{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC SINGLE CELL\", technology = \"generic-scrnaseq-only\" and tissue_curation_coarse = \"All anatomical structures\"", "rows": [[25324, "SRR25820349", "SRX21542119", "SRS18751470", "SRP457651", "PRJNA1010830", "Identifying hand2 downstream targets in cardiomyocyte during early cardiogenesis", "GSE241971", "Other", "hand2 reporter expressing cardiac cells fail to migrate to the midline.  To investigate the underlying molecular changes  we sequenced mRNA from 3900 and 3836 hand2 reporter expressing single cells from 24 hpf hand2 FLD /  and hand2 FLD+/? sibling embryos  respectively.  Furthermore  hand2 is broadly expressed within the LPM  which gives rise to various cell lineages and tissues including the cardiovascular system  blood  kidneys  mesothelium  and limb connective tissue.  To further investigate the requirement of Hand2 in the early events of cardiac lineage specification in zebrafish  we aim to characterize the early hand2 expressing cardiac precursors by using embryonic CM H3K27ac ChIP seq and ATAC seq data. Overall design: scRNA seq: WT: hand2 reporter expressing single cells from 24 hpf  hand2 FLD+/?  Embryos; mutants: hand2 reporter expressing single cells from 24 hpf hand2 FLD /  sibling embryos.  ATAC seq and CGIP seq: Comparing myl7:GFP+ CMs with  myl7:GFP  cells", null, "pubmed:39658721", null, "MUT  replicate1  scRNA", "GSM7746945", null, "source name:whole embryo|tissue:whole embryo|cell type:hand2 reporter expressing single cells|genotype:hand2 mutants|geo loc name:missing|collection date:missing", "MUT  replicate1  scRNA", "demultiplexing star solo mapping: '  soloType CB UMI Simple   soloBarcodeReadLength 0   soloCellFilter EmptyDrops CR 5000 0.99 10 45000 90000 500 0.01 20000 0.01 10000' Assembly: danio rerio/101 Supplementary files format and content: 10x based mtx raw count matrix  barcodes and genes", "whole embryo", null, "10xGenomics", null, "tissue:whole embryo|cell type:hand2 reporter expressing single cells|genotype:hand2 mutants", "GSM7746945", "GSM7746945: MUT  replicate1  scRNA; Danio rerio; RNA Seq", "GSM7746945 r1", "GSM7746945", "1", "10xGenomics", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP457651", null, null, "Yanli_10x_Mut_24hpf_R2.fastq.gz Yanli_10x_Mut_24hpf_R1.fastq.gz", "fastq fastq", 12703207777.0, 159786155.0, "GSM7746945 r1", "0:28 1:51.50", "A:3417159154;C:2758515982;G:2823785724;T:3638099229;N:65647688", 28, 51, null, null, 3417159154, 2758515982, 2823785724, 3638099229, 65647688, "SRX21542119", "SRS18751470", "SRA1702565", "Max Planck Institute for Heart and Lung Research", "Max Planck Institute for Heart and Lung Research", 2, 0.00189, 0.93843, 0.0006, 0.12822, 0.99571, 0.781, 0.38429, 0.49855, 28, 52, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "Germany", "2023-08-30", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [25325, "SRR25820350", "SRX21542118", "SRS18751469", "SRP457651", "PRJNA1010830", "Identifying hand2 downstream targets in cardiomyocyte during early cardiogenesis", "GSE241971", "Other", "hand2 reporter expressing cardiac cells fail to migrate to the midline.  To investigate the underlying molecular changes  we sequenced mRNA from 3900 and 3836 hand2 reporter expressing single cells from 24 hpf hand2 FLD /  and hand2 FLD+/? sibling embryos  respectively.  Furthermore  hand2 is broadly expressed within the LPM  which gives rise to various cell lineages and tissues including the cardiovascular system  blood  kidneys  mesothelium  and limb connective tissue.  To further investigate the requirement of Hand2 in the early events of cardiac lineage specification in zebrafish  we aim to characterize the early hand2 expressing cardiac precursors by using embryonic CM H3K27ac ChIP seq and ATAC seq data. Overall design: scRNA seq: WT: hand2 reporter expressing single cells from 24 hpf  hand2 FLD+/?  Embryos; mutants: hand2 reporter expressing single cells from 24 hpf hand2 FLD /  sibling embryos.  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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.", null, "expt2.broad.48.enzymatic.P01.F01.fq.gz", null, "seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  48hpf  enzymatic dissociation  replicate 6", "100", "100", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.", null, "expt2.broad.48.enzymatic.P01.E01.fq.gz", null, "seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  48hpf  enzymatic dissociation  replicate 5", "99", "99", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "expt2.broad.48.enzymatic.P01.E01.fq.gz", "fastq", 496356.0, 5909.0, "expt2.broad.48.enzymatic.P01.E01.fq.gz", "0:84", "A:156600;C:99183;G:113282;T:127036;N:255", 84, null, null, null, 156600, 99183, 113282, 127036, 255, "SRX28203118", "SRS24552823", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-03-31", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [35569, "SRR32928201", "SRX28203117", "SRS24552824", "SRP575522", "PRJNA1244443", "An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing", "PRJNA1244443", "Other", "Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.", null, "expt2.broad.48.enzymatic.P01.D01.fq.gz", null, "seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  48hpf  enzymatic dissociation  replicate 4", "98", "98", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "expt2.broad.48.enzymatic.P01.D01.fq.gz", "fastq", 2053800.0, 24450.0, "expt2.broad.48.enzymatic.P01.D01.fq.gz", "0:84", "A:668634;C:393806;G:431279;T:559022;N:1059", 84, null, null, null, 668634, 393806, 431279, 559022, 1059, "SRX28203117", "SRS24552824", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-03-31", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [35570, "SRR32928202", "SRX28203116", "SRS24552821", "SRP575522", "PRJNA1244443", "An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing", "PRJNA1244443", "Other", "Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. 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This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.", null, "expt2.broad.48.enzymatic.P01.C01.fq.gz", null, "seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  48hpf  enzymatic dissociation  replicate 3", "97", "97", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "expt2.broad.48.enzymatic.P01.C01.fq.gz", "fastq", 2159052.0, 25703.0, "expt2.broad.48.enzymatic.P01.C01.fq.gz", "0:84", "A:837784;C:348085;G:463530;T:508544;N:1109", 84, null, null, null, 837784, 348085, 463530, 508544, 1109, "SRX28203116", "SRS24552821", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-03-31", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [35571, "SRR32928203", "SRX28203115", "SRS24552822", "SRP575522", "PRJNA1244443", "An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing", "PRJNA1244443", "Other", "Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. 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This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.", null, "expt2.broad.48.enzymatic.P01.B01.fq.gz", null, "seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  48hpf  enzymatic dissociation  replicate 2", "96", "96", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. 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This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.", null, "expt2.broad.48.enzymatic.P01.A01.fq.gz", null, "seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  48hpf  enzymatic dissociation  replicate 1", "95", "95", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.G12.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 7", "212", "212", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.F12.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 6", "211", "211", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt1.12.bead.P1.H3.fq.gz", null, "seq depth:NA|Experiment id:1|dissociation method:bead|replicate:22|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 22", "22", "22", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.E12.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 5", "210", "210", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.D12.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 4", "209", "209", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.C12.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 3", "208", "208", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.B12.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 2", "207", "207", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.A12.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 1", "206", "206", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.H11.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:bead|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  bead dissociation  replicate 8", "205", "205", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.G11.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:bead|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  bead dissociation  replicate 7", "204", "204", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.F11.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:bead|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  bead dissociation  replicate 6", "203", "203", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.E11.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:bead|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  bead dissociation  replicate 5", "202", "202", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.D11.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:bead|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  bead dissociation  replicate 4", "201", "201", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt1.12.bead.P1.G5.fq.gz", null, "seq depth:NA|Experiment id:1|dissociation method:bead|replicate:21|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 21", "21", "21", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt1.12.bead.P1.A5.fq.gz", null, "seq depth:NA|Experiment id:1|dissociation method:bead|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 3", "3", "3", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.C11.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:bead|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  bead dissociation  replicate 3", "200", "200", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.B11.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:bead|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  bead dissociation  replicate 2", "199", "199", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.A11.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:bead|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  bead dissociation  replicate 1", "198", "198", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt1.12.bead.P1.D3.fq.gz", null, "seq depth:NA|Experiment id:1|dissociation method:bead|replicate:10|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 10", "10", "10", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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[experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_source\" = :p0 and \"technology\" = :p1 and \"tissue_curation_coarse\" = :p2 order by rowid limit 101", "params": {"p0": "TRANSCRIPTOMIC SINGLE CELL", "p1": "generic-scrnaseq-only", "p2": "All anatomical structures"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=generic-scrnaseq-only&tissue_curation_coarse=All+anatomical+structures", "results": [{"value": "OTHER", "label": "OTHER", "count": 213, "toggle_url": 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