70, null, null, 492818908, 346137294, 317211835, 694001591, 6314772, "SRX9557250", "SRS7765592", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.30002, 0.7268, 0.28482, 0.56738, 0.9791, 0.82049, 0.73227, 0.35775, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62052, "SRR13115036", "SRX9557249", "SRS7762249", "SRP293760", "PRJNA680334", "Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development", "GSE162031", "Transcriptome Analysis", "Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.", null, "pubmed:33749326", null, "ZN MAX P1 11", "GSM4930008", null, "source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "ZN MAX P1 11", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3\u2019 UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "Pronephros", "The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg", "line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf", "GSM4930008", "GSM4930008: ZN MAX P1 11; Danio rerio; RNA Seq", "GSM4930008", null, "1", "Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol", "GEO Accession:GSM4930008", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP293760", null, null, "ZN_MAX_P1_11_R1.fastq.gz ZN_MAX_P1_11_R2.fastq.gz", "fastq fastq", 1999710700.0, 19997107.0, "GSM4930008 r1", "0:30 1:70", "A:530172026;C:366347543;G:346790681;T:749549554;N:6850896", 30, 70, null, null, 530172026, 366347543, 346790681, 749549554, 6850896, "SRX9557249", "SRS7762249", "SRA1162774", "GEO", "Renal Division, Department of Medicine, University Freiburg Medical Center", 2, 0.36165, 0.7372, 0.34294, 0.57352, 0.98023, 0.8118, 0.6141, 0.3196, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2020-11-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [69933, "SRR19178789", "SRX15244119", "SRS12977047", "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  homogenized", "GSM6135030", null, "tissue:whole larvae  48hpf|cell type:whole larvae  48hpf|genotype:WT|treatment:homogenized|age:48hpf", "larvae  homogenized", "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 larvae were anesthesized on ice and homogenized 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:homogenized|age:48hpf", "GSM6135030", "GSM6135030: larvae  homogenized; Danio rerio; RNA Seq", "GSM6135030 r1", "GSM6135030", "1", "10 larvae were anesthesized on ice and homogenized 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, null, "l_homogenised_R1.fastq.gz l_homogenised_R2.fastq.gz", "fastq fastq", 2128952100.0, 14193014.0, "GSM6135030 r1", "0:120 1:30", "A:640803723;C:366701707;G:389171070;T:732243074;N:32526", 120, 30, null, null, 640803723, 366701707, 389171070, 732243074, 32526, "SRX15244119", "SRS12977047", "SRA1419460", "Junker, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker, Max-Delbr\u00fcck-Center for Molecular Medicine", 2, 0.74632, 0.19814, 0.18356, 0.19806, 0.8454, 0.99975, 0.49504, 0.58333, 120, 30, "B", "T", "mate2 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2022-05-12", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [69934, "SRR19178790", "SRX15244118", "SRS12977046", "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  injected", "GSM6135029", null, "tissue:whole larvae  48hpf|cell type:whole larvae  48hpf|genotype:WT|treatment:30 min 4sU injected|age:48hpf", "larvae  injected", "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 larvae injected with 5nl 4sU 100mM in 10 mM Tris\u2022HCl pH 7.4  Carl Roth with Dextran fluorescein Thermo Fisher Scientific #7136 were incubated at 28\u00b0C for 30 minutes  anesthesized on ice and homogenized 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 injected|age:48hpf", "GSM6135029", "GSM6135029: larvae  injected; Danio rerio; RNA Seq", "GSM6135029 r1", "GSM6135029", "1", "10 larvae injected with 5nl 4sU 100mM in 10 mM Tris\u2022HCl pH 7.4  Carl Roth with Dextran fluorescein Thermo Fisher Scientific #7136 were incubated at 28\u00b0C for 30 minutes  anesthesized on ice and homogenized 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, null, "l_injected_R1.fastq.gz l_injected_R2.fastq.gz", "fastq fastq", 1235050200.0, 8233668.0, "GSM6135029 r1", "0:120 1:30", "A:378943760;C:185923499;G:307183410;T:362956267;N:43264", 120, 30, null, null, 378943760, 185923499, 307183410, 362956267, 43264, "SRX15244118", "SRS12977046", "SRA1419460", "Junker, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker, Max-Delbr\u00fcck-Center for Molecular Medicine", 2, 0.65413, 0.25162, 0.12157, 0.25153, 0.8757, 0.99969, 0.58973, 0.66666, 120, 30, "B", "T", "mate2 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2022-05-12", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [69935, "SRR19178791", "SRX15244117", "SRS12977045", "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  dissociated", "GSM6135028", null, "tissue:whole larvae  48hpf|cell type:whole larvae  48hpf|genotype:WT|treatment:30 min 4sU during dissociation|age:48hpf", "larvae  dissociated", "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  anaesthetized larvae were washed twice in ice cold HBSS Life Technologies GmbH #14175095 and resuspended in 500 l TryplE Mix 1xTrypleE Life Technologies GmbH #A1217701 in HBSS   1mM EDTA pH 8 Molekula #900493 10 mM 4sU Merck Chemicals GmbH #T4509 for labelled sample and incubated at 37\u00b0C for 30 min. 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|age:48hpf", "GSM6135028", "GSM6135028: larvae  dissociated; Danio rerio; RNA Seq", "GSM6135028 r1", "GSM6135028", "1", "10  anaesthetized larvae were washed twice in ice cold HBSS Life Technologies GmbH #14175095 and resuspended in 500 l TryplE Mix 1xTrypleE Life Technologies GmbH #A1217701 in HBSS   1mM EDTA pH 8 Molekula #900493 10 mM 4sU Merck Chemicals GmbH #T4509 for labelled sample and incubated at 37\u00b0C for 30 min. 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. 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