{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Juvenile\" and technology = \"10x\"", "rows": [[25326, "SRR25868015", "SRX21589423", "SRS18766996", "SRP457977", "PRJNA1011833", "Single cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity", "GSE242133", "Transcriptome Analysis", "The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However knowledge about the properties of kidney hematopoietic cells and the functionality of kidney in fish immune systems remain to be elucidated. To this end our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell HSPC and immune cell types from zebrafish kidney via single cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity and displayed differential responses to viral infection indicating their diverse functional roles in antiviral immunity. Remarkably HSPCs were found to have extensive reactivities to viral infection and the trained immunity can be effectively induced in certain HSPCs. In addition the antigen stimulated adaptive immunity can be fully generated in kidney suggesting kidney acting as a secondary lymphoid organ. These results indicated that fish kidney is a dual functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune system and highlighted the multifaced biology of kidney in ancient vertebrates. Overall design: Kidney leukocyte PBS administered control SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:38497789", null, "vaccinated+SVCV scRNAseq Kidney leukocyte", "GSM7749529", null, "source name:Kidney|cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:vaccinated+SVCV|geo loc name:missing|collection date:missing", "vaccinated+SVCV scRNAseq Kidney leukocyte", "The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files", "Kidney", null, "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 \u03bcg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:vaccinated+SVCV", "GSM7749529", "GSM7749529: vaccinated+SVCV scRNAseq Kidney leukocyte; Danio rerio; RNA Seq", "GSM7749529 r1", "GSM7749529", "1", "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 \u03bcg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP457977", null, null, "vaccinated+SVCV_S1_L001_R1_001.fastq.gz vaccinated+SVCV_S1_L001_R2_001.fastq.gz", "fastq fastq", 48964415682.0, 411465678.0, "GSM7749529 r1", "0:28 1:91", "A:13575624351;C:10984755198;G:11582424564;T:12820058148;N:1553421", 28, 91, null, null, 13575624351, 10984755198, 11582424564, 12820058148, 1553421, "SRX21589423", "SRS18766996", "SRA1703997", "College of Life Sciences, Zhejiang University", "College of Life Sciences, Zhejiang University", 2, 0.00754, 0.93029, 0.00274, 0.13414, 0.99168, 0.81527, 0.35, 0.50044, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-09-01", "Juvenile", "Juvenile", "Kidney", "Renal System"], [25327, "SRR25868016", "SRX21589422", "SRS18766995", "SRP457977", "PRJNA1011833", "Single cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity", "GSE242133", "Transcriptome Analysis", "The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However knowledge about the properties of kidney hematopoietic cells and the functionality of kidney in fish immune systems remain to be elucidated. To this end our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell HSPC and immune cell types from zebrafish kidney via single cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity and displayed differential responses to viral infection indicating their diverse functional roles in antiviral immunity. Remarkably HSPCs were found to have extensive reactivities to viral infection and the trained immunity can be effectively induced in certain HSPCs. In addition the antigen stimulated adaptive immunity can be fully generated in kidney suggesting kidney acting as a secondary lymphoid organ. These results indicated that fish kidney is a dual functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune system and highlighted the multifaced biology of kidney in ancient vertebrates. Overall design: Kidney leukocyte PBS administered control SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:38497789", null, "SVCV scRNAseq Kidney leukocyte", "GSM7749528", null, "source name:Kidney|cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:SVCV|geo loc name:missing|collection date:missing", "SVCV scRNAseq Kidney leukocyte", "The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files", "Kidney", null, "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 \u03bcg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:SVCV", "GSM7749528", "GSM7749528: SVCV scRNAseq Kidney leukocyte; Danio rerio; RNA Seq", "GSM7749528 r1", "GSM7749528", "1", "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 \u03bcg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP457977", null, null, "SVCV_S1_L001_R2_001.fastq.gz SVCV_S1_L001_R1_001.fastq.gz", "fastq fastq", 48037908933.0, 403679907.0, "GSM7749528 r1", "0:28 1:91", "A:13476452185;C:10712519121;G:11200837365;T:12646404590;N:1695672", 28, 91, null, null, 13476452185, 10712519121, 11200837365, 12646404590, 1695672, "SRX21589422", "SRS18766995", "SRA1703997", "College of Life Sciences, Zhejiang University", "College of Life Sciences, Zhejiang University", 2, 0.00795, 0.92383, 0.00261, 0.14, 0.98948, 0.7806, 0.36862, 0.54549, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-09-01", "Juvenile", "Juvenile", "Kidney", "Renal System"], [25328, "SRR25868017", "SRX21589421", "SRS18766994", "SRP457977", "PRJNA1011833", "Single cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity", "GSE242133", "Transcriptome Analysis", "The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However knowledge about the properties of kidney hematopoietic cells and the functionality of kidney in fish immune systems remain to be elucidated. To this end our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell HSPC and immune cell types from zebrafish kidney via single cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity and displayed differential responses to viral infection indicating their diverse functional roles in antiviral immunity. Remarkably HSPCs were found to have extensive reactivities to viral infection and the trained immunity can be effectively induced in certain HSPCs. In addition the antigen stimulated adaptive immunity can be fully generated in kidney suggesting kidney acting as a secondary lymphoid organ. These results indicated that fish kidney is a dual functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune system and highlighted the multifaced biology of kidney in ancient vertebrates. Overall design: Kidney leukocyte PBS administered control SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:38497789", null, "PBS scRNAseq Kidney leukocyte", "GSM7749527", null, "source name:Kidney|cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:PBS|geo loc name:missing|collection date:missing", "PBS scRNAseq Kidney leukocyte", "The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files", "Kidney", null, "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 \u03bcg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:PBS", "GSM7749527", "GSM7749527: PBS scRNAseq Kidney leukocyte; Danio rerio; RNA Seq", "GSM7749527 r1", "GSM7749527", "1", "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 \u03bcg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP457977", null, null, "PBS_S1_L001_R1_001.fastq.gz PBS_S1_L001_R2_001.fastq.gz", "fastq fastq", 49559940115.0, 416470085.0, "GSM7749527 r1", "0:28 1:91", "A:13856071803;C:11114011608;G:11616674427;T:12971434952;N:1747325", 28, 91, null, null, 13856071803, 11114011608, 11616674427, 12971434952, 1747325, "SRX21589421", "SRS18766994", "SRA1703997", "College of Life Sciences, Zhejiang University", "College of Life Sciences, Zhejiang University", 2, 0.00648, 0.92681, 0.00213, 0.1376, 0.99056, 0.79866, 0.40117, 0.5487, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-09-01", "Juvenile", "Juvenile", "Kidney", "Renal System"], [29188, "SRR8176753", "SRX4996870", "SRS4031878", "SRP480945", "PRJNA1055160", "Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain", "PRJNA1055160", "Other", "We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf", null, "pubmed:38529407", null, "Nadia 30dpf ZZ Gonad Single Cell RNA Seq", "Nadia 30dpf ZZ Gonad Single Cell RNA Seq", null, "strain:Nadia|age:30 dpf provider:John H. Postlethwait University of Oregon|genotype:ZZ|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA Seq of Danio rerio: Nadia 30dpf ZZ gonad", "Nadia 30dpf ZZ gonad", "Nadia 30dpf ZZ gonad", "A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP480945", null, "loader:fastq load.py", null, null, 23587173438.0, 167284918.0, "1 I1 001.fastq.gz", "0:8 1:133", "A:6732844252;C:4934497997;G:5685086026;T:6219863789;N:14881374", 8, 133, null, null, 6732844252, 4934497997, 5685086026, 6219863789, 14881374, "SRX4996870", "SRS4031878", "SRA807619", "University of Oregon|Institute of Neuroscience", "University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2018-11-08", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [29189, "SRR8176754", "SRX4996869", "SRS4031877", "SRP480945", "PRJNA1055160", "Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain", "PRJNA1055160", "Other", "We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf", null, "pubmed:38529407", null, "Nadia 30dpf ZW Gonad Single Cell RNA Seq", "Nadia 30dpf ZW Gonad Single Cell RNA Seq", null, "strain:Nadia|age:30 dpf provider:John H. Postlethwait University of Oregon|genotype:ZW|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA Seq of Danio rerio: Nadia 30dpf ZW gonad", "Nadia 30dpf ZW gonad", "Nadia 30dpf ZW gonad", "A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP480945", null, "loader:fastq load.py", null, null, 43358808480.0, 307509280.0, "2 I1 001.fastq.gz", "0:8 1:133", "A:12290612367;C:8880655083;G:10261318751;T:11898771792;N:27450487", 8, 133, null, null, 12290612367, 8880655083, 10261318751, 11898771792, 27450487, "SRX4996869", "SRS4031877", "SRA807619", "University of Oregon|Institute of Neuroscience", "University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2018-11-08", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [30738, "SRR28346485", "SRX23952998", "SRS20753493", "SRP495277", "PRJNA1088100", "Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo", "GSE261604", "Transcriptome Analysis", "To identify the crosstalk between Wnt/\u00df catenin signaling activated cardiomyocytes \u00df cat ON CMs and coronary endothelial cells coECs we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/\u00df catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/\u00df catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between \u00df cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 \u00b5M IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.", "parent bioproject:PRJNA926354", "pubmed:39395410", null, "AVC IWR1 scRNAseq", "GSM8147318", null, "source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1|geo loc name:missing|collection date:missing", "AVC IWR1 scRNAseq", "The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample", "Heart", "Fish were treated with DMSO or 10 \u03bcM MTZ dissolved in fish water for 48 h in the dark.", "Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCF\u0394C;5xUAS:NTR mCherry fish treated with DMSO or 10 \u03bcM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 \u00baC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4\u00baC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3\u2019reagent kits v3.1 10X Genomics 1000128 according to the manufacturer\u2019s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.", null, "tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1", "GSM8147318", "GSM8147318: AVC IWR1 scRNAseq; Danio rerio; RNA Seq", "GSM8147318 r1", "GSM8147318", "1", "Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCF\u0394C;5xUAS:NTR mCherry fish treated with DMSO or 10 \u03bcM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 \u00baC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4\u00baC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP495277", null, "loader:fastq load.py", "AVC_IWR1_S1_L001_I1_001.fastq.gz AVC_IWR1_S1_L001_I2_001.fastq.gz AVC_IWR1_S1_L001_R1_001.fastq.gz AVC_IWR1_S1_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 8596842480.0, 62295960.0, "GSM8147318 r1", "0:10 1:10 2:28 3:90", "A:1570400090;C:1308581548;G:1326249813;T:1399966642;N:1438307", 10, 10, 28, 90, 1570400090, 1308581548, 1326249813, 1399966642, 1438307, "SRX23952998", "SRS20753493", "SRA1824323", "Department of Pharmacology, Yamagata University", "Department of Pharmacology, Yamagata University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Japan", "2024-03-14", "Juvenile", "Juvenile", "Heart", "Cardiovascular System"], [30739, "SRR28346486", "SRX23952998", "SRS20753493", "SRP495277", "PRJNA1088100", "Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo", "GSE261604", "Transcriptome Analysis", "To identify the crosstalk between Wnt/\u00df catenin signaling activated cardiomyocytes \u00df cat ON CMs and coronary endothelial cells coECs we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/\u00df catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/\u00df catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between \u00df cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 \u00b5M IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.", "parent bioproject:PRJNA926354", "pubmed:39395410", null, "AVC IWR1 scRNAseq", "GSM8147318", null, "source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1|geo loc name:missing|collection date:missing", "AVC IWR1 scRNAseq", "The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample", "Heart", "Fish were treated with DMSO or 10 \u03bcM MTZ dissolved in fish water for 48 h in the dark.", "Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCF\u0394C;5xUAS:NTR mCherry fish treated with DMSO or 10 \u03bcM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 \u00baC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4\u00baC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3\u2019reagent kits v3.1 10X Genomics 1000128 according to the manufacturer\u2019s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.", null, "tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1", "GSM8147318", "GSM8147318: AVC IWR1 scRNAseq; Danio rerio; RNA Seq", "GSM8147318 r1", "GSM8147318", "1", "Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCF\u0394C;5xUAS:NTR mCherry fish treated with DMSO or 10 \u03bcM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 \u00baC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4\u00baC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP495277", null, "loader:fastq load.py", "AVC_IWR1_S1_L002_I1_001.fastq.gz AVC_IWR1_S1_L002_I2_001.fastq.gz AVC_IWR1_S1_L002_R1_001.fastq.gz AVC_IWR1_S1_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 8505185502.0, 61631779.0, "GSM8147318 r2", "0:10 1:10 2:28 3:90", "A:1553616390;C:1294687778;G:1312612882;T:1384504011;N:1439049", 10, 10, 28, 90, 1553616390, 1294687778, 1312612882, 1384504011, 1439049, "SRX23952998", "SRS20753493", "SRA1824323", "Department of Pharmacology, Yamagata University", "Department of Pharmacology, Yamagata University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Japan", "2024-03-14", "Juvenile", "Juvenile", "Heart", "Cardiovascular System"], [30740, "SRR28346487", "SRX23952998", "SRS20753493", "SRP495277", "PRJNA1088100", "Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo", "GSE261604", "Transcriptome Analysis", "To identify the crosstalk between Wnt/\u00df catenin signaling activated cardiomyocytes \u00df cat ON CMs and coronary endothelial cells coECs we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/\u00df catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/\u00df catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between \u00df cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 \u00b5M IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.", "parent bioproject:PRJNA926354", "pubmed:39395410", null, "AVC IWR1 scRNAseq", "GSM8147318", null, "source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1|geo loc name:missing|collection date:missing", "AVC IWR1 scRNAseq", "The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample", "Heart", "Fish were treated with DMSO or 10 \u03bcM MTZ dissolved in fish water for 48 h in the dark.", "Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCF\u0394C;5xUAS:NTR mCherry fish treated with DMSO or 10 \u03bcM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 \u00baC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4\u00baC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3\u2019reagent kits v3.1 10X Genomics 1000128 according to the manufacturer\u2019s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.", null, "tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1", "GSM8147318", "GSM8147318: AVC IWR1 scRNAseq; Danio rerio; RNA Seq", "GSM8147318 r1", "GSM8147318", "1", "Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCF\u0394C;5xUAS:NTR mCherry fish treated with DMSO or 10 \u03bcM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 \u00baC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4\u00baC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP495277", null, "loader:fastq load.py", "AVC_IWR1_S1_L003_I1_001.fastq.gz AVC_IWR1_S1_L003_I2_001.fastq.gz AVC_IWR1_S1_L003_R1_001.fastq.gz AVC_IWR1_S1_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 8699205498.0, 63037721.0, "GSM8147318 r3", "0:10 1:10 2:28 3:90", "A:1588465122;C:1324147204;G:1343996634;T:1415623074;N:1162856", 10, 10, 28, 90, 1588465122, 1324147204, 1343996634, 1415623074, 1162856, "SRX23952998", "SRS20753493", "SRA1824323", "Department of Pharmacology, Yamagata University", "Department of Pharmacology, Yamagata University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Japan", "2024-03-14", "Juvenile", "Juvenile", "Heart", "Cardiovascular System"], [30741, "SRR28346488", "SRX23952998", "SRS20753493", "SRP495277", "PRJNA1088100", "Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo", "GSE261604", "Transcriptome Analysis", "To identify the crosstalk between Wnt/\u00df catenin signaling activated cardiomyocytes \u00df cat ON CMs and coronary endothelial cells coECs we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/\u00df catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/\u00df catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between \u00df cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 \u00b5M IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.", "parent bioproject:PRJNA926354", "pubmed:39395410", null, "AVC IWR1 scRNAseq", "GSM8147318", null, "source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1|geo loc name:missing|collection date:missing", "AVC IWR1 scRNAseq", "The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample", "Heart", "Fish were treated with DMSO or 10 \u03bcM MTZ dissolved in fish water for 48 h in the dark.", "Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCF\u0394C;5xUAS:NTR mCherry fish treated with DMSO or 10 \u03bcM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 \u00baC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4\u00baC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3\u2019reagent kits v3.1 10X Genomics 1000128 according to the manufacturer\u2019s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.", null, "tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1", "GSM8147318", "GSM8147318: AVC IWR1 scRNAseq; Danio rerio; RNA Seq", "GSM8147318 r1", "GSM8147318", "1", "Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCF\u0394C;5xUAS:NTR mCherry fish treated with DMSO or 10 \u03bcM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 \u00baC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4\u00baC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP495277", null, "loader:fastq load.py", "AVC_IWR1_S1_L004_I1_001.fastq.gz AVC_IWR1_S1_L004_I2_001.fastq.gz AVC_IWR1_S1_L004_R1_001.fastq.gz AVC_IWR1_S1_L004_R2_001.fastq.gz", "fastq fastq fastq fastq", 8627728812.0, 62519774.0, "GSM8147318 r4", "0:10 1:10 2:28 3:90", "A:1576009383;C:1313466786;G:1332114241;T:1404392019;N:797231", 10, 10, 28, 90, 1576009383, 1313466786, 1332114241, 1404392019, 797231, "SRX23952998", "SRS20753493", "SRA1824323", "Department of Pharmacology, Yamagata University", "Department of Pharmacology, Yamagata University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Japan", "2024-03-14", "Juvenile", "Juvenile", "Heart", "Cardiovascular System"], [30742, "SRR28346489", "SRX23952997", "SRS20753492", "SRP495277", "PRJNA1088100", "Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo", "GSE261604", "Transcriptome Analysis", "To identify the crosstalk between Wnt/\u00df catenin signaling activated cardiomyocytes \u00df cat ON CMs and coronary endothelial cells coECs we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/\u00df catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/\u00df catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between \u00df cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 \u00b5M IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.", "parent bioproject:PRJNA926354", "pubmed:39395410", null, "AVC DMSO scRNAseq", "GSM8147317", null, "source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO|geo loc name:missing|collection date:missing", "AVC DMSO scRNAseq", "The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample", "Heart", "Fish were treated with DMSO or 10 \u03bcM MTZ dissolved in fish water for 48 h in the dark.", "Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCF\u0394C;5xUAS:NTR mCherry fish treated with DMSO or 10 \u03bcM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 \u00baC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4\u00baC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3\u2019reagent kits v3.1 10X Genomics 1000128 according to the manufacturer\u2019s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.", null, "tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO", "GSM8147317", "GSM8147317: AVC DMSO scRNAseq; Danio rerio; RNA Seq", "GSM8147317 r1", "GSM8147317", "1", "Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCF\u0394C;5xUAS:NTR mCherry fish treated with DMSO or 10 \u03bcM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 \u00baC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4\u00baC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP495277", null, "loader:fastq load.py", "AVC_Ctrl_S1_L001_I1_001.fastq.gz AVC_Ctrl_S1_L001_I2_001.fastq.gz AVC_Ctrl_S1_L001_R1_001.fastq.gz AVC_Ctrl_S1_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 7385103810.0, 53515245.0, "GSM8147317 r1", "0:10 1:10 2:28 3:90", "A:1329371520;C:1135299252;G:1143250549;T:1207226310;N:1224419", 10, 10, 28, 90, 1329371520, 1135299252, 1143250549, 1207226310, 1224419, "SRX23952997", "SRS20753492", "SRA1824323", "Department of Pharmacology, Yamagata University", "Department of Pharmacology, Yamagata University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Japan", "2024-03-14", "Juvenile", "Juvenile", "Heart", "Cardiovascular System"], [30743, "SRR28346490", "SRX23952997", "SRS20753492", "SRP495277", "PRJNA1088100", "Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo", "GSE261604", "Transcriptome Analysis", "To identify the crosstalk between Wnt/\u00df catenin signaling activated cardiomyocytes \u00df cat ON CMs and coronary endothelial cells coECs we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/\u00df catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/\u00df catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between \u00df cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 \u00b5M IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.", "parent bioproject:PRJNA926354", "pubmed:39395410", null, "AVC DMSO scRNAseq", "GSM8147317", null, "source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO|geo loc name:missing|collection date:missing", "AVC DMSO scRNAseq", "The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample", "Heart", "Fish were treated with DMSO or 10 \u03bcM MTZ dissolved in fish water for 48 h in the dark.", "Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCF\u0394C;5xUAS:NTR mCherry fish treated with DMSO or 10 \u03bcM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 \u00baC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4\u00baC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3\u2019reagent kits v3.1 10X Genomics 1000128 according to the manufacturer\u2019s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.", null, "tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO", "GSM8147317", "GSM8147317: AVC DMSO scRNAseq; Danio rerio; RNA Seq", "GSM8147317 r1", "GSM8147317", "1", "Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCF\u0394C;5xUAS:NTR mCherry fish treated with DMSO or 10 \u03bcM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 \u00baC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4\u00baC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP495277", null, "loader:fastq load.py", "AVC_Ctrl_S1_L002_I1_001.fastq.gz AVC_Ctrl_S1_L002_I2_001.fastq.gz AVC_Ctrl_S1_L002_R1_001.fastq.gz AVC_Ctrl_S1_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 7313299098.0, 52994921.0, "GSM8147317 r2", "0:10 1:10 2:28 3:90", "A:1316101332;C:1124200896;G:1133146934;T:1194866024;N:1227704", 10, 10, 28, 90, 1316101332, 1124200896, 1133146934, 1194866024, 1227704, "SRX23952997", "SRS20753492", "SRA1824323", "Department of Pharmacology, Yamagata University", "Department of Pharmacology, Yamagata University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Japan", "2024-03-14", "Juvenile", "Juvenile", "Heart", "Cardiovascular System"], [30744, "SRR28346491", "SRX23952997", "SRS20753492", "SRP495277", "PRJNA1088100", "Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo", "GSE261604", "Transcriptome Analysis", "To identify the crosstalk between Wnt/\u00df catenin signaling activated cardiomyocytes \u00df cat ON CMs and coronary endothelial cells coECs we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/\u00df catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/\u00df catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between \u00df cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 \u00b5M IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.", "parent bioproject:PRJNA926354", "pubmed:39395410", null, "AVC DMSO scRNAseq", "GSM8147317", null, "source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO|geo loc name:missing|collection date:missing", "AVC DMSO scRNAseq", "The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample", "Heart", "Fish were treated with DMSO or 10 \u03bcM MTZ dissolved in fish water for 48 h in the dark.", "Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCF\u0394C;5xUAS:NTR mCherry fish treated with DMSO or 10 \u03bcM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 \u00baC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4\u00baC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3\u2019reagent kits v3.1 10X Genomics 1000128 according to the manufacturer\u2019s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.", null, "tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO", "GSM8147317", "GSM8147317: AVC DMSO scRNAseq; Danio rerio; RNA Seq", "GSM8147317 r1", "GSM8147317", "1", "Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCF\u0394C;5xUAS:NTR mCherry fish treated with DMSO or 10 \u03bcM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 \u00baC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4\u00baC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP495277", null, "loader:fastq load.py", "AVC_Ctrl_S1_L003_I1_001.fastq.gz AVC_Ctrl_S1_L003_I2_001.fastq.gz AVC_Ctrl_S1_L003_R1_001.fastq.gz AVC_Ctrl_S1_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 7457857272.0, 54042444.0, "GSM8147317 r3", "0:10 1:10 2:28 3:90", "A:1341763332;C:1146520201;G:1156131488;T:1218395804;N:1009135", 10, 10, 28, 90, 1341763332, 1146520201, 1156131488, 1218395804, 1009135, "SRX23952997", "SRS20753492", "SRA1824323", "Department of Pharmacology, Yamagata University", "Department of Pharmacology, Yamagata University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Japan", "2024-03-14", "Juvenile", "Juvenile", "Heart", "Cardiovascular System"], [30745, "SRR28346492", "SRX23952997", "SRS20753492", "SRP495277", "PRJNA1088100", "Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo", "GSE261604", "Transcriptome Analysis", "To identify the crosstalk between Wnt/\u00df catenin signaling activated cardiomyocytes \u00df cat ON CMs and coronary endothelial cells coECs we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/\u00df catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/\u00df catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between \u00df cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 \u00b5M IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.", "parent bioproject:PRJNA926354", "pubmed:39395410", null, "AVC DMSO scRNAseq", "GSM8147317", null, "source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO|geo loc name:missing|collection date:missing", "AVC DMSO scRNAseq", "The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample", "Heart", "Fish were treated with DMSO or 10 \u03bcM MTZ dissolved in fish water for 48 h in the dark.", "Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCF\u0394C;5xUAS:NTR mCherry fish treated with DMSO or 10 \u03bcM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 \u00baC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4\u00baC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3\u2019reagent kits v3.1 10X Genomics 1000128 according to the manufacturer\u2019s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.", null, "tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO", "GSM8147317", "GSM8147317: AVC DMSO scRNAseq; Danio rerio; RNA Seq", "GSM8147317 r1", "GSM8147317", "1", "Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCF\u0394C;5xUAS:NTR mCherry fish treated with DMSO or 10 \u03bcM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 \u00baC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4\u00baC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP495277", null, "loader:fastq load.py", "AVC_Ctrl_S1_L004_I1_001.fastq.gz AVC_Ctrl_S1_L004_I2_001.fastq.gz AVC_Ctrl_S1_L004_R1_001.fastq.gz AVC_Ctrl_S1_L004_R2_001.fastq.gz", "fastq fastq fastq fastq", 7430049030.0, 53840935.0, "GSM8147317 r4", "0:10 1:10 2:28 3:90", "A:1337094348;C:1142353903;G:1151539276;T:1214006711;N:689912", 10, 10, 28, 90, 1337094348, 1142353903, 1151539276, 1214006711, 689912, "SRX23952997", "SRS20753492", "SRA1824323", "Department of Pharmacology, Yamagata University", "Department of Pharmacology, Yamagata University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Japan", "2024-03-14", "Juvenile", "Juvenile", "Heart", "Cardiovascular System"], [50847, "SRR8312900", "SRX5126276", "SRS4139398", "SRP173304", "PRJNA509469", "Single cell RNA sequencing of zebrafish pancreatic cells", "GSE123662", "Other", "The pancreatic beta cells regulate blood glucose levels by secreting the hormone insulin in response to increasing glucose levels. Recent work has identified molecular and functional heterogeneity among the beta cell community. To ontain an unbiased picture into the molecular heterogeneity present in zebrafish pancreatic cells we performed droplet based next generation sequencing of individual pancreatic cells. Using unsupervised clustering we could identify all the major cell types present in the pancreas. Moreover we could define sub populations within the major cell types demonstrating the presence of molecular heterogeneity within nominally homogenous cell populations. Overall design: We used 10x Genomics to profile pancreatic cells from zebrafish. Pancreatic islets from six animals were dissociated and single cell library prepared using 10x Genomics Chromium pipeline. Sequencing was performed on llumina NextSeq 550 machine using a HighOutput flowcell in paired end mode R1: 26 cycles; I1: 8 cycles; R2: 57 cycles thus generating 45 mio fragments. The raw sequencing data was then processed with the 'count' command of the Cell Ranger software v2.1.0 provided by 10X Genomics with the option ' expect cells' set to 5000 all other options were used as per default. To build the reference for Cell Ranger zebrafish genome GRCz10 as well as gene annotation Ensembl 87 were downloaded from Ensembl and the annotation was filtered with the 'mkgtf' command of Cell Ranger options: ' attribute=gene biotype:protein coding attribute=gene biotype:lincRNA \u2013attribute=gene biotype:antisense'. Genome sequence and filtered annotation were then used as input to the 'mkref' command of Cell Ranger to build the appropriate Cellranger Reference.", null, "pubmed:32694805", null, "2mpf Pancreas", "GSM3509161", null, "tissue:pancreatic cells|age:2mpf|strain:Tgins:BB1.0L|disease state:Normal", "2mpf Pancreas", "The raw sequencing data was then processed with the \u2018count\u2019 command of the Cell Ranger software v2.1.0 provided by 10X Genomics with the option \u2018 expect cells\u2019 set to 5000 all other options were used as per default. To build the reference for Cell Ranger zebrafish genome GRCz10 as well as gene annotation Ensembl 87 were downloaded from Ensembl and the annotation was filtered with the \u2018mkgtf\u2019 command of Cell Ranger options: \u2018 attribute=gene biotype:protein coding attribute=gene biotype:lincRNA \u2013attribute=gene biotype:antisense\u2019. Genome sequence and filtered annotation were then used as input to the \u2018mkref\u2019 command of Cell Ranger to build the appropriate Cellranger Reference. Genome build: Zebrafish GRCz10 Supplementary files format and content: csv format with rows as genes and columns as cells", "pancreatic cells", null, "Enzymatic Dissociation The single cell suspension was adjusted to a concentration of about 800 cells per microliter and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 5000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system Zheng et al. 2016. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The cDNA was amplified with 10 cycles following the guidelines of the 10x Genomics user manual. The 10X Genomics single cell RNA seq library preparation involving fragmentation dA Tailing adapter ligation and indexing PCR \u2013 was performed based on the manufacturer\u2019s protocol.", null, "age:2mpf|strain:Tgins:BB1.0L|disease state:Normal", "GSM3509161", "GSM3509161: 2mpf Pancreas; Danio rerio; RNA Seq", "GSM3509161", null, "1", "Enzymatic Dissociation The single cell suspension was adjusted to a concentration of about 800 cells per microliter and diluted with nuclease free water according to the manufacturer's instructions to yield 5000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system Zheng et al. 2016. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The cDNA was amplified with 10 cycles following the guidelines of the 10x Genomics user manual. The 10X Genomics single cell RNA seq library preparation involving fragmentation dA Tailing adapter ligation and indexing PCR \u2013 was performed based on the manufacturer's protocol.", "GEO Accession:GSM3509161", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP173304", null, null, "s2mpf_R1.fastq.gz s2mpf_R2.fastq.gz", "fastq fastq", 3682641276.0, 44369172.0, "GSM3509161 r1", "0:26 1:57", "A:950388419;C:876060179;G:944476013;T:911635661;N:81004", 26, 57, null, null, 950388419, 876060179, 944476013, 911635661, 81004, "SRX5126276", "SRS4139398", "SRA822849", "GEO", "Single Cell Endocrinology, IRIBHM", 2, 0.00373, 0.9564, 0.0008, 0.03195, 0.99508, 0.9024, 0.38273, 0.59374, 26, 57, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2018-12-11", "Juvenile", "Juvenile", "Pancreas", "Endocrine System"], [52954, "SRR9609653", "SRX6373047", "SRS5034104", "SRP212225", "PRJNA551501", "Single cell RNA sequencing of zebrafish thyroid cells", "GSE133466", "Transcriptome Analysis", "The thyroid gland is responsible for supplying the thyroid hormones to the body. The gland is an endocrine organ with an intricate structure enabling production storage and release of the thyroid hormones. The gland is composed of numerous spherical follicles of varying sizes surrounded by thyroid follicular epithelial cells or thyrocytes. The thyrocytes surrounding the follicles generate the thyroid hormones in a multi step process. Though the machinery responsible for the production of thyroid hormones by thyrocytes is well established it remains unknown if all the thyrocytes resident in the thyroid gland are equally capable of generating thyroid hormones. In other words the extent of molecular homogeneity between individual thyrocytes has not yet been investigated. To obtain an unbiased picture into the molecular heterogeneity present in zebrafish thyrocytes we performed droplet based next generation sequencing of individual thyrod gland cells. Using unsupervised clustering we could identify all the major cell types present in the thyroid gland. Moreover we could define sub populations within the major cell types demonstrating the presence of molecular heterogeneity within nominally homogenous cell populations. Overall design: We used 10x Genomics to profile thyroid cells from zebrafish. Thyroid gland was enzymatically dissociated and single cell library prepared using 10x Genomics Chromium pipeline. Sequencing was performed on llumina NextSeq 550 machine using a HighOutput flowcell in paired end mode R1: 26 cycles; I1: 8 cycles; R2: 57 cycles thus generating 45 mio fragments. The raw sequencing data was then processed with the 'count' command of the Cell Ranger software v2.1.0 provided by 10X Genomics with the option ' expect cells' set to 6000 all other options were used as per default. To build the reference for Cell Ranger zebrafish genome GRCz10 as well as gene annotation Ensembl 87 were downloaded from Ensembl and the annotation was filtered with the 'mkgtf' command of Cell Ranger options: ' attribute=gene biotype:protein coding attribute=gene biotype:lincRNA \u2013attribute=gene biotype:antisense'. Genome sequence and filtered annotation were then used as input to the 'mkref' command of Cell Ranger to build the appropriate Cellranger Reference.", null, null, null, "2mpf Thyroid", "GSM3909771", null, "tissue:thyroid gland|treatment:2mpf|strain:Tgtg:mVenus T2A NTR|tag:Normal", "2mpf Thyroid", "The raw sequencing data was then processed with the \u2018count\u2019 command of the Cell Ranger software v2.1.0 provided by 10X Genomics with the option \u2018 expect cells\u2019 set to 6000 all other options were used as per default. To build the reference for Cell Ranger zebrafish genome GRCz10 as well as gene annotation Ensembl 87 were downloaded from Ensembl and the annotation was filtered with the \u2018mkgtf\u2019 command of Cell Ranger options: \u2018 attribute=gene biotype:protein coding attribute=gene biotype:lincRNA \u2013attribute=gene biotype:antisense\u2019. Genome sequence and filtered annotation were then used as input to the \u2018mkref\u2019 command of Cell Ranger to build the appropriate Cellranger Reference. Genome build: Zebrafish GRCz10 Supplementary files format and content: Matrix with rows as genes and columns as cells.", "thyroid gland", null, "Enzymatic Dissociation The single cell suspension was adjusted to a concentration of about 800 cells per microliter and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 12000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system Zheng et al. 2016. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The cDNA was amplified with 10 cycles following the guidelines of the 10x Genomics user manual. The 10X Genomics single cell RNA seq library preparation involving fragmentation dA Tailing adapter ligation and indexing PCR \u2013 was performed based on the manufacturer\u2019s protocol.", null, "treatment:2mpf|strain:Tgtg:mVenus T2A NTR|tag:Normal", "GSM3909771", "GSM3909771: 2mpf Thyroid; Danio rerio; RNA Seq", "GSM3909771", null, "1", "Enzymatic Dissociation The single cell suspension was adjusted to a concentration of about 800 cells per microliter and diluted with nuclease free water according to the manufacturer's instructions to yield 12000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system Zheng et al. 2016. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The cDNA was amplified with 10 cycles following the guidelines of the 10x Genomics user manual. The 10X Genomics single cell RNA seq library preparation involving fragmentation dA Tailing adapter ligation and indexing PCR \u2013 was performed based on the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP212225", null, null, "L38695_Track-76231_R2.fastq.gz L38695_Track-76231_R1.fastq.gz", "fastq fastq", 9092057268.0, 108238777.0, "GSM3909771 r1", "0:28 1:56", "A:2584354341;C:1956113829;G:2086486284;T:2461142498;N:3960316", 28, 56, null, null, 2584354341, 1956113829, 2086486284, 2461142498, 3960316, "SRX6373047", "SRS5034104", "SRA914541", "GEO", "Singh Lab, IRIBHM", 2, 0.01005, 0.87575, 0.00435, 0.23392, 0.99192, 0.80344, 0.39812, 0.53402, 28, 56, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2019-06-27", "Juvenile", "Juvenile", "Thyroid", "Endocrine System"], [54727, "SRR10150436", "SRX6875873", "SRS5411730", "SRP222654", "PRJNA571187", "single cell RNA Seq of juvenile zebrafish", "PRJNA571187", "Other", "single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit", null, null, null, "whole organism single cell RNA seq of juvenile zebrafish", "SC2S3", null, "strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "single cell RNA Seq of zebrafish: whole organism of juvenile", "I4S2", "I4S2", "A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP222654", null, null, "S3-I4-Hiseq_S2_L001_R1_001.fastq.gz S3-I4-Hiseq_S2_L001_R2_001.fastq.gz", "fastq fastq", 3487596300.0, 11625321.0, "S3 I4 Hiseq S2 L001 R1 001.fastq.gz", "0:150 1:150", "A:892777135;C:554604922;G:602698080;T:1437353489;N:162674", 150, 150, null, null, 892777135, 554604922, 602698080, 1437353489, 162674, "SRX6875873", "SRS5411730", "SRA965192", "Sun Yat- sen University|Life Sicence School", "Sun Yat- sen University", 2, 0.20171, 0.89797, 0.05294, 0.15018, 0.98557, 0.78865, 0.5155, 0.57581, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-09-20", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [54728, "SRR10150437", "SRX6875872", "SRS5411730", "SRP222654", "PRJNA571187", "single cell RNA Seq of juvenile zebrafish", "PRJNA571187", "Other", "single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit", null, null, null, "whole organism single cell RNA seq of juvenile zebrafish", "SC2S3", null, "strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "single cell RNA Seq of zebrafish: whole organism of juvenile", "I4S1", "I4S1", "A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP222654", null, null, "S3-I4-Hiseq_S1_L001_R1_001.fastq.gz S3-I4-Hiseq_S1_L001_R2_001.fastq.gz", "fastq fastq", 7508763300.0, 25029211.0, "S3 I4 Hiseq S1 L001 R1 001.fastq.gz", "0:150 1:150", "A:1913388616;C:1347525105;G:1432782100;T:2815014523;N:52956", 150, 150, null, null, 1913388616, 1347525105, 1432782100, 2815014523, 52956, "SRX6875872", "SRS5411730", "SRA965192", "Sun Yat- sen University|Life Sicence School", "Sun Yat- sen University", 2, 0.07221, 0.85601, 0.01751, 0.14578, 0.98569, 0.78642, 0.49143, 0.56028, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-09-20", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [54729, "SRR10150438", "SRX6875871", "SRS5411730", "SRP222654", "PRJNA571187", "single cell RNA Seq of juvenile zebrafish", "PRJNA571187", "Other", "single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit", null, null, null, "whole organism single cell RNA seq of juvenile zebrafish", "SC2S3", null, "strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "single cell RNA Seq of zebrafish: whole organism of juvenile", "I3S2", "I3S2", "A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP222654", null, null, "S3-I3-Hiseq_S2_L001_R1_001.fastq.gz S3-I3-Hiseq_S2_L001_R2_001.fastq.gz", "fastq fastq", 4273728900.0, 14245763.0, "S3 I3 Hiseq S2 L001 R1 001.fastq.gz", "0:150 1:150", "A:1093044190;C:680068409;G:740119940;T:1760292389;N:203972", 150, 150, null, null, 1093044190, 680068409, 740119940, 1760292389, 203972, "SRX6875871", "SRS5411730", "SRA965192", "Sun Yat- sen University|Life Sicence School", "Sun Yat- sen University", 2, 0.20465, 0.90036, 0.05289, 0.14865, 0.98553, 0.7877, 0.49162, 0.55234, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-09-20", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [54730, "SRR10150439", "SRX6875870", "SRS5411730", "SRP222654", "PRJNA571187", "single cell RNA Seq of juvenile zebrafish", "PRJNA571187", "Other", "single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit", null, null, null, "whole organism single cell RNA seq of juvenile zebrafish", "SC2S3", null, "strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "single cell RNA Seq of zebrafish: whole organism of juvenile", "I3S1", "I3S1", "A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP222654", null, null, "S3-I3-Hiseq_S1_L001_R1_001.fastq.gz S3-I3-Hiseq_S1_L001_R2_001.fastq.gz", "fastq fastq", 9027772200.0, 30092574.0, "S3 I3 Hiseq S1 L001 R1 001.fastq.gz", "0:150 1:150", "A:2295058606;C:1618993604;G:1725968569;T:3387689160;N:62261", 150, 150, null, null, 2295058606, 1618993604, 1725968569, 3387689160, 62261, "SRX6875870", "SRS5411730", "SRA965192", "Sun Yat- sen University|Life Sicence School", "Sun Yat- sen University", 2, 0.07429, 0.86204, 0.01816, 0.14367, 0.98638, 0.78754, 0.51152, 0.56418, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-09-20", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [54731, "SRR10150440", "SRX6875869", "SRS5411730", "SRP222654", "PRJNA571187", "single cell RNA Seq of juvenile zebrafish", "PRJNA571187", "Other", "single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit", null, null, null, "whole organism single cell RNA seq of juvenile zebrafish", "SC2S3", null, "strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "single cell RNA Seq of zebrafish: whole organism of juvenile", "I2S2", "I2S2", "A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP222654", null, null, "S3-I2-Hiseq_S2_L001_R1_001.fastq.gz S3-I2-Hiseq_S2_L001_R2_001.fastq.gz", "fastq fastq", 3198554400.0, 10661848.0, "S3 I2 Hiseq S2 L001 R1 001.fastq.gz", "0:150 1:150", "A:818748615;C:508568675;G:554517575;T:1316569216;N:150319", 150, 150, null, null, 818748615, 508568675, 554517575, 1316569216, 150319, "SRX6875869", "SRS5411730", "SRA965192", "Sun Yat- sen University|Life Sicence School", "Sun Yat- sen University", 2, 0.2074, 0.89961, 0.05315, 0.14953, 0.98514, 0.78849, 0.48568, 0.56678, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-09-20", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [54732, "SRR10150441", "SRX6875868", "SRS5411730", "SRP222654", "PRJNA571187", "single cell RNA Seq of juvenile zebrafish", "PRJNA571187", "Other", "single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit", null, null, null, "whole organism single cell RNA seq of juvenile zebrafish", "SC2S3", null, "strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "single cell RNA Seq of zebrafish: whole organism of juvenile", "I2S1", "I2S1", "A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP222654", null, null, "S3-I2-Hiseq_S1_L001_R1_001.fastq.gz S3-I2-Hiseq_S1_L001_R2_001.fastq.gz", "fastq fastq", 7025021100.0, 23416737.0, "S3 I2 Hiseq S1 L001 R1 001.fastq.gz", "0:150 1:150", "A:1791257403;C:1265471598;G:1350119282;T:2618125524;N:47293", 150, 150, null, null, 1791257403, 1265471598, 1350119282, 2618125524, 47293, "SRX6875868", "SRS5411730", "SRA965192", "Sun Yat- sen University|Life Sicence School", "Sun Yat- sen University", 2, 0.0595, 0.8397, 0.01378, 0.14017, 0.98602, 0.78618, 0.49684, 0.57243, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-09-20", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [54733, "SRR10150442", "SRX6875867", "SRS5411730", "SRP222654", "PRJNA571187", "single cell RNA Seq of juvenile zebrafish", "PRJNA571187", "Other", "single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit", null, null, null, "whole organism single cell RNA seq of juvenile zebrafish", "SC2S3", null, "strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "single cell RNA Seq of zebrafish: whole organism of juvenile", "I1S2", "I1S2", "A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP222654", null, null, "S3-I1-Hiseq_S2_L001_R1_001.fastq.gz S3-I1-Hiseq_S2_L001_R2_001.fastq.gz", "fastq fastq", 3657667800.0, 12192226.0, "S3 I1 Hiseq S2 L001 R1 001.fastq.gz", "0:150 1:150", "A:936855915;C:580324428;G:630608753;T:1509707910;N:170794", 150, 150, null, null, 936855915, 580324428, 630608753, 1509707910, 170794, "SRX6875867", "SRS5411730", "SRA965192", "Sun Yat- sen University|Life Sicence School", "Sun Yat- sen University", 2, 0.20478, 0.89817, 0.05194, 0.15048, 0.98543, 0.78817, 0.49956, 0.57664, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-09-20", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [54734, "SRR10150443", "SRX6875866", "SRS5411730", "SRP222654", "PRJNA571187", "single cell RNA Seq of juvenile zebrafish", "PRJNA571187", "Other", "single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit", null, null, null, "whole organism single cell RNA seq of juvenile zebrafish", "SC2S3", null, "strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "single cell RNA Seq of zebrafish: whole organism of juvenile", "I1S1", "I1S1", "A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP222654", null, null, "S3-I1-Hiseq_S1_L001_R1_001.fastq.gz S3-I1-Hiseq_S1_L001_R2_001.fastq.gz", "fastq fastq", 7809763800.0, 26032546.0, "S3 I1 Hiseq S1 L001 R1 001.fastq.gz", "0:150 1:150", "A:1991021603;C:1400155384;G:1489635110;T:2928896892;N:54811", 150, 150, null, null, 1991021603, 1400155384, 1489635110, 2928896892, 54811, "SRX6875866", "SRS5411730", "SRA965192", "Sun Yat- sen University|Life Sicence School", "Sun Yat- sen University", 2, 0.06891, 0.85095, 0.01881, 0.14251, 0.98555, 0.78772, 0.49154, 0.57233, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-09-20", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [65060, "SRR14923998", "SRX11237268", "SRS9283142", "SRP325759", "PRJNA741770", "Single cell profiling of cranial neural crest diversification across a vertebrate lifetime", "GSE178969", "Other", "The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.", null, "pubmed:35013168", null, "scRNAseq Sox10 Cre bact BtR 60dpf rep 2", "GSM5402440", null, "tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+", "scRNAseq Sox10 Cre bact BtR 60dpf rep 2", "For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 \u2013 30 000 for 5 dpf 1 000 \u2013 11 000 for 14 dpf and 1 000 \u2013 20 000 for the rest. To\u00a0 recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf which then subjected to neighbor finding FindNeighbors k = 20 and clustering FindClusters resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding clustering and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv a sparse matrix of count table mtx and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.", "Cranial neural crest derived cells", null, "Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer\u2019s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5\u00b0C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 \u00b0C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies twice. Final volumes of 500 \u00b5l resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer\u2019s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults in the institute vivarium according to Protocol 20771.", "cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+", "GSM5402440", "GSM5402440: scRNAseq Sox10 Cre bact BtR 60dpf rep 2; Danio rerio; RNA Seq", "GSM5402440", null, "1", "Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5\u00b0C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 \u00b0C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 \u00b5l resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.", "GEO Accession:GSM5402440", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP325759", null, null, "scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_2_S17_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_2_S17_L001_R2_001.fastq.gz", "fastq fastq", 7297507744.0, 49499870.0, "GSM5402440 r1", "0:27 1:120.42", "A:2154834707;C:1571012695;G:1612449699;T:1955051784;N:4158859", 27, 120, null, null, 2154834707, 1571012695, 1612449699, 1955051784, 4158859, "SRX11237268", "SRS9283142", "SRA1250944", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.00118, 0.86503, 0.00059, 0.14289, 0.99793, 0.85385, 0.46902, 0.50643, 27, 119, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-06-27", "Juvenile", "Juvenile", "Brain", "Nervous System"], [65061, "SRR14923999", "SRX11237268", "SRS9283142", "SRP325759", "PRJNA741770", "Single cell profiling of cranial neural crest diversification across a vertebrate lifetime", "GSE178969", "Other", "The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.", null, "pubmed:35013168", null, "scRNAseq Sox10 Cre bact BtR 60dpf rep 2", "GSM5402440", null, "tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+", "scRNAseq Sox10 Cre bact BtR 60dpf rep 2", "For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 \u2013 30 000 for 5 dpf 1 000 \u2013 11 000 for 14 dpf and 1 000 \u2013 20 000 for the rest. To\u00a0 recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf which then subjected to neighbor finding FindNeighbors k = 20 and clustering FindClusters resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding clustering and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv a sparse matrix of count table mtx and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.", "Cranial neural crest derived cells", null, "Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer\u2019s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5\u00b0C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 \u00b0C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies twice. Final volumes of 500 \u00b5l resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer\u2019s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults in the institute vivarium according to Protocol 20771.", "cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+", "GSM5402440", "GSM5402440: scRNAseq Sox10 Cre bact BtR 60dpf rep 2; Danio rerio; RNA Seq", "GSM5402440", null, "1", "Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5\u00b0C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 \u00b0C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 \u00b5l resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.", "GEO Accession:GSM5402440", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP325759", null, null, "scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_2_S18_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_2_S18_L001_R2_001.fastq.gz", "fastq fastq", 4258953868.0, 28889131.0, "GSM5402440 r2", "0:27 1:120.42", "A:1263874552;C:912254586;G:936347287;T:1144040879;N:2436564", 27, 120, null, null, 1263874552, 912254586, 936347287, 1144040879, 2436564, "SRX11237268", "SRS9283142", "SRA1250944", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.00124, 0.86353, 0.00061, 0.14235, 0.99782, 0.85251, 0.45967, 0.51575, 27, 120, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-06-27", "Juvenile", "Juvenile", "Brain", "Nervous System"], [65062, "SRR14924000", "SRX11237268", "SRS9283142", "SRP325759", "PRJNA741770", "Single cell profiling of cranial neural crest diversification across a vertebrate lifetime", "GSE178969", "Other", "The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.", null, "pubmed:35013168", null, "scRNAseq Sox10 Cre bact BtR 60dpf rep 2", "GSM5402440", null, "tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+", "scRNAseq Sox10 Cre bact BtR 60dpf rep 2", "For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 \u2013 30 000 for 5 dpf 1 000 \u2013 11 000 for 14 dpf and 1 000 \u2013 20 000 for the rest. To\u00a0 recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf which then subjected to neighbor finding FindNeighbors k = 20 and clustering FindClusters resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding clustering and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv a sparse matrix of count table mtx and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.", "Cranial neural crest derived cells", null, "Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer\u2019s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5\u00b0C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 \u00b0C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies twice. Final volumes of 500 \u00b5l resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer\u2019s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults in the institute vivarium according to Protocol 20771.", "cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+", "GSM5402440", "GSM5402440: scRNAseq Sox10 Cre bact BtR 60dpf rep 2; Danio rerio; RNA Seq", "GSM5402440", null, "1", "Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5\u00b0C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 \u00b0C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 \u00b5l resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.", "GEO Accession:GSM5402440", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP325759", null, null, "scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_2_S19_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_2_S19_L001_R2_001.fastq.gz", "fastq fastq", 4050808878.0, 27477008.0, "GSM5402440 r3", "0:27 1:120.43", "A:1201699026;C:868704481;G:891671655;T:1086426372;N:2307344", 27, 120, null, null, 1201699026, 868704481, 891671655, 1086426372, 2307344, "SRX11237268", "SRS9283142", "SRA1250944", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.00124, 0.86647, 0.0006, 0.14333, 0.99778, 0.85407, 0.4065, 0.52778, 27, 120, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-06-27", "Juvenile", "Juvenile", "Brain", "Nervous System"], [65063, "SRR14924001", "SRX11237268", "SRS9283142", "SRP325759", "PRJNA741770", "Single cell profiling of cranial neural crest diversification across a vertebrate lifetime", "GSE178969", "Other", "The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.", null, "pubmed:35013168", null, "scRNAseq Sox10 Cre bact BtR 60dpf rep 2", "GSM5402440", null, "tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+", "scRNAseq Sox10 Cre bact BtR 60dpf rep 2", "For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 \u2013 30 000 for 5 dpf 1 000 \u2013 11 000 for 14 dpf and 1 000 \u2013 20 000 for the rest. To\u00a0 recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf which then subjected to neighbor finding FindNeighbors k = 20 and clustering FindClusters resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding clustering and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv a sparse matrix of count table mtx and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.", "Cranial neural crest derived cells", null, "Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer\u2019s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5\u00b0C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 \u00b0C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies twice. Final volumes of 500 \u00b5l resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer\u2019s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults in the institute vivarium according to Protocol 20771.", "cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+", "GSM5402440", "GSM5402440: scRNAseq Sox10 Cre bact BtR 60dpf rep 2; Danio rerio; RNA Seq", "GSM5402440", null, "1", "Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5\u00b0C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 \u00b0C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 \u00b5l resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.", "GEO Accession:GSM5402440", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP325759", null, null, "scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_2_S20_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_2_S20_L001_R2_001.fastq.gz", "fastq fastq", 5532406222.0, 37527113.0, "GSM5402440 r4", "0:27 1:120.42", "A:1639053013;C:1186314122;G:1218280877;T:1485607687;N:3150523", 27, 120, null, null, 1639053013, 1186314122, 1218280877, 1485607687, 3150523, "SRX11237268", "SRS9283142", "SRA1250944", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.00122, 0.86507, 0.00058, 0.14242, 0.99772, 0.85385, 0.4, 0.51687, 27, 120, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-06-27", "Juvenile", "Juvenile", "Brain", "Nervous System"], [65064, "SRR14923994", "SRX11237267", "SRS9283141", "SRP325759", "PRJNA741770", "Single cell profiling of cranial neural crest diversification across a vertebrate lifetime", "GSE178969", "Other", "The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.", null, "pubmed:35013168", null, "scRNAseq Sox10 Cre bact BtR 60dpf rep 1", "GSM5402439", null, "tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+", "scRNAseq Sox10 Cre bact BtR 60dpf rep 1", "For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 \u2013 30 000 for 5 dpf 1 000 \u2013 11 000 for 14 dpf and 1 000 \u2013 20 000 for the rest. To\u00a0 recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf which then subjected to neighbor finding FindNeighbors k = 20 and clustering FindClusters resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding clustering and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv a sparse matrix of count table mtx and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.", "Cranial neural crest derived cells", null, "Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer\u2019s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5\u00b0C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 \u00b0C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies twice. Final volumes of 500 \u00b5l resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer\u2019s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults in the institute vivarium according to Protocol 20771.", "cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+", "GSM5402439", "GSM5402439: scRNAseq Sox10 Cre bact BtR 60dpf rep 1; Danio rerio; RNA Seq", "GSM5402439", null, "1", "Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5\u00b0C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 \u00b0C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 \u00b5l resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.", "GEO Accession:GSM5402439", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP325759", null, null, "scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_1_S13_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_1_S13_L001_R2_001.fastq.gz", "fastq fastq", 9936865506.0, 67405339.0, "GSM5402439 r1", "0:27 1:120.42", "A:2906745689;C:2166283632;G:2206772222;T:2651323922;N:5740041", 27, 120, null, null, 2906745689, 2166283632, 2206772222, 2651323922, 5740041, "SRX11237267", "SRS9283141", "SRA1250944", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.00134, 0.84917, 0.0006, 0.12877, 0.99746, 0.84944, 0.36363, 0.52247, 27, 119, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-06-27", "Juvenile", "Juvenile", "Brain", "Nervous System"], [65065, "SRR14923995", "SRX11237267", "SRS9283141", "SRP325759", "PRJNA741770", "Single cell profiling of cranial neural crest diversification across a vertebrate lifetime", "GSE178969", "Other", "The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.", null, "pubmed:35013168", null, "scRNAseq Sox10 Cre bact BtR 60dpf rep 1", "GSM5402439", null, "tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+", "scRNAseq Sox10 Cre bact BtR 60dpf rep 1", "For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 \u2013 30 000 for 5 dpf 1 000 \u2013 11 000 for 14 dpf and 1 000 \u2013 20 000 for the rest. To\u00a0 recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf which then subjected to neighbor finding FindNeighbors k = 20 and clustering FindClusters resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding clustering and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv a sparse matrix of count table mtx and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.", "Cranial neural crest derived cells", null, "Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer\u2019s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5\u00b0C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 \u00b0C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies twice. Final volumes of 500 \u00b5l resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer\u2019s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults in the institute vivarium according to Protocol 20771.", "cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+", "GSM5402439", "GSM5402439: scRNAseq Sox10 Cre bact BtR 60dpf rep 1; Danio rerio; RNA Seq", "GSM5402439", null, "1", "Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5\u00b0C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 \u00b0C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 \u00b5l resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.", "GEO Accession:GSM5402439", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP325759", null, null, "scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_1_S14_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_1_S14_L001_R2_001.fastq.gz", "fastq fastq", 7897275260.0, 53567183.0, "GSM5402439 r2", "0:27 1:120.43", "A:2323096260;C:1712849172;G:1740350109;T:2116414828;N:4564891", 27, 120, null, null, 2323096260, 1712849172, 1740350109, 2116414828, 4564891, "SRX11237267", "SRS9283141", "SRA1250944", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.00136, 0.85419, 0.00056, 0.13524, 0.99709, 0.85989, 0.38853, 0.51984, 27, 120, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-06-27", "Juvenile", "Juvenile", "Brain", "Nervous System"], [65066, "SRR14923996", "SRX11237267", "SRS9283141", "SRP325759", "PRJNA741770", "Single cell profiling of cranial neural crest diversification across a vertebrate lifetime", "GSE178969", "Other", "The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.", null, "pubmed:35013168", null, "scRNAseq Sox10 Cre bact BtR 60dpf rep 1", "GSM5402439", null, "tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+", "scRNAseq Sox10 Cre bact BtR 60dpf rep 1", "For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 \u2013 30 000 for 5 dpf 1 000 \u2013 11 000 for 14 dpf and 1 000 \u2013 20 000 for the rest. To\u00a0 recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf which then subjected to neighbor finding FindNeighbors k = 20 and clustering FindClusters resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding clustering and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv a sparse matrix of count table mtx and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.", "Cranial neural crest derived cells", null, "Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer\u2019s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5\u00b0C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 \u00b0C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies twice. Final volumes of 500 \u00b5l resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer\u2019s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults in the institute vivarium according to Protocol 20771.", "cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+", "GSM5402439", "GSM5402439: scRNAseq Sox10 Cre bact BtR 60dpf rep 1; Danio rerio; RNA Seq", "GSM5402439", null, "1", "Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5\u00b0C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 \u00b0C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 \u00b5l resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.", "GEO Accession:GSM5402439", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP325759", null, null, "scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_1_S15_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_1_S15_L001_R2_001.fastq.gz", "fastq fastq", 7765136197.0, 52676458.0, "GSM5402439 r3", "0:27 1:120.41", "A:2285912113;C:1683626385;G:1719251520;T:2071793622;N:4552557", 27, 120, null, null, 2285912113, 1683626385, 1719251520, 2071793622, 4552557, "SRX11237267", "SRS9283141", "SRA1250944", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.00115, 0.85166, 0.00046, 0.13288, 0.99766, 0.85163, 0.35877, 0.5154, 27, 121, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-06-27", "Juvenile", "Juvenile", "Brain", "Nervous System"], [65067, "SRR14923997", "SRX11237267", "SRS9283141", "SRP325759", "PRJNA741770", "Single cell profiling of cranial neural crest diversification across a vertebrate lifetime", "GSE178969", "Other", "The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.", null, "pubmed:35013168", null, "scRNAseq Sox10 Cre bact BtR 60dpf rep 1", "GSM5402439", null, "tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+", "scRNAseq Sox10 Cre bact BtR 60dpf rep 1", "For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 \u2013 30 000 for 5 dpf 1 000 \u2013 11 000 for 14 dpf and 1 000 \u2013 20 000 for the rest. To\u00a0 recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf which then subjected to neighbor finding FindNeighbors k = 20 and clustering FindClusters resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding clustering and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv a sparse matrix of count table mtx and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.", "Cranial neural crest derived cells", null, "Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer\u2019s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5\u00b0C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 \u00b0C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies twice. Final volumes of 500 \u00b5l resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer\u2019s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults in the institute vivarium according to Protocol 20771.", "cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+", "GSM5402439", "GSM5402439: scRNAseq Sox10 Cre bact BtR 60dpf rep 1; Danio rerio; RNA Seq", "GSM5402439", null, "1", "Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5\u00b0C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 \u00b0C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 \u00b5l resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.", "GEO Accession:GSM5402439", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP325759", null, null, "scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_1_S16_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_1_S16_L001_R2_001.fastq.gz", "fastq fastq", 10430563739.0, 70754033.0, "GSM5402439 r4", "0:27 1:120.42", "A:3057357215;C:2269896192;G:2312685494;T:2784595449;N:6029389", 27, 120, null, null, 3057357215, 2269896192, 2312685494, 2784595449, 6029389, "SRX11237267", "SRS9283141", "SRA1250944", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.00148, 0.85451, 0.00069, 0.13182, 0.99715, 0.85397, 0.41721, 0.50684, 27, 121, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-06-27", "Juvenile", "Juvenile", "Brain", "Nervous System"], [66846, "SRR16681977", "SRX12882565", "SRS10825217", "SRP344071", "PRJNA776888", "Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts", "GSE186957", "Transcriptome Analysis", "Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana\u2122 miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT\u2013PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation which potentially provides a basis for breeding strains of fish without xxx to improve the safe consumption and economic value of many aquaculture species and in this way boost the proportion of fish for the supply of animal protein worldwide Fig. 6. For this reason we needed to verify that the content of fatty acid in the runx2b / mutant was higher than that in runx2b+/+ fish as well as the expression of key genes related to IBs in the runx2b / and runx2b+/+ strains obtained by scRNA seq data. This study also provides materials and directions for further study to clarify the specific regulatory mechanism of IB formation and will help to discover more specific genetic resources that can be used for IB trait improvement in fish. Overall design: the scRNA seq and bulk seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish", null, "pubmed:39741296", null, "runx2b / scRNA seq", "GSM5664293", null, "source name:muscle and IB|strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:runx2b / ", "runx2b / scRNA seq", "Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample", "muscle and IB", null, "tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.", null, "strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:runx2b / ", "GSM5664293", "GSM5664293: runx2b / scRNA seq; Danio rerio; RNA Seq", "GSM5664293", null, "1", "tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.", "GEO Accession:GSM5664293", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP344071", null, "loader:fastq load.py", "MU_S2_L003_R2_001.fastq MU_S2_L003_R1_001.fastq", "fastq fastq", 112565768100.0, 375219227.0, "GSM5664293 r1", "0:150 1:150", "A:34329910863;C:17430450121;G:18090145246;T:42713500460;N:1761410", 150, 150, null, null, 34329910863, 17430450121, 18090145246, 42713500460, 1761410, "SRX12882565", "SRS10825217", "SRA1320685", "GEO", "huazhong agricultural university", 2, 0.34718, 0.92478, 0.05085, 0.09377, 0.98545, 0.82375, 0.7209, 0.73759, 150, 150, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_droplet", "10x", null, "China", "2021-11-01", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [66847, "SRR16681976", "SRX12882564", "SRS10825216", "SRP344071", "PRJNA776888", "Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts", "GSE186957", "Transcriptome Analysis", "Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana\u2122 miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT\u2013PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation which potentially provides a basis for breeding strains of fish without xxx to improve the safe consumption and economic value of many aquaculture species and in this way boost the proportion of fish for the supply of animal protein worldwide Fig. 6. For this reason we needed to verify that the content of fatty acid in the runx2b / mutant was higher than that in runx2b+/+ fish as well as the expression of key genes related to IBs in the runx2b / and runx2b+/+ strains obtained by scRNA seq data. This study also provides materials and directions for further study to clarify the specific regulatory mechanism of IB formation and will help to discover more specific genetic resources that can be used for IB trait improvement in fish. Overall design: the scRNA seq and bulk seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish", null, "pubmed:39741296", null, "runx2b+/+ scRNA seq", "GSM5664292", null, "source name:muscle and IB|strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:wild type", "runx2b+/+ scRNA seq", "Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample", "muscle and IB", null, "tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.", null, "strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:wild type", "GSM5664292", "GSM5664292: runx2b+/+ scRNA seq; Danio rerio; RNA Seq", "GSM5664292", null, "1", "tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.", "GEO Accession:GSM5664292", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP344071", null, "loader:fastq load.py|options: doNotUseSharq", "WT_S1_L003_R1_001.fastq WT_S1_L003_R2_001.fastq", "fastq fastq", 99838157100.0, 332793857.0, "GSM5664292 r1", "0:150 1:150", "A:30283010374;C:15529232903;G:16181518775;T:37842782328;N:1612720", 150, 150, null, null, 30283010374, 15529232903, 16181518775, 37842782328, 1612720, "SRX12882564", "SRS10825216", "SRA1320685", "GEO", "huazhong agricultural university", 2, 0.34316, 0.92608, 0.04623, 0.09467, 0.98701, 0.83644, 0.72084, 0.76059, 150, 150, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_droplet", "10x", null, "China", "2021-11-01", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [66848, "SRR16681984", "SRX12882563", "SRS10825218", "SRP344071", "PRJNA776888", "Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts", "GSE186957", "Transcriptome Analysis", "Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana\u2122 miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT\u2013PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation which potentially provides a basis for breeding strains of fish without xxx to improve the safe consumption and economic value of many aquaculture species and in this way boost the proportion of fish for the supply of animal protein worldwide Fig. 6. For this reason we needed to verify that the content of fatty acid in the runx2b / mutant was higher than that in runx2b+/+ fish as well as the expression of key genes related to IBs in the runx2b / and runx2b+/+ strains obtained by scRNA seq data. This study also provides materials and directions for further study to clarify the specific regulatory mechanism of IB formation and will help to discover more specific genetic resources that can be used for IB trait improvement in fish. Overall design: the scRNA seq and bulk seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish", null, "pubmed:39741296", null, "runx2b / bulk RNA seq rep3", "GSM5664299", null, "source name:muscle and IB|strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:runx2b / ", "runx2b / bulk RNA seq rep3", "Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample", "muscle and IB", null, "tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.", null, "strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:runx2b / ", "GSM5664299", "GSM5664299: runx2b / bulk RNA seq rep3; Danio rerio; RNA Seq", "GSM5664299", null, "1", "tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.", "GEO Accession:GSM5664299", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP344071", null, "loader:fastq load.py", "MUT_3_60dpf.R1.fq MUT_3_60dpf.R2.fq", "fastq fastq", 7358370600.0, 24527902.0, "GSM5664299 r1", "0:150 1:150", "A:1781646726;C:1790446433;G:2025455441;T:1760804227;N:17773", 150, 150, null, null, 1781646726, 1790446433, 2025455441, 1760804227, 17773, "SRX12882563", "SRS10825218", "SRA1320685", "GEO", "huazhong agricultural university", 2, 0.92553, 0.92182, 0.01196, 0.01201, 0.86239, 0.86348, 0.70266, 0.63893, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_droplet", "10x", null, "China", "2021-11-01", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [66849, "SRR16681983", "SRX12882562", "SRS10825219", "SRP344071", "PRJNA776888", "Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts", "GSE186957", "Transcriptome Analysis", "Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana\u2122 miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT\u2013PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation which potentially provides a basis for breeding strains of fish without xxx to improve the safe consumption and economic value of many aquaculture species and in this way boost the proportion of fish for the supply of animal protein worldwide Fig. 6. For this reason we needed to verify that the content of fatty acid in the runx2b / mutant was higher than that in runx2b+/+ fish as well as the expression of key genes related to IBs in the runx2b / and runx2b+/+ strains obtained by scRNA seq data. This study also provides materials and directions for further study to clarify the specific regulatory mechanism of IB formation and will help to discover more specific genetic resources that can be used for IB trait improvement in fish. Overall design: the scRNA seq and bulk seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish", null, "pubmed:39741296", null, "runx2b / bulk RNA seq rep2", "GSM5664298", null, "source name:muscle and IB|strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:runx2b / ", "runx2b / bulk RNA seq rep2", "Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample", "muscle and IB", null, "tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.", null, "strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:runx2b / ", "GSM5664298", "GSM5664298: runx2b / bulk RNA seq rep2; Danio rerio; RNA Seq", "GSM5664298", null, "1", "tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.", "GEO Accession:GSM5664298", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP344071", null, "loader:fastq load.py", "MUT_2_60dpf.R2.fq MUT_2_60dpf.R1.fq", "fastq fastq", 5983046100.0, 19943487.0, "GSM5664298 r1", "0:150 1:150", "A:1456794159;C:1460953692;G:1613536834;T:1451747111;N:14304", 150, 150, null, null, 1456794159, 1460953692, 1613536834, 1451747111, 14304, "SRX12882562", "SRS10825219", "SRA1320685", "GEO", "huazhong agricultural university", 2, 0.9349, 0.92939, 0.01147, 0.01123, 0.85488, 0.85687, 0.69455, 0.61732, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_droplet", "10x", null, "China", "2021-11-01", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [66850, "SRR16681982", "SRX12882561", "SRS10825215", "SRP344071", "PRJNA776888", "Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts", "GSE186957", "Transcriptome Analysis", "Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana\u2122 miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT\u2013PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation which potentially provides a basis for breeding strains of fish without xxx to improve the safe consumption and economic value of many aquaculture species and in this way boost the proportion of fish for the supply of animal protein worldwide Fig. 6. For this reason we needed to verify that the content of fatty acid in the runx2b / mutant was higher than that in runx2b+/+ fish as well as the expression of key genes related to IBs in the runx2b / and runx2b+/+ strains obtained by scRNA seq data. This study also provides materials and directions for further study to clarify the specific regulatory mechanism of IB formation and will help to discover more specific genetic resources that can be used for IB trait improvement in fish. Overall design: the scRNA seq and bulk seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish", null, "pubmed:39741296", null, "runx2b / bulk RNA seq rep1", "GSM5664297", null, "source name:muscle and IB|strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:runx2b / ", "runx2b / bulk RNA seq rep1", "Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample", "muscle and IB", null, "tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.", null, "strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:runx2b / ", "GSM5664297", "GSM5664297: runx2b / bulk RNA seq rep1; Danio rerio; RNA Seq", "GSM5664297", null, "1", "tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.", "GEO Accession:GSM5664297", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP344071", null, "loader:fastq load.py", "MUT_1_60dpf.R1.fq MUT_1_60dpf.R2.fq", "fastq fastq", 6876053100.0, 22920177.0, "GSM5664297 r1", "0:150 1:150", "A:1683687632;C:1665466650;G:1862910858;T:1663971371;N:16589", 150, 150, null, null, 1683687632, 1665466650, 1862910858, 1663971371, 16589, "SRX12882561", "SRS10825215", "SRA1320685", "GEO", "huazhong agricultural university", 2, 0.9327, 0.92802, 0.01178, 0.0113, 0.84861, 0.84987, 0.62221, 0.67729, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_droplet", "10x", null, "China", "2021-11-01", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [66851, "SRR16681981", "SRX12882560", "SRS10825214", "SRP344071", "PRJNA776888", "Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts", "GSE186957", "Transcriptome Analysis", "Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana\u2122 miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT\u2013PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation which potentially provides a basis for breeding strains of fish without xxx to improve the safe consumption and economic value of many aquaculture species and in this way boost the proportion of fish for the supply of animal protein worldwide Fig. 6. For this reason we needed to verify that the content of fatty acid in the runx2b / mutant was higher than that in runx2b+/+ fish as well as the expression of key genes related to IBs in the runx2b / and runx2b+/+ strains obtained by scRNA seq data. This study also provides materials and directions for further study to clarify the specific regulatory mechanism of IB formation and will help to discover more specific genetic resources that can be used for IB trait improvement in fish. Overall design: the scRNA seq and bulk seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish", null, "pubmed:39741296", null, "runx2b+/+ bulk RNA seq rep3", "GSM5664296", null, "source name:muscle and IB|strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:wild type", "runx2b+/+ bulk RNA seq rep3", "Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample", "muscle and IB", null, "tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.", null, "strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:wild type", "GSM5664296", "GSM5664296: runx2b+/+ bulk RNA seq rep3; Danio rerio; RNA Seq", "GSM5664296", null, "1", "tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.", "GEO Accession:GSM5664296", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP344071", null, "loader:fastq load.py", "WT_3_60dpf.R1.fq WT_3_60dpf.R2.fq", "fastq fastq", 6834033900.0, 22780113.0, "GSM5664296 r1", "0:150 1:150", "A:1665713519;C:1660512523;G:1864685424;T:1643106338;N:16096", 150, 150, null, null, 1665713519, 1660512523, 1864685424, 1643106338, 16096, "SRX12882560", "SRS10825214", "SRA1320685", "GEO", "huazhong agricultural university", 2, 0.92969, 0.92347, 0.01017, 0.01012, 0.85807, 0.86001, 0.63698, 0.67717, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_droplet", "10x", null, "China", "2021-11-01", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [66852, "SRR16681980", "SRX12882559", "SRS10825212", "SRP344071", "PRJNA776888", "Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts", "GSE186957", "Transcriptome Analysis", "Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana\u2122 miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT\u2013PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation which potentially provides a basis for breeding strains of fish without xxx to improve the safe consumption and economic value of many aquaculture species and in this way boost the proportion of fish for the supply of animal protein worldwide Fig. 6. For this reason we needed to verify that the content of fatty acid in the runx2b / mutant was higher than that in runx2b+/+ fish as well as the expression of key genes related to IBs in the runx2b / and runx2b+/+ strains obtained by scRNA seq data. This study also provides materials and directions for further study to clarify the specific regulatory mechanism of IB formation and will help to discover more specific genetic resources that can be used for IB trait improvement in fish. Overall design: the scRNA seq and bulk seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish", null, "pubmed:39741296", null, "runx2b+/+ bulk RNA seq rep2", "GSM5664295", null, "source name:muscle and IB|strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:wild type", "runx2b+/+ bulk RNA seq rep2", "Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample", "muscle and IB", null, "tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.", null, "strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:wild type", "GSM5664295", "GSM5664295: runx2b+/+ bulk RNA seq rep2; Danio rerio; RNA Seq", "GSM5664295", null, "1", "tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.", "GEO Accession:GSM5664295", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP344071", null, "loader:fastq load.py", "WT_2_60dpf.R1.fq WT_2_60dpf.R2.fq", "fastq fastq", 7007750400.0, 23359168.0, "GSM5664295 r1", "0:150 1:150", "A:1714498514;C:1702913716;G:1897215939;T:1693105532;N:16699", 150, 150, null, null, 1714498514, 1702913716, 1897215939, 1693105532, 16699, "SRX12882559", "SRS10825212", "SRA1320685", "GEO", "huazhong agricultural university", 2, 0.93182, 0.92608, 0.01221, 0.01171, 0.8478, 0.85023, 0.67158, 0.65917, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_droplet", "10x", null, "China", "2021-11-01", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [66853, "SRR16681979", "SRX12882558", "SRS10825213", "SRP344071", "PRJNA776888", "Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts", "GSE186957", "Transcriptome Analysis", "Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana\u2122 miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT\u2013PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation which potentially provides a basis for breeding strains of fish without xxx to improve the safe consumption and economic value of many aquaculture species and in this way boost the proportion of fish for the supply of animal protein worldwide Fig. 6. For this reason we needed to verify that the content of fatty acid in the runx2b / mutant was higher than that in runx2b+/+ fish as well as the expression of key genes related to IBs in the runx2b / and runx2b+/+ strains obtained by scRNA seq data. This study also provides materials and directions for further study to clarify the specific regulatory mechanism of IB formation and will help to discover more specific genetic resources that can be used for IB trait improvement in fish. Overall design: the scRNA seq and bulk seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish", null, "pubmed:39741296", null, "runx2b+/+ bulk RNA seq rep1", "GSM5664294", null, "source name:muscle and IB|strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:wild type", "runx2b+/+ bulk RNA seq rep1", "Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample", "muscle and IB", null, "tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.", null, "strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:wild type", "GSM5664294", "GSM5664294: runx2b+/+ bulk RNA seq rep1; Danio rerio; RNA Seq", "GSM5664294", null, "1", "tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.", "GEO Accession:GSM5664294", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP344071", null, "loader:fastq load.py", "WT_1_60dpf.R1.fq WT_1_60dpf.R2.fq", "fastq fastq", 6785203800.0, 22617346.0, "GSM5664294 r1", "0:150 1:150", "A:1660992152;C:1637869425;G:1843210897;T:1643114944;N:16382", 150, 150, null, null, 1660992152, 1637869425, 1843210897, 1643114944, 16382, "SRX12882558", "SRS10825213", "SRA1320685", "GEO", "huazhong agricultural university", 2, 0.92763, 0.92196, 0.00968, 0.00949, 0.84295, 0.84593, 0.65456, 0.65914, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_droplet", "10x", null, "China", "2021-11-01", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [67758, "SRR17262950", "SRX13441050", "SRS11340479", "SRP351377", "PRJNA789855", "Single cell transcriptome reveals insights into the development and function of the zebrafish ovary", "GSE191137", "Transcriptome Analysis", "Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development yet there are still significant gaps in our understanding of the genes that regulate gonad development sex and reproduction. Unlike the development of many organs such as the brain and heart that form during the first few days of development zebrafish gonads do not begin to form until the larval stage =5 dpf. Thus forward genetic screens have identified very few genes required for gonad development. In addition bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations we have used single cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10 658 germ cells and 14 431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types including follicle cells theca cells and interstitial stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance we determined the location of these cell subpopulations within the ovary. Finally for select examples we used gene knockout experiments to determine the role of newly identified genes. Our results reveal novel insights into ovarian development and function and the sequencing information will provide a valuable resource for future studies. Overall design: Single cell RNA sequencing of 40 dpf zebrafish ovaries", null, "pubmed:35588359", null, "40 dpf zebrafish ovaries cells zx4", "GSM5739896", null, "tissue:40 dpf zebrafish ovaries|cell type:Ovary cells|genotype:AB wildtype", "40 dpf zebrafish ovaries cells zx4", "A General Transfer Format GTF gene annotation filerelease 96 for the GRCz11 zebrafish genome was downloaded from Ensembl Genome Browser and filtered using the \u201cmkgtf\u201d function in Cell Ranger v3.0.2; 10x Genomic to retain the following attributes: protein coding lincRNA and antisense. A genome reference file was generated with Cell Ranger\u2019s \u201cmkref\u201d function using the GRCz11 zebrafish genome obtained from the Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file. GRCz11 zebrafish genome FASTQ file from Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file described above were used to generate the count file using the \u201ccount\u201d function in Cell Ranger v3.0.2; 10x Genomic. \u201cexpect cells\u201d was setted to 10000 based on estimated cell recovery.\u00a0 Genome build: GRCz11 Supplementary files format and content: Filtered or raw matrix files generated from Cell Ranger in one zip file.", "40 dpf zebrafish ovaries", null, "Somatic ovary cells were dissociated using a modification of Elkouby and Mullins 2016. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfp transgenic fish Leu et al. 2010 were dissected and stored in a LoBind tube containing 2mL of L15. Tissues were minced with microdissection scissors into < 1 mm pieces. post the tissue had settled to the bottom of the tube the media was replaced with 5mL of digestive enzyme mixture 3 mg/mL collagenase I Cat.No. C0130; Sigma Aldrich 3 mg/mL collagenase II Cat.No. C6885; Sigma Aldrich and 1.6 mg/mL hyaluronidase Cat.No. H4272; Sigma Aldrich in L15 and incubated on an orbital rotator at room temperature . The suspension was monitored every 10 mins until a minimal number of cell clumps were observed 30 min.. Cells were centrifuged for 3 mins at 300 x g and resuspended in 5 mL of 5x TrypLE Cat.No. A1217701; Thermo Fisher in L15 and incubated on an orbital rotator at room temperature for 15 min. The trypsin reaction was stopped by adding 500 \u00b5L of 2.8 mg/mL trypsin inhibitor in L15 and incubated on an orbital rotator at room temperature for 1 min. The cell suspension was then added to 25 ml of L15 in a 50 ml conical tube to dilute the trypsin and centrifuged for 3 min at 300 x g. The cell pellet was resuspended and washed two times with 5 mL of L15 using a P1000 pipette and centrifuged for 3 mins at 300 x g. The cell pellet was then resuspended and filtered as described above. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly barcoded 3\u2019 single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell 3\u2019 Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer\u2019s recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent. The libraries were quantified by fluorometry on a Qubit instrument LifeTechnologies and by qPCR with a Kapa Library Quant kit Kapa Biosystems prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer Illumina with paired end 100 bp reads.", "Zebrafish husbandry was performed as previously described Westerfield 2000.", "cell type:Ovary cells|genotype:AB wildtype", "GSM5739896", "GSM5739896: 40 dpf zebrafish ovaries cells zx4; Danio rerio; ssRNA seq", "GSM5739896 r1", "GSM5739896", "1", "Somatic ovary cells were dissociated using a modification of Elkouby and Mullins 2016. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfp transgenic fish Leu et al. 2010 were dissected and stored in a LoBind tube containing 2mL of L15. Tissues were minced with microdissection scissors into < 1 mm pieces. post the tissue had settled to the bottom of the tube the media was replaced with 5mL of digestive enzyme mixture 3 mg/mL collagenase I Cat.No. C0130; Sigma Aldrich 3 mg/mL collagenase II Cat.No. C6885; Sigma Aldrich and 1.6 mg/mL hyaluronidase Cat.No. H4272; Sigma Aldrich in L15 and incubated on an orbital rotator at room temperature . The suspension was monitored every 10 mins until a minimal number of cell clumps were observed 30 min.. Cells were centrifuged for 3 mins at 300 x g and resuspended in 5 mL of 5x TrypLE Cat.No. A1217701; Thermo Fisher in L15 and incubated on an orbital rotator at room temperature for 15 min. The trypsin reaction was stopped by adding 500 \u00b5L of 2.8 mg/mL trypsin inhibitor in L15 and incubated on an orbital rotator at room temperature for 1 min. The cell suspension was then added to 25 ml of L15 in a 50 ml conical tube to dilute the trypsin and centrifuged for 3 min at 300 x g. The cell pellet was resuspended and washed two times with 5 mL of L15 using a P1000 pipette and centrifuged for 3 mins at 300 x g. The cell pellet was then resuspended and filtered as described above. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly barcoded three prime single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell three prime Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer's recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent. The libraries were quantified by fluorometry on a Qubit instrument LifeTechnologies and by qPCR with a Kapa Library Quant kit Kapa Biosystems prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer Illumina with paired end 100 bp reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP351377", null, null, "40dpf_ova_2_S1_L001_R1_001.fastq.gz 40dpf_ova_2_S1_L001_R2_001.fastq.gz", "fastq fastq", 109199255578.0, 361586939.0, "GSM5739896 r1", "0:151 1:151", "A:26889567766;C:19012911507;G:17705256458;T:45580417154;N:11102693", 151, 151, null, null, 26889567766, 19012911507, 17705256458, 45580417154, 11102693, "SRX13441050", "SRS11340479", "SRA1345465", "Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis", "Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis", 2, 0.00012, 0.84311, 5e-05, 0.10842, 0.99997, 0.78486, 1.0, 0.53946, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-17", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [67759, "SRR17262951", "SRX13441049", "SRS11340478", "SRP351377", "PRJNA789855", "Single cell transcriptome reveals insights into the development and function of the zebrafish ovary", "GSE191137", "Transcriptome Analysis", "Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development yet there are still significant gaps in our understanding of the genes that regulate gonad development sex and reproduction. Unlike the development of many organs such as the brain and heart that form during the first few days of development zebrafish gonads do not begin to form until the larval stage =5 dpf. Thus forward genetic screens have identified very few genes required for gonad development. In addition bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations we have used single cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10 658 germ cells and 14 431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types including follicle cells theca cells and interstitial stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance we determined the location of these cell subpopulations within the ovary. Finally for select examples we used gene knockout experiments to determine the role of newly identified genes. Our results reveal novel insights into ovarian development and function and the sequencing information will provide a valuable resource for future studies. Overall design: Single cell RNA sequencing of 40 dpf zebrafish ovaries", null, "pubmed:35588359", null, "40 dpf zebrafish ovaries cells zx2", "GSM5739895", null, "tissue:40 dpf zebrafish ovaries|cell type:Ovary cells|genotype:AB wildtype", "40 dpf zebrafish ovaries cells zx2", "A General Transfer Format GTF gene annotation filerelease 96 for the GRCz11 zebrafish genome was downloaded from Ensembl Genome Browser and filtered using the \u201cmkgtf\u201d function in Cell Ranger v3.0.2; 10x Genomic to retain the following attributes: protein coding lincRNA and antisense. A genome reference file was generated with Cell Ranger\u2019s \u201cmkref\u201d function using the GRCz11 zebrafish genome obtained from the Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file. GRCz11 zebrafish genome FASTQ file from Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file described above were used to generate the count file using the \u201ccount\u201d function in Cell Ranger v3.0.2; 10x Genomic. \u201cexpect cells\u201d was setted to 10000 based on estimated cell recovery.\u00a0 Genome build: GRCz11 Supplementary files format and content: Filtered or raw matrix files generated from Cell Ranger in one zip file.", "40 dpf zebrafish ovaries", null, "Somatic ovary cells were dissociated using a modification of Elkouby and Mullins 2016. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfp transgenic fish Leu et al. 2010 were dissected and stored in a LoBind tube containing 2mL of L15. Tissues were minced with microdissection scissors into < 1 mm pieces. post the tissue had settled to the bottom of the tube the media was replaced with 5mL of digestive enzyme mixture 3 mg/mL collagenase I Cat.No. C0130; Sigma Aldrich 3 mg/mL collagenase II Cat.No. C6885; Sigma Aldrich and 1.6 mg/mL hyaluronidase Cat.No. H4272; Sigma Aldrich in L15 and incubated on an orbital rotator at room temperature . The suspension was monitored every 10 mins until a minimal number of cell clumps were observed 30 min.. Cells were centrifuged for 3 mins at 300 x g and resuspended in 5 mL of 5x TrypLE Cat.No. A1217701; Thermo Fisher in L15 and incubated on an orbital rotator at room temperature for 15 min. The trypsin reaction was stopped by adding 500 \u00b5L of 2.8 mg/mL trypsin inhibitor in L15 and incubated on an orbital rotator at room temperature for 1 min. The cell suspension was then added to 25 ml of L15 in a 50 ml conical tube to dilute the trypsin and centrifuged for 3 min at 300 x g. The cell pellet was resuspended and washed two times with 5 mL of L15 using a P1000 pipette and centrifuged for 3 mins at 300 x g. The cell pellet was then resuspended and filtered as described above. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly barcoded 3\u2019 single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell 3\u2019 Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer\u2019s recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent. The libraries were quantified by fluorometry on a Qubit instrument LifeTechnologies and by qPCR with a Kapa Library Quant kit Kapa Biosystems prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer Illumina with paired end 100 bp reads.", "Zebrafish husbandry was performed as previously described Westerfield 2000.", "cell type:Ovary cells|genotype:AB wildtype", "GSM5739895", "GSM5739895: 40 dpf zebrafish ovaries cells zx2; Danio rerio; ssRNA seq", "GSM5739895 r1", "GSM5739895", "1", "Somatic ovary cells were dissociated using a modification of Elkouby and Mullins 2016. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfp transgenic fish Leu et al. 2010 were dissected and stored in a LoBind tube containing 2mL of L15. Tissues were minced with microdissection scissors into < 1 mm pieces. post the tissue had settled to the bottom of the tube the media was replaced with 5mL of digestive enzyme mixture 3 mg/mL collagenase I Cat.No. C0130; Sigma Aldrich 3 mg/mL collagenase II Cat.No. C6885; Sigma Aldrich and 1.6 mg/mL hyaluronidase Cat.No. H4272; Sigma Aldrich in L15 and incubated on an orbital rotator at room temperature . The suspension was monitored every 10 mins until a minimal number of cell clumps were observed 30 min.. Cells were centrifuged for 3 mins at 300 x g and resuspended in 5 mL of 5x TrypLE Cat.No. A1217701; Thermo Fisher in L15 and incubated on an orbital rotator at room temperature for 15 min. The trypsin reaction was stopped by adding 500 \u00b5L of 2.8 mg/mL trypsin inhibitor in L15 and incubated on an orbital rotator at room temperature for 1 min. The cell suspension was then added to 25 ml of L15 in a 50 ml conical tube to dilute the trypsin and centrifuged for 3 min at 300 x g. The cell pellet was resuspended and washed two times with 5 mL of L15 using a P1000 pipette and centrifuged for 3 mins at 300 x g. The cell pellet was then resuspended and filtered as described above. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly barcoded three prime single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell three prime Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer's recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent. The libraries were quantified by fluorometry on a Qubit instrument LifeTechnologies and by qPCR with a Kapa Library Quant kit Kapa Biosystems prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer Illumina with paired end 100 bp reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP351377", null, null, "40dpf_ova_1_S146_L004_R2_001.fastq.gz 40dpf_ova_1_S146_L004_R1_001.fastq.gz", "fastq fastq", 109753922368.0, 363423584.0, "GSM5739895 r1", "0:151 1:151", "A:26550231612;C:18985464266;G:18837331344;T:45367377509;N:13517637", 151, 151, null, null, 26550231612, 18985464266, 18837331344, 45367377509, 13517637, "SRX13441049", "SRS11340478", "SRA1345465", "Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis", "Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis", 2, 9e-05, 0.84548, 8e-05, 0.09287, 1.0, 0.78589, null, 0.54454, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-17", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [67760, "SRR17262952", "SRX13441048", "SRS11340477", "SRP351377", "PRJNA789855", "Single cell transcriptome reveals insights into the development and function of the zebrafish ovary", "GSE191137", "Transcriptome Analysis", "Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development yet there are still significant gaps in our understanding of the genes that regulate gonad development sex and reproduction. Unlike the development of many organs such as the brain and heart that form during the first few days of development zebrafish gonads do not begin to form until the larval stage =5 dpf. Thus forward genetic screens have identified very few genes required for gonad development. In addition bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations we have used single cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10 658 germ cells and 14 431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types including follicle cells theca cells and interstitial stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance we determined the location of these cell subpopulations within the ovary. Finally for select examples we used gene knockout experiments to determine the role of newly identified genes. Our results reveal novel insights into ovarian development and function and the sequencing information will provide a valuable resource for future studies. Overall design: Single cell RNA sequencing of 40 dpf zebrafish ovaries", null, "pubmed:35588359", null, "40 dpf zebrafish ovaries cells sorted germ cells", "GSM5739894", null, "tissue:40 dpf zebrafish ovaries|cell type:Germ cells|genotype:AB wildtype", "40 dpf zebrafish ovaries cells sorted germ cells", "A General Transfer Format GTF gene annotation filerelease 96 for the GRCz11 zebrafish genome was downloaded from Ensembl Genome Browser and filtered using the \u201cmkgtf\u201d function in Cell Ranger v3.0.2; 10x Genomic to retain the following attributes: protein coding lincRNA and antisense. A genome reference file was generated with Cell Ranger\u2019s \u201cmkref\u201d function using the GRCz11 zebrafish genome obtained from the Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file. GRCz11 zebrafish genome FASTQ file from Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file described above were used to generate the count file using the \u201ccount\u201d function in Cell Ranger v3.0.2; 10x Genomic. \u201cexpect cells\u201d was setted to 10000 based on estimated cell recovery.\u00a0 Genome build: GRCz11 Supplementary files format and content: Filtered or raw matrix files generated from Cell Ranger in one zip file.", "40 dpf zebrafish ovaries", null, "Germ cells were dissociated from the somatic gonad using a modification of Blokhina et al. 2019. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfpuc02 transgenic fish Leu et al. 2010 and stored in a LoBind tube Cat.No. 0030108302; Eppendorf containing 2 mL of L15 mediumCat.No. L5520; Sigma Aldrich. The tissue was minced with small scissors into <1 mm pieces. 200 \u00b5L of 20 mg/mL of type 2 collagenase in L15 Cat.No. NC9870009; Worthington were added and incubated on an orbital rotator at 28\u00b0C for 35 min. The cell suspension was then gently passed through a 23g needle five times to break up large cell clumps. 200 \u00b5L of 7 mg/mL trypsin Cat.No. LS003708; Worthington in L15 were added and incubated on an orbital rotator for 10 min or until a minimal amount of cell clumps was observed. The trypsin reaction was stopped by adding 500 \u00b5L of 20 mg/mL trypsin Inhibitor Cat.No. 100612; MP Biomedicals in L15. The cells were centrifuged for 3 min at 300 x g and the supernatant carefully removed. The cells were then resuspended and washed two times with 5 mL of L15 using a P1000 pipette tip and then centrifuged for 3 min at 300 x g. Cells were then resuspended in 1 mL L15 and filtered through a 100 \u00b5m nylon filter Cat.No. 431752; Corning and then through a 40 \u00b5m nylon filter Cat.No. 431750; Corning to remove cell clumps. The filtrate was centrifuged for 3 min at 300 x g and resuspended in 1 mL of 50 mg/mL BSA Cat.No. A8806; Sigma Aldrich in Phosphate Buffered Saline. Cell viability and number were assessed using propidium iodine Cat. No. P1304MP; Thermo Fisher and Hoechst 33342 Cat.No. H3570; Thermo Fisher staining on a Fuchs Rosenthal hemocytometer Cat.No. DHC F01; Incyto. Following cell dissociation of Tgpiwil1:egfp transgenic ovaries GFP+ germ cells were sorted using a MoFlo Astrios EQ Cell Sorter Beckman Coulter with a 70 \u00b5m nozzle. Cells were sorted using side scatter and GFP purify to identify single germ cells. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly barcoded 3\u2019 single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell 3\u2019 Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer\u2019s recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent. The libraries were quantified by fluorometry on a Qubit instrument LifeTechnologies and by qPCR with a Kapa Library Quant kit Kapa Biosystems prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer Illumina with paired end 100 bp reads.", "Zebrafish husbandry was performed as previously described Westerfield 2000.", "cell type:Germ cells|genotype:AB wildtype", "GSM5739894", "GSM5739894: 40 dpf zebrafish ovaries cells sorted germ cells; Danio rerio; ssRNA seq", "GSM5739894 r1", "GSM5739894", "1", "Germ cells were dissociated from the somatic gonad using a modification of Blokhina et al. 2019. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfpuc02 transgenic fish Leu et al. 2010 and stored in a LoBind tube Cat.No. 0030108302; Eppendorf containing 2 mL of L15 mediumCat.No. L5520; Sigma Aldrich. The tissue was minced with small scissors into <1 mm pieces. 200 \u00b5L of 20 mg/mL of type 2 collagenase in L15 Cat.No. NC9870009; Worthington were added and incubated on an orbital rotator at 28\u00b0C for 35 min. The cell suspension was then gently passed through a 23g needle five times to break up large cell clumps. 200 \u00b5L of 7 mg/mL trypsin Cat.No. LS003708; Worthington in L15 were added and incubated on an orbital rotator for 10 min or until a minimal amount of cell clumps was observed. The trypsin reaction was stopped by adding 500 \u00b5L of 20 mg/mL trypsin Inhibitor Cat.No. 100612; MP Biomedicals in L15. The cells were centrifuged for 3 min at 300 x g and the supernatant carefully removed. The cells were then resuspended and washed two times with 5 mL of L15 using a P1000 pipette tip and then centrifuged for 3 min at 300 x g. Cells were then resuspended in 1 mL L15 and filtered through a 100 \u00b5m nylon filter Cat.No. 431752; Corning and then through a 40 \u00b5m nylon filter Cat.No. 431750; Corning to remove cell clumps. The filtrate was centrifuged for 3 min at 300 x g and resuspended in 1 mL of 50 mg/mL BSA Cat.No. A8806; Sigma Aldrich in Phosphate Buffered Saline. Cell viability and number were assessed using propidium iodine Cat. No. P1304MP; Thermo Fisher and Hoechst 33342 Cat.No. H3570; Thermo Fisher staining on a Fuchs Rosenthal hemocytometer Cat.No. DHC F01; Incyto. Following cell dissociation of Tgpiwil1:egfp transgenic ovaries GFP+ germ cells were sorted using a MoFlo Astrios EQ Cell Sorter Beckman Coulter with a 70 \u00b5m nozzle. Cells were sorted using side scatter and GFP purify to identify single germ cells. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly barcoded three prime single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell three prime Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer's recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent. The libraries were quantified by fluorometry on a Qubit instrument LifeTechnologies and by qPCR with a Kapa Library Quant kit Kapa Biosystems prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer Illumina with paired end 100 bp reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP351377", null, null, "40d_Germ_S67_L007_R1_001.fastq.gz 40d_Germ_S67_L007_R2_001.fastq.gz", "fastq fastq", 97157899800.0, 321714900.0, "GSM5739894 r1", "0:151 1:151", "A:25130180865;C:15016964022;G:17255588720;T:39751154898;N:4011295", 151, 151, null, null, 25130180865, 15016964022, 17255588720, 39751154898, 4011295, "SRX13441048", "SRS11340477", "SRA1345465", "Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis", "Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis", 2, 0.00058, 0.83872, 0.00016, 0.05616, 0.99989, 0.77873, 0.4, 0.51521, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-17", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68139, "SRR17630961", "SRX13799339", "SRS11681628", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "scRNA seq TCDD testes rep 2", "GSM5820556", null, "tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension", "scRNA seq TCDD testes rep 2", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820556", "GSM5820556: scRNA seq TCDD testes rep 2; Danio rerio; RNA Seq", "GSM5820556 r1", "GSM5820556", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, "loader:fastq load.py", "SC_T2_S5_L001_I1_001.fastq.gz SC_T2_S5_L001_R1_001.fastq.gz SC_T2_S5_L001_R2_001.fastq.gz", "fastq fastq fastq", 11262679659.0, 88682517.0, "GSM5820556 r1", "0:8 1:28 2:91", "A:2329833844;C:1736580490;G:2028746154;T:1974513391;N:435168", 8, 28, 91, null, 2329833844, 1736580490, 2028746154, 1974513391, 435168, "SRX13799339", "SRS11681628", "SRA1357269", "University of Florida", "University of Florida", 1, 0.89663, null, 0.23137, null, 0.75166, null, 0.55299, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68140, "SRR17630962", "SRX13799339", "SRS11681628", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "scRNA seq TCDD testes rep 2", "GSM5820556", null, "tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension", "scRNA seq TCDD testes rep 2", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820556", "GSM5820556: scRNA seq TCDD testes rep 2; Danio rerio; RNA Seq", "GSM5820556 r1", "GSM5820556", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, "loader:fastq load.py", "SC_T2_S5_L002_I1_001.fastq.gz SC_T2_S5_L002_R1_001.fastq.gz SC_T2_S5_L002_R2_001.fastq.gz", "fastq fastq fastq", 11384315052.0, 89640276.0, "GSM5820556 r2", "0:8 1:28 2:91", "A:2351124750;C:1758531934;G:2054452297;T:1992620872;N:535263", 8, 28, 91, null, 2351124750, 1758531934, 2054452297, 1992620872, 535263, "SRX13799339", "SRS11681628", "SRA1357269", "University of Florida", "University of Florida", 1, 0.89836, null, 0.23263, null, 0.7543, null, 0.55738, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68141, "SRR17630963", "SRX13799338", "SRS11681627", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "scRNA seq TCDD testes rep 1", "GSM5820555", null, "tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension", "scRNA seq TCDD testes rep 1", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820555", "GSM5820555: scRNA seq TCDD testes rep 1; Danio rerio; RNA Seq", "GSM5820555 r1", "GSM5820555", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, "loader:fastq load.py", "SC_T1_S4_L001_I1_001.fastq.gz SC_T1_S4_L001_R1_001.fastq.gz SC_T1_S4_L001_R2_001.fastq.gz", "fastq fastq fastq", 10978768873.0, 86446999.0, "GSM5820555 r1", "0:8 1:28 2:91", "A:2363149906;C:1616901304;G:1945888469;T:1940298056;N:439174", 8, 28, 91, null, 2363149906, 1616901304, 1945888469, 1940298056, 439174, "SRX13799338", "SRS11681627", "SRA1357269", "University of Florida", "University of Florida", 1, 0.87562, null, 0.208, null, 0.75511, null, 0.5329, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68142, "SRR17630964", "SRX13799338", "SRS11681627", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "scRNA seq TCDD testes rep 1", "GSM5820555", null, "tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension", "scRNA seq TCDD testes rep 1", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820555", "GSM5820555: scRNA seq TCDD testes rep 1; Danio rerio; RNA Seq", "GSM5820555 r1", "GSM5820555", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, "loader:fastq load.py", "SC_T1_S4_L002_I1_001.fastq.gz SC_T1_S4_L002_R1_001.fastq.gz SC_T1_S4_L002_R2_001.fastq.gz", "fastq fastq fastq", 11084990022.0, 87283386.0, "GSM5820555 r2", "0:8 1:28 2:91", "A:2382115862;C:1635424114;G:1968060449;T:1956671635;N:516066", 8, 28, 91, null, 2382115862, 1635424114, 1968060449, 1956671635, 516066, "SRX13799338", "SRS11681627", "SRA1357269", "University of Florida", "University of Florida", 1, 0.8745, null, 0.20808, null, 0.7585, null, 0.52692, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68143, "SRR17630965", "SRX13799337", "SRS11681626", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "scRNA seq control testes rep 3", "GSM5820554", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "scRNA seq control testes rep 3", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820554", "GSM5820554: scRNA seq control testes rep 3; Danio rerio; RNA Seq", "GSM5820554 r1", "GSM5820554", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, "loader:fastq load.py", "SC_C3_S3_L001_I1_001.fastq.gz SC_C3_S3_L001_R1_001.fastq.gz SC_C3_S3_L001_R2_001.fastq.gz", "fastq fastq fastq", 11736916836.0, 92416668.0, "GSM5820554 r1", "0:8 1:28 2:91", "A:2491182657;C:1749727321;G:2001921423;T:2166620469;N:464918", 8, 28, 91, null, 2491182657, 1749727321, 2001921423, 2166620469, 464918, "SRX13799337", "SRS11681626", "SRA1357269", "University of Florida", "University of Florida", 1, 0.89927, null, 0.17983, null, 0.71601, null, 0.52261, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68144, "SRR17630966", "SRX13799337", "SRS11681626", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "scRNA seq control testes rep 3", "GSM5820554", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "scRNA seq control testes rep 3", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820554", "GSM5820554: scRNA seq control testes rep 3; Danio rerio; RNA Seq", "GSM5820554 r1", "GSM5820554", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, "loader:fastq load.py", "SC_C3_S3_L002_I1_001.fastq.gz SC_C3_S3_L002_R1_001.fastq.gz SC_C3_S3_L002_R2_001.fastq.gz", "fastq fastq fastq", 11862480339.0, 93405357.0, "GSM5820554 r2", "0:8 1:28 2:91", "A:2515246562;C:1770645118;G:2026263526;T:2187182415;N:549866", 8, 28, 91, null, 2515246562, 1770645118, 2026263526, 2187182415, 549866, "SRX13799337", "SRS11681626", "SRA1357269", "University of Florida", "University of Florida", 1, 0.89922, null, 0.1803, null, 0.71419, null, 0.52093, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68145, "SRR17630967", "SRX13799336", "SRS11681625", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "scRNA seq control testes rep 2", "GSM5820553", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "scRNA seq control testes rep 2", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820553", "GSM5820553: scRNA seq control testes rep 2; Danio rerio; RNA Seq", "GSM5820553 r1", "GSM5820553", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, "loader:fastq load.py", "SC_C2_S2_L001_I1_001.fastq.gz SC_C2_S2_L001_R1_001.fastq.gz SC_C2_S2_L001_R2_001.fastq.gz", "fastq fastq fastq", 11597196897.0, 91316511.0, "GSM5820553 r1", "0:8 1:28 2:91", "A:2441188567;C:1731265684;G:2062239362;T:2074648513;N:460375", 8, 28, 91, null, 2441188567, 1731265684, 2062239362, 2074648513, 460375, "SRX13799336", "SRS11681625", "SRA1357269", "University of Florida", "University of Florida", 1, 0.87524, null, 0.22302, null, 0.75893, null, 0.55047, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68146, "SRR17630968", "SRX13799336", "SRS11681625", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "scRNA seq control testes rep 2", "GSM5820553", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "scRNA seq control testes rep 2", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820553", "GSM5820553: scRNA seq control testes rep 2; Danio rerio; RNA Seq", "GSM5820553 r1", "GSM5820553", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, "loader:fastq load.py", "SC_C2_S2_L002_I1_001.fastq.gz SC_C2_S2_L002_R1_001.fastq.gz SC_C2_S2_L002_R2_001.fastq.gz", "fastq fastq fastq", 11724309038.0, 92317394.0, "GSM5820553 r2", "0:8 1:28 2:91", "A:2464546352;C:1753014248;G:2088164317;T:2094592155;N:565782", 8, 28, 91, null, 2464546352, 1753014248, 2088164317, 2094592155, 565782, "SRX13799336", "SRS11681625", "SRA1357269", "University of Florida", "University of Florida", 1, 0.87809, null, 0.22205, null, 0.75272, null, 0.55306, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68147, "SRR17630969", "SRX13799335", "SRS11681624", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "scRNA seq control testes rep 1", "GSM5820552", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "scRNA seq control testes rep 1", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820552", "GSM5820552: scRNA seq control testes rep 1; Danio rerio; RNA Seq", "GSM5820552 r1", "GSM5820552", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, "loader:fastq load.py", "SC_C1_S1_L001_I1_001.fastq.gz SC_C1_S1_L001_R1_001.fastq.gz SC_C1_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 11845124392.0, 93268696.0, "GSM5820552 r1", "0:8 1:28 2:91", "A:2554285232;C:1757437977;G:2060709302;T:2114543968;N:474857", 8, 28, 91, null, 2554285232, 1757437977, 2060709302, 2114543968, 474857, "SRX13799335", "SRS11681624", "SRA1357269", "University of Florida", "University of Florida", 1, 0.89006, null, 0.16375, null, 0.74714, null, 0.51816, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68148, "SRR17630970", "SRX13799335", "SRS11681624", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "scRNA seq control testes rep 1", "GSM5820552", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "scRNA seq control testes rep 1", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820552", "GSM5820552: scRNA seq control testes rep 1; Danio rerio; RNA Seq", "GSM5820552 r1", "GSM5820552", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, "loader:fastq load.py", "SC_C1_S1_L002_I1_001.fastq.gz SC_C1_S1_L002_R1_001.fastq.gz SC_C1_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 11974253293.0, 94285459.0, "GSM5820552 r2", "0:8 1:28 2:91", "A:2577816465;C:1779883368;G:2086781140;T:2134925822;N:569974", 8, 28, 91, null, 2577816465, 1779883368, 2086781140, 2134925822, 569974, "SRX13799335", "SRS11681624", "SRA1357269", "University of Florida", "University of Florida", 1, 0.89007, null, 0.16458, null, 0.74986, null, 0.52005, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68149, "SRR17630939", "SRX13799350", "SRS11681639", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "dissociated bulk seq control testes rep 3 compared to intact control testes", "GSM5820567", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "dissociated bulk seq control testes rep 3 compared to intact control testes", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820567", "GSM5820567: dissociated bulk seq control testes rep 3 compared to intact control testes; Danio rerio; RNA Seq", "GSM5820567 r1", "GSM5820567", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "I_C3_S14_L001_R1_001.fastq.gz", "fastq", 1847371623.0, 36222973.0, "GSM5820567 r1", "0:51 1:0", "A:535632392;C:366862698;G:429979337;T:514873991;N:23205", 51, 0, null, null, 535632392, 366862698, 429979337, 514873991, 23205, "SRX13799350", "SRS11681639", "SRA1357269", "University of Florida", "University of Florida", 1, 0.87212, null, 0.1857, null, 0.69372, null, 0.56886, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68150, "SRR17630940", "SRX13799350", "SRS11681639", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "dissociated bulk seq control testes rep 3 compared to intact control testes", "GSM5820567", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "dissociated bulk seq control testes rep 3 compared to intact control testes", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820567", "GSM5820567: dissociated bulk seq control testes rep 3 compared to intact control testes; Danio rerio; RNA Seq", "GSM5820567 r1", "GSM5820567", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "I_C3_S14_L002_R1_001.fastq.gz", "fastq", 1823230824.0, 35749624.0, "GSM5820567 r2", "0:51 1:0", "A:529009592;C:361883074;G:424030274;T:508289743;N:18141", 51, 0, null, null, 529009592, 361883074, 424030274, 508289743, 18141, "SRX13799350", "SRS11681639", "SRA1357269", "University of Florida", "University of Florida", 1, 0.8708, null, 0.18714, null, 0.6955, null, 0.5716, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68151, "SRR17630941", "SRX13799349", "SRS11681638", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "dissociated bulk seq control testes rep 2 compared to intact control testes", "GSM5820566", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "dissociated bulk seq control testes rep 2 compared to intact control testes", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820566", "GSM5820566: dissociated bulk seq control testes rep 2 compared to intact control testes; Danio rerio; RNA Seq", "GSM5820566 r1", "GSM5820566", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "I_C2_S13_L001_R1_001.fastq.gz", "fastq", 536561208.0, 10520808.0, "GSM5820566 r1", "0:51 1:0", "A:163430759;C:106016694;G:122059136;T:145048023;N:6596", 51, 0, null, null, 163430759, 106016694, 122059136, 145048023, 6596, "SRX13799349", "SRS11681638", "SRA1357269", "University of Florida", "University of Florida", 1, 0.83573, null, 0.2005, null, 0.71056, null, 0.52825, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68152, "SRR17630942", "SRX13799349", "SRS11681638", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "dissociated bulk seq control testes rep 2 compared to intact control testes", "GSM5820566", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "dissociated bulk seq control testes rep 2 compared to intact control testes", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820566", "GSM5820566: dissociated bulk seq control testes rep 2 compared to intact control testes; Danio rerio; RNA Seq", "GSM5820566 r1", "GSM5820566", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "I_C2_S13_L002_R1_001.fastq.gz", "fastq", 530978238.0, 10411338.0, "GSM5820566 r2", "0:51 1:0", "A:161875304;C:104815309;G:120705456;T:143576873;N:5296", 51, 0, null, null, 161875304, 104815309, 120705456, 143576873, 5296, "SRX13799349", "SRS11681638", "SRA1357269", "University of Florida", "University of Florida", 1, 0.83663, null, 0.19964, null, 0.71104, null, 0.54143, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68153, "SRR17630943", "SRX13799348", "SRS11681637", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "dissociated bulk seq control testes rep 1 compared to intact control testes", "GSM5820565", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "dissociated bulk seq control testes rep 1 compared to intact control testes", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820565", "GSM5820565: dissociated bulk seq control testes rep 1 compared to intact control testes; Danio rerio; RNA Seq", "GSM5820565 r1", "GSM5820565", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "I_C1_S12_L001_R1_001.fastq.gz", "fastq", 523779282.0, 10270182.0, "GSM5820565 r1", "0:51 1:0", "A:155891194;C:103400919;G:120028554;T:144451616;N:6999", 51, 0, null, null, 155891194, 103400919, 120028554, 144451616, 6999, "SRX13799348", "SRS11681637", "SRA1357269", "University of Florida", "University of Florida", 1, 0.85957, null, 0.19557, null, 0.69501, null, 0.56637, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68154, "SRR17630944", "SRX13799348", "SRS11681637", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "dissociated bulk seq control testes rep 1 compared to intact control testes", "GSM5820565", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "dissociated bulk seq control testes rep 1 compared to intact control testes", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820565", "GSM5820565: dissociated bulk seq control testes rep 1 compared to intact control testes; Danio rerio; RNA Seq", "GSM5820565 r1", "GSM5820565", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "I_C1_S12_L002_R1_001.fastq.gz", "fastq", 516901983.0, 10135333.0, "GSM5820565 r2", "0:51 1:0", "A:153923180;C:101966413;G:118359254;T:142647450;N:5686", 51, 0, null, null, 153923180, 101966413, 118359254, 142647450, 5686, "SRX13799348", "SRS11681637", "SRA1357269", "University of Florida", "University of Florida", 1, 0.85795, null, 0.19403, null, 0.69627, null, 0.57159, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68155, "SRR17630945", "SRX13799347", "SRS11681636", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq intact control testes rep 3", "GSM5820564", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes", "bulk seq intact control testes rep 3", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes", "GSM5820564", "GSM5820564: bulk seq intact control testes rep 3; Danio rerio; RNA Seq", "GSM5820564 r1", "GSM5820564", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "D_C3_S16_L001_R1_001.fastq.gz", "fastq", 1673456880.0, 32812880.0, "GSM5820564 r1", "0:51 1:0", "A:496655744;C:334242155;G:387205466;T:455330132;N:23383", 51, 0, null, null, 496655744, 334242155, 387205466, 455330132, 23383, "SRX13799347", "SRS11681636", "SRA1357269", "University of Florida", "University of Florida", 1, 0.8707, null, 0.22045, null, 0.71078, null, 0.60605, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68156, "SRR17630946", "SRX13799347", "SRS11681636", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq intact control testes rep 3", "GSM5820564", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes", "bulk seq intact control testes rep 3", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes", "GSM5820564", "GSM5820564: bulk seq intact control testes rep 3; Danio rerio; RNA Seq", "GSM5820564 r1", "GSM5820564", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "D_C3_S16_L002_R1_001.fastq.gz", "fastq", 1647184587.0, 32297737.0, "GSM5820564 r2", "0:51 1:0", "A:489182217;C:328774657;G:380849646;T:448358863;N:19204", 51, 0, null, null, 489182217, 328774657, 380849646, 448358863, 19204, "SRX13799347", "SRS11681636", "SRA1357269", "University of Florida", "University of Florida", 1, 0.87032, null, 0.22081, null, 0.71261, null, 0.60917, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68157, "SRR17630947", "SRX13799346", "SRS11681635", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes", "GSM5820561", null, "tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension", "bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820561", "GSM5820561: bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes; Danio rerio; RNA Seq", "GSM5820561 r1", "GSM5820561", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "BS_T2_S7_L001_R1_001.fastq.gz", "fastq", 1583815608.0, 31055208.0, "GSM5820561 r1", "0:51 1:0", "A:447529477;C:312467507;G:374130013;T:449667219;N:21392", 51, 0, null, null, 447529477, 312467507, 374130013, 449667219, 21392, "SRX13799346", "SRS11681635", "SRA1357269", "University of Florida", "University of Florida", 1, 0.86982, null, 0.25275, null, 0.70774, null, 0.5721, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68158, "SRR17630948", "SRX13799346", "SRS11681635", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes", "GSM5820561", null, "tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension", "bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820561", "GSM5820561: bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes; Danio rerio; RNA Seq", "GSM5820561 r1", "GSM5820561", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "BS_T2_S7_L002_R1_001.fastq.gz", "fastq", 1564087941.0, 30668391.0, "GSM5820561 r2", "0:51 1:0", "A:442209708;C:308400147;G:369229792;T:444230646;N:17648", 51, 0, null, null, 442209708, 308400147, 369229792, 444230646, 17648, "SRX13799346", "SRS11681635", "SRA1357269", "University of Florida", "University of Florida", 1, 0.87035, null, 0.2527, null, 0.70682, null, 0.57673, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68159, "SRR17630949", "SRX13799345", "SRS11681634", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq intact control testes rep 2", "GSM5820563", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes", "bulk seq intact control testes rep 2", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes", "GSM5820563", "GSM5820563: bulk seq intact control testes rep 2; Danio rerio; RNA Seq", "GSM5820563 r1", "GSM5820563", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "D_C2_S15_L001_R1_001.fastq.gz", "fastq", 1493724669.0, 29288719.0, "GSM5820563 r1", "0:51 1:0", "A:445588125;C:289131502;G:340459665;T:418525850;N:19527", 51, 0, null, null, 445588125, 289131502, 340459665, 418525850, 19527, "SRX13799345", "SRS11681634", "SRA1357269", "University of Florida", "University of Florida", 1, 0.85779, null, 0.20343, null, 0.69887, null, 0.56808, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68160, "SRR17630950", "SRX13799345", "SRS11681634", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq intact control testes rep 2", "GSM5820563", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes", "bulk seq intact control testes rep 2", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes", "GSM5820563", "GSM5820563: bulk seq intact control testes rep 2; Danio rerio; RNA Seq", "GSM5820563 r1", "GSM5820563", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "D_C2_S15_L002_R1_001.fastq.gz", "fastq", 1475012565.0, 28921815.0, "GSM5820563 r2", "0:51 1:0", "A:440339743;C:285301590;G:335922618;T:413432380;N:16234", 51, 0, null, null, 440339743, 285301590, 335922618, 413432380, 16234, "SRX13799345", "SRS11681634", "SRA1357269", "University of Florida", "University of Florida", 1, 0.85783, null, 0.20221, null, 0.70102, null, 0.57116, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68161, "SRR17630957", "SRX13799344", "SRS11681633", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq intact control testes rep 1", "GSM5820562", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes", "bulk seq intact control testes rep 1", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes", "GSM5820562", "GSM5820562: bulk seq intact control testes rep 1; Danio rerio; RNA Seq", "GSM5820562 r1", "GSM5820562", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "D_C1_S2_L001_R1_001.fastq.gz", "fastq", 1783515696.0, 34970896.0, "GSM5820562 r1", "0:51 1:0", "A:503613569;C:361648917;G:420357217;T:497872153;N:23840", 51, 0, null, null, 503613569, 361648917, 420357217, 497872153, 23840, "SRX13799344", "SRS11681633", "SRA1357269", "University of Florida", "University of Florida", 1, 0.88797, null, 0.22692, null, 0.69522, null, 0.57676, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68162, "SRR17630958", "SRX13799344", "SRS11681633", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq intact control testes rep 1", "GSM5820562", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes", "bulk seq intact control testes rep 1", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes", "GSM5820562", "GSM5820562: bulk seq intact control testes rep 1; Danio rerio; RNA Seq", "GSM5820562 r1", "GSM5820562", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "D_C1_S2_L002_R1_001.fastq.gz", "fastq", 1758067563.0, 34471913.0, "GSM5820562 r2", "0:51 1:0", "A:496669418;C:356271536;G:414028881;T:491077933;N:19795", 51, 0, null, null, 496669418, 356271536, 414028881, 491077933, 19795, "SRX13799344", "SRS11681633", "SRA1357269", "University of Florida", "University of Florida", 1, 0.88843, null, 0.22792, null, 0.69619, null, 0.57488, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68163, "SRR17630951", "SRX13799343", "SRS11681632", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes", "GSM5820560", null, "tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension", "bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820560", "GSM5820560: bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes; Danio rerio; RNA Seq", "GSM5820560 r1", "GSM5820560", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "BS_T1_S6_L001_R1_001.fastq.gz", "fastq", 3525780042.0, 69132942.0, "GSM5820560 r1", "0:51 1:0", "A:1025376436;C:691776192;G:829134506;T:979443851;N:49057", 51, 0, null, null, 1025376436, 691776192, 829134506, 979443851, 49057, "SRX13799343", "SRS11681632", "SRA1357269", "University of Florida", "University of Florida", 1, 0.86505, null, 0.30929, null, 0.72074, null, 0.6373, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68164, "SRR17630952", "SRX13799343", "SRS11681632", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes", "GSM5820560", null, "tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension", "bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820560", "GSM5820560: bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes; Danio rerio; RNA Seq", "GSM5820560 r1", "GSM5820560", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "BS_T1_S6_L002_R1_001.fastq.gz", "fastq", 3479799156.0, 68231356.0, "GSM5820560 r2", "0:51 1:0", "A:1012622841;C:682305804;G:817948602;T:966881210;N:40699", 51, 0, null, null, 1012622841, 682305804, 817948602, 966881210, 40699, "SRX13799343", "SRS11681632", "SRA1357269", "University of Florida", "University of Florida", 1, 0.86392, null, 0.30933, null, 0.71863, null, 0.63706, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68165, "SRR17630953", "SRX13799342", "SRS11681631", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq control testes rep 2 to be compared to scRNA seq control testes", "GSM5820558", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "bulk seq control testes rep 2 to be compared to scRNA seq control testes", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820558", "GSM5820558: bulk seq control testes rep 2 to be compared to scRNA seq control testes; Danio rerio; RNA Seq", "GSM5820558 r1", "GSM5820558", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "BS_C2_S8_L001_R1_001.fastq.gz", "fastq", 1264687137.0, 24797787.0, "GSM5820558 r1", "0:51 1:0", "A:361072135;C:254984535;G:302043978;T:346569617;N:16872", 51, 0, null, null, 361072135, 254984535, 302043978, 346569617, 16872, "SRX13799342", "SRS11681631", "SRA1357269", "University of Florida", "University of Florida", 1, 0.86972, null, 0.31888, null, 0.71561, null, 0.6242, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68166, "SRR17630954", "SRX13799342", "SRS11681631", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq control testes rep 2 to be compared to scRNA seq control testes", "GSM5820558", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "bulk seq control testes rep 2 to be compared to scRNA seq control testes", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820558", "GSM5820558: bulk seq control testes rep 2 to be compared to scRNA seq control testes; Danio rerio; RNA Seq", "GSM5820558 r1", "GSM5820558", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "BS_C2_S8_L002_R1_001.fastq.gz", "fastq", 1247134620.0, 24453620.0, "GSM5820558 r2", "0:51 1:0", "A:356333809;C:251264657;G:297639103;T:341883185;N:13866", 51, 0, null, null, 356333809, 251264657, 297639103, 341883185, 13866, "SRX13799342", "SRS11681631", "SRA1357269", "University of Florida", "University of Florida", 1, 0.8683, null, 0.31544, null, 0.71332, null, 0.62605, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68167, "SRR17630955", "SRX13799341", "SRS11681630", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq control testes rep 3 to be compared to scRNA seq control testes", "GSM5820559", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "bulk seq control testes rep 3 to be compared to scRNA seq control testes", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820559", "GSM5820559: bulk seq control testes rep 3 to be compared to scRNA seq control testes; Danio rerio; RNA Seq", "GSM5820559 r1", "GSM5820559", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "BS_C3_S5_L001_R1_001.fastq.gz", "fastq", 1298470557.0, 25460207.0, "GSM5820559 r1", "0:51 1:0", "A:370125548;C:258465981;G:307735443;T:362125609;N:17976", 51, 0, null, null, 370125548, 258465981, 307735443, 362125609, 17976, "SRX13799341", "SRS11681630", "SRA1357269", "University of Florida", "University of Florida", 1, 0.87017, null, 0.23168, null, 0.7049, null, 0.43404, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68168, "SRR17630956", "SRX13799341", "SRS11681630", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq control testes rep 3 to be compared to scRNA seq control testes", "GSM5820559", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "bulk seq control testes rep 3 to be compared to scRNA seq control testes", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820559", "GSM5820559: bulk seq control testes rep 3 to be compared to scRNA seq control testes; Danio rerio; RNA Seq", "GSM5820559 r1", "GSM5820559", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "BS_C3_S5_L002_R1_001.fastq.gz", "fastq", 1282277445.0, 25142695.0, "GSM5820559 r2", "0:51 1:0", "A:365706822;C:255117242;G:303741803;T:357696714;N:14864", 51, 0, null, null, 365706822, 255117242, 303741803, 357696714, 14864, "SRX13799341", "SRS11681630", "SRA1357269", "University of Florida", "University of Florida", 1, 0.86967, null, 0.23412, null, 0.70447, null, 0.60084, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68169, "SRR17630959", "SRX13799340", "SRS11681629", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq control testes rep 1 to be compared to scRNA seq control testes", "GSM5820557", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "bulk seq control testes rep 1 to be compared to scRNA seq control testes", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820557", "GSM5820557: bulk seq control testes rep 1 to be compared to scRNA seq control testes; Danio rerio; RNA Seq", "GSM5820557 r1", "GSM5820557", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "BS_C1_S4_L001_R1_001.fastq.gz", "fastq", 363711651.0, 7131601.0, "GSM5820557 r1", "0:51 1:0", "A:101645255;C:77359657;G:89895787;T:94805817;N:5135", 51, 0, null, null, 101645255, 77359657, 89895787, 94805817, 5135, "SRX13799340", "SRS11681629", "SRA1357269", "University of Florida", "University of Florida", 1, 0.86049, null, 0.29611, null, 0.72293, null, 0.54071, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [68170, "SRR17630960", "SRX13799340", "SRS11681629", "SRP355202", "PRJNA797655", "Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue", "GSE193758", "Transcriptome Analysis", "Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq control testes rep 1 to be compared to scRNA seq control testes", "GSM5820557", null, "tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "bulk seq control testes rep 1 to be compared to scRNA seq control testes", "Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. \u00a0 Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the \"FindMarkers\" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq", "testes", "Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", "Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27\u00b0C\u2013 30\u00b0C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.", "strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension", "GSM5820557", "GSM5820557: bulk seq control testes rep 1 to be compared to scRNA seq control testes; Danio rerio; RNA Seq", "GSM5820557 r1", "GSM5820557", "1", "Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "BS_C1_S4_L002_R1_001.fastq.gz", "fastq", 358349460.0, 7026460.0, "GSM5820557 r2", "0:51 1:0", "A:100176173;C:76199709;G:88532838;T:93436578;N:4162", 51, 0, null, null, 100176173, 76199709, 88532838, 93436578, 4162, "SRX13799340", "SRS11681629", "SRA1357269", "University of Florida", "University of Florida", 1, 0.86034, null, 0.29588, null, 0.72346, null, 0.54277, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [71018, "SRR21091734", "SRX17106223", "SRS14681693", "SRP392539", "PRJNA870096", "Single cell transcriptome profiling reveals diverse immune cell populations and their responses to viral infection in the spleen of zebrafish", "GSE211396", "Transcriptome Analysis", "Teleost fish are indispensable model organisms for comparative immunology research that should provide fundamental insights into the evolutionary history of vertebrate immunity and eventually lead to an improved understanding of the general principles of immune system design. Although numerous studies on ?sh immunology have been conducted knowledge about the cell types that orchestrate piscine immune systems remains limited. In this study we generated a comprehensive atlas of immune cell types in a zebrafish model on the basis of single cell transcriptome profiling. Overall design: Spleen leukocyte PBS administered control SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated byFicoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:37227178;pubmed:40392591", null, "vaccinated+SVCV scRNAseq", "GSM6469457", null, "source name:Spleen|cell type:leukocyte|tissue:Spleen|strain:AB|age:5 wpf 7 wpf|geo loc name:missing|collection date:missing", "vaccinated+SVCV scRNAseq", "The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files", "Spleen", null, "Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a 62] Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 \u03bcg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "cell type:leukocyte|tissue:Spleen|strain:AB|age:5 wpf 7 wpf", "GSM6469457", "GSM6469457: vaccinated+SVCV scRNAseq; Danio rerio; RNA Seq", "GSM6469457 r1", "GSM6469457", "1", "Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a 62] Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 \u03bcg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP392539", null, null, "vaccinated+SVCV_S1_L001_R1_001.fastq.gz vaccinated+SVCV_S1_L001_R2_001.fastq.gz", "fastq fastq", 54148439576.0, 455028904.0, "GSM6469457 r1", "0:28 1:91", "A:15899568894;C:11520113647;G:12620718617;T:14107197313;N:841105", 28, 91, null, null, 15899568894, 11520113647, 12620718617, 14107197313, 841105, "SRX17106223", "SRS14681693", "SRA1477254", "College of Life Sciences, Zhejiang University", "College of Life Sciences, Zhejiang University", 2, 0.01082, 0.82759, 0.00393, 0.19284, 0.99093, 0.82164, 0.42631, 0.61086, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-08-16", "Juvenile", "Juvenile", "Spleen", "Hematopoietic System"], [71019, "SRR21091735", "SRX17106222", "SRS14681692", "SRP392539", "PRJNA870096", "Single cell transcriptome profiling reveals diverse immune cell populations and their responses to viral infection in the spleen of zebrafish", "GSE211396", "Transcriptome Analysis", "Teleost fish are indispensable model organisms for comparative immunology research that should provide fundamental insights into the evolutionary history of vertebrate immunity and eventually lead to an improved understanding of the general principles of immune system design. Although numerous studies on ?sh immunology have been conducted knowledge about the cell types that orchestrate piscine immune systems remains limited. In this study we generated a comprehensive atlas of immune cell types in a zebrafish model on the basis of single cell transcriptome profiling. Overall design: Spleen leukocyte PBS administered control SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated byFicoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:37227178;pubmed:40392591", null, "SVCV scRNAseq", "GSM6469456", null, "source name:Spleen|cell type:leukocyte|tissue:Spleen|strain:AB|age:5 wpf 7 wpf|geo loc name:missing|collection date:missing", "SVCV scRNAseq", "The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files", "Spleen", null, "Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a 62] Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 \u03bcg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "cell type:leukocyte|tissue:Spleen|strain:AB|age:5 wpf 7 wpf", "GSM6469456", "GSM6469456: SVCV scRNAseq; Danio rerio; RNA Seq", "GSM6469456 r1", "GSM6469456", "1", "Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a 62] Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 \u03bcg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP392539", null, null, "SVCV_S1_L001_R1_001.fastq.gz SVCV_S1_L001_R2_001.fastq.gz", "fastq fastq", 52273900644.0, 439276476.0, "GSM6469456 r1", "0:28 1:91", "A:15161666574;C:11232538299;G:11962650688;T:13914991728;N:2053355", 28, 91, null, null, 15161666574, 11232538299, 11962650688, 13914991728, 2053355, "SRX17106222", "SRS14681692", "SRA1477254", "College of Life Sciences, Zhejiang University", "College of Life Sciences, Zhejiang University", 2, 0.0088, 0.86697, 0.00319, 0.19264, 0.99251, 0.78289, 0.46167, 0.59016, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-08-16", "Juvenile", "Juvenile", "Spleen", "Hematopoietic System"], [71020, "SRR21091736", "SRX17106221", "SRS14681691", "SRP392539", "PRJNA870096", "Single cell transcriptome profiling reveals diverse immune cell populations and their responses to viral infection in the spleen of zebrafish", "GSE211396", "Transcriptome Analysis", "Teleost fish are indispensable model organisms for comparative immunology research that should provide fundamental insights into the evolutionary history of vertebrate immunity and eventually lead to an improved understanding of the general principles of immune system design. Although numerous studies on ?sh immunology have been conducted knowledge about the cell types that orchestrate piscine immune systems remains limited. In this study we generated a comprehensive atlas of immune cell types in a zebrafish model on the basis of single cell transcriptome profiling. Overall design: Spleen leukocyte PBS administered control SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated byFicoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:37227178;pubmed:40392591", null, "PBS scRNAseq", "GSM6469455", null, "source name:Spleen|cell type:leukocyte|tissue:Spleen|strain:AB|age:5 wpf 7 wpf|geo loc name:missing|collection date:missing", "PBS scRNAseq", "The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files", "Spleen", null, "Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a 62] Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 \u03bcg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "cell type:leukocyte|tissue:Spleen|strain:AB|age:5 wpf 7 wpf", "GSM6469455", "GSM6469455: PBS scRNAseq; Danio rerio; RNA Seq", "GSM6469455 r1", "GSM6469455", "1", "Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a 62] Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 \u03bcg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP392539", null, null, "PBS_S1_L001_R1_001.fastq.gz PBS_S1_L001_R2_001.fastq.gz", "fastq fastq", 48934762310.0, 411216490.0, "GSM6469455 r1", "0:28 1:91", "A:14053810123;C:10679154471;G:11495668034;T:12705747178;N:382504", 28, 91, null, null, 14053810123, 10679154471, 11495668034, 12705747178, 382504, "SRX17106221", "SRS14681691", "SRA1477254", "College of Life Sciences, Zhejiang University", "College of Life Sciences, Zhejiang University", 2, 0.00845, 0.84491, 0.00304, 0.17543, 0.99212, 0.78833, 0.45994, 0.6033, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-08-16", "Juvenile", "Juvenile", "Spleen", "Hematopoietic System"], [71807, "SRR22058034", "SRX18039091", "SRS15545647", "SRP404721", "PRJNA894591", "hapln1a+ cells guide coronary growth during heart morphogenesis and regeneration [Dev hapln1a+ cells]", "GSE216646", "Other", "As cardiac regeneration requires new coronary vessels exploring the underlying mechanisms behind revascularization will facilitate the development of regenerative therapies for heart failure. Although multiple tissues and chemokines likely orchestrate coronary formation the interaction between coronary growth and guidance cues remains unclear. Here by applying single cell RNA sequencing scRNA seq analysis we examined gene expression in zebrafish epicardial cells during coronary vascularization and identified hapln1a expressing epicardial cells enriched with vascular regulating genes. Fluorescence reporter assays indicated hapln1a+ cells not only envelop coronary vessels but also form cellular shear structures in ahead of coronary tips. Live imaging analyses demonstrated coronary growth along the pre formed shears with depletion of hapln1a+ cells blocking this growth. Further we found hapln1a+ cells also pre lead coronary tips in the regenerating area and hapln1a+ cell loss inhibits coronary revascularization. To characterize the molecular nature of hapln1a+ cells during coronary growth we profiled hapln1a+ cells in juvenile and regenerating hearts and detected expression of the cell adhesion and migration regulator serpine1 in hapln1a+ cells adjacent to coronary tips. Pharmacological inhibition of serpine1 function blocked coronary vascularization and revascularization. Altogether our studies reveal that hapln1a+ cells are required for coronary production during heart morphogenesis and regeneration by establishing a microenvironment to facilitate guided coronary growth. Overall design: hapln1a+ cells of zebrafish heart were isolated by Fluorescence activated cell sorting FACS according to the presence or absence of eGFP signal and analyzed using scRNAseq.", "parent bioproject:PRJNA894685", "pubmed:37311876", null, "hapln1a+ development scRNAseq", "GSM6685234", null, "source name:heart|strain:EK|tissue:heart|cell type:epicardial cells|age:7 weeks|geo loc name:missing|collection date:missing", "hapln1a+ development scRNAseq", "All processing was performed in 10X Genomics CellRanger v3.1.0 using default parameters Assembly: Danio rerio GRCz11 Supplementary files format and content: Cell Ranger outputs a .mtx file with the feature barcode matrix. This matrix contains the counts of molecules per cell UMI/cell as determined post filtering and counting by Cell Ranger. The matrix is in market exchange format while the row gene or feature and columns cell barcodes are provided as TSV files. File formats are documented in the Cell Ranger software manual", "heart", null, "Hearts were dissected from juvenile zebrafish and ventricles were digested with Liberase TM 0.26 U/ml . Dissociated cells were spun down and live EGFP+ cells were sorted by flow cytometry. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v3.1 protocol 10x Genomics ", null, "strain:EK|tissue:heart|cell type:epicardial cells|cell type sorted:hapln1a+|age:7 weeks", "GSM6685234", "GSM6685234: hapln1a+ development scRNAseq; Danio rerio; RNA Seq", "GSM6685234 r1", "GSM6685234", "1", "Hearts were dissected from juvenile zebrafish and ventricles were digested with Liberase TM 0.26 U/ml . Dissociated cells were spun down and live EGFP+ cells were sorted by flow cytometry. Library was performed according to the manufacter's instructions single cell three prime v3.1 protocol 10x Genomics ", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP404721", null, "loader:fastq load.py", "1_S1_L001_I1_001.fastq.gz 1_S1_L001_R1_001.fastq.gz 1_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 1606360897.0, 12648511.0, "GSM6685234 r1", "0:8 1:28 2:91", "A:339791226;C:243552181;G:266423271;T:301107277;N:140546", 8, 28, 91, null, 339791226, 243552181, 266423271, 301107277, 140546, "SRX18039091", "SRS15545647", "SRA1528482", "Emory University", "Emory University", 1, 0.92176, null, 0.1499, null, 0.81781, null, 0.50927, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-10-26", "Juvenile", "Juvenile", "Heart", "Cardiovascular System"], [71808, "SRR22058035", "SRX18039091", "SRS15545647", "SRP404721", "PRJNA894591", "hapln1a+ cells guide coronary growth during heart morphogenesis and regeneration [Dev hapln1a+ cells]", "GSE216646", "Other", "As cardiac regeneration requires new coronary vessels exploring the underlying mechanisms behind revascularization will facilitate the development of regenerative therapies for heart failure. Although multiple tissues and chemokines likely orchestrate coronary formation the interaction between coronary growth and guidance cues remains unclear. Here by applying single cell RNA sequencing scRNA seq analysis we examined gene expression in zebrafish epicardial cells during coronary vascularization and identified hapln1a expressing epicardial cells enriched with vascular regulating genes. Fluorescence reporter assays indicated hapln1a+ cells not only envelop coronary vessels but also form cellular shear structures in ahead of coronary tips. Live imaging analyses demonstrated coronary growth along the pre formed shears with depletion of hapln1a+ cells blocking this growth. Further we found hapln1a+ cells also pre lead coronary tips in the regenerating area and hapln1a+ cell loss inhibits coronary revascularization. To characterize the molecular nature of hapln1a+ cells during coronary growth we profiled hapln1a+ cells in juvenile and regenerating hearts and detected expression of the cell adhesion and migration regulator serpine1 in hapln1a+ cells adjacent to coronary tips. Pharmacological inhibition of serpine1 function blocked coronary vascularization and revascularization. Altogether our studies reveal that hapln1a+ cells are required for coronary production during heart morphogenesis and regeneration by establishing a microenvironment to facilitate guided coronary growth. Overall design: hapln1a+ cells of zebrafish heart were isolated by Fluorescence activated cell sorting FACS according to the presence or absence of eGFP signal and analyzed using scRNAseq.", "parent bioproject:PRJNA894685", "pubmed:37311876", null, "hapln1a+ development scRNAseq", "GSM6685234", null, "source name:heart|strain:EK|tissue:heart|cell type:epicardial cells|age:7 weeks|geo loc name:missing|collection date:missing", "hapln1a+ development scRNAseq", "All processing was performed in 10X Genomics CellRanger v3.1.0 using default parameters Assembly: Danio rerio GRCz11 Supplementary files format and content: Cell Ranger outputs a .mtx file with the feature barcode matrix. This matrix contains the counts of molecules per cell UMI/cell as determined post filtering and counting by Cell Ranger. The matrix is in market exchange format while the row gene or feature and columns cell barcodes are provided as TSV files. File formats are documented in the Cell Ranger software manual", "heart", null, "Hearts were dissected from juvenile zebrafish and ventricles were digested with Liberase TM 0.26 U/ml . Dissociated cells were spun down and live EGFP+ cells were sorted by flow cytometry. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v3.1 protocol 10x Genomics ", null, "strain:EK|tissue:heart|cell type:epicardial cells|cell type sorted:hapln1a+|age:7 weeks", "GSM6685234", "GSM6685234: hapln1a+ development scRNAseq; Danio rerio; RNA Seq", "GSM6685234 r1", "GSM6685234", "1", "Hearts were dissected from juvenile zebrafish and ventricles were digested with Liberase TM 0.26 U/ml . Dissociated cells were spun down and live EGFP+ cells were sorted by flow cytometry. Library was performed according to the manufacter's instructions single cell three prime v3.1 protocol 10x Genomics ", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP404721", null, "loader:fastq load.py", "1_S2_L001_I1_001.fastq.gz 1_S2_L001_R1_001.fastq.gz 1_S2_L001_R2_001.fastq.gz", "fastq fastq fastq", 1332426088.0, 10491544.0, "GSM6685234 r2", "0:8 1:28 2:91", "A:281795062;C:202126091;G:221122322;T:249574256;N:112773", 8, 28, 91, null, 281795062, 202126091, 221122322, 249574256, 112773, "SRX18039091", "SRS15545647", "SRA1528482", "Emory University", "Emory University", 1, 0.92141, null, 0.14909, null, 0.81714, null, 0.50543, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-10-26", "Juvenile", "Juvenile", "Heart", "Cardiovascular System"], [71809, "SRR22058036", "SRX18039091", "SRS15545647", "SRP404721", "PRJNA894591", "hapln1a+ cells guide coronary growth during heart morphogenesis and regeneration [Dev hapln1a+ cells]", "GSE216646", "Other", "As cardiac regeneration requires new coronary vessels exploring the underlying mechanisms behind revascularization will facilitate the development of regenerative therapies for heart failure. Although multiple tissues and chemokines likely orchestrate coronary formation the interaction between coronary growth and guidance cues remains unclear. Here by applying single cell RNA sequencing scRNA seq analysis we examined gene expression in zebrafish epicardial cells during coronary vascularization and identified hapln1a expressing epicardial cells enriched with vascular regulating genes. Fluorescence reporter assays indicated hapln1a+ cells not only envelop coronary vessels but also form cellular shear structures in ahead of coronary tips. Live imaging analyses demonstrated coronary growth along the pre formed shears with depletion of hapln1a+ cells blocking this growth. Further we found hapln1a+ cells also pre lead coronary tips in the regenerating area and hapln1a+ cell loss inhibits coronary revascularization. To characterize the molecular nature of hapln1a+ cells during coronary growth we profiled hapln1a+ cells in juvenile and regenerating hearts and detected expression of the cell adhesion and migration regulator serpine1 in hapln1a+ cells adjacent to coronary tips. Pharmacological inhibition of serpine1 function blocked coronary vascularization and revascularization. Altogether our studies reveal that hapln1a+ cells are required for coronary production during heart morphogenesis and regeneration by establishing a microenvironment to facilitate guided coronary growth. Overall design: hapln1a+ cells of zebrafish heart were isolated by Fluorescence activated cell sorting FACS according to the presence or absence of eGFP signal and analyzed using scRNAseq.", "parent bioproject:PRJNA894685", "pubmed:37311876", null, "hapln1a+ development scRNAseq", "GSM6685234", null, "source name:heart|strain:EK|tissue:heart|cell type:epicardial cells|age:7 weeks|geo loc name:missing|collection date:missing", "hapln1a+ development scRNAseq", "All processing was performed in 10X Genomics CellRanger v3.1.0 using default parameters Assembly: Danio rerio GRCz11 Supplementary files format and content: Cell Ranger outputs a .mtx file with the feature barcode matrix. This matrix contains the counts of molecules per cell UMI/cell as determined post filtering and counting by Cell Ranger. The matrix is in market exchange format while the row gene or feature and columns cell barcodes are provided as TSV files. File formats are documented in the Cell Ranger software manual", "heart", null, "Hearts were dissected from juvenile zebrafish and ventricles were digested with Liberase TM 0.26 U/ml . Dissociated cells were spun down and live EGFP+ cells were sorted by flow cytometry. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v3.1 protocol 10x Genomics ", null, "strain:EK|tissue:heart|cell type:epicardial cells|cell type sorted:hapln1a+|age:7 weeks", "GSM6685234", "GSM6685234: hapln1a+ development scRNAseq; Danio rerio; RNA Seq", "GSM6685234 r1", "GSM6685234", "1", "Hearts were dissected from juvenile zebrafish and ventricles were digested with Liberase TM 0.26 U/ml . Dissociated cells were spun down and live EGFP+ cells were sorted by flow cytometry. Library was performed according to the manufacter's instructions single cell three prime v3.1 protocol 10x Genomics ", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP404721", null, "loader:fastq load.py", "1_S3_L001_I1_001.fastq.gz 1_S3_L001_R1_001.fastq.gz 1_S3_L001_R2_001.fastq.gz", "fastq fastq fastq", 1187072175.0, 9347025.0, "GSM6685234 r3", "0:8 1:28 2:91", "A:251072030;C:180002392;G:196984629;T:222418470;N:101754", 8, 28, 91, null, 251072030, 180002392, 196984629, 222418470, 101754, "SRX18039091", "SRS15545647", "SRA1528482", "Emory University", "Emory University", 1, 0.92231, null, 0.15014, null, 0.8174, null, 0.50735, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-10-26", "Juvenile", "Juvenile", "Heart", "Cardiovascular System"], [71810, "SRR22058037", "SRX18039091", "SRS15545647", "SRP404721", "PRJNA894591", "hapln1a+ cells guide coronary growth during heart morphogenesis and regeneration [Dev hapln1a+ cells]", "GSE216646", "Other", "As cardiac regeneration requires new coronary vessels exploring the underlying mechanisms behind revascularization will facilitate the development of regenerative therapies for heart failure. Although multiple tissues and chemokines likely orchestrate coronary formation the interaction between coronary growth and guidance cues remains unclear. Here by applying single cell RNA sequencing scRNA seq analysis we examined gene expression in zebrafish epicardial cells during coronary vascularization and identified hapln1a expressing epicardial cells enriched with vascular regulating genes. Fluorescence reporter assays indicated hapln1a+ cells not only envelop coronary vessels but also form cellular shear structures in ahead of coronary tips. Live imaging analyses demonstrated coronary growth along the pre formed shears with depletion of hapln1a+ cells blocking this growth. Further we found hapln1a+ cells also pre lead coronary tips in the regenerating area and hapln1a+ cell loss inhibits coronary revascularization. To characterize the molecular nature of hapln1a+ cells during coronary growth we profiled hapln1a+ cells in juvenile and regenerating hearts and detected expression of the cell adhesion and migration regulator serpine1 in hapln1a+ cells adjacent to coronary tips. Pharmacological inhibition of serpine1 function blocked coronary vascularization and revascularization. Altogether our studies reveal that hapln1a+ cells are required for coronary production during heart morphogenesis and regeneration by establishing a microenvironment to facilitate guided coronary growth. Overall design: hapln1a+ cells of zebrafish heart were isolated by Fluorescence activated cell sorting FACS according to the presence or absence of eGFP signal and analyzed using scRNAseq.", "parent bioproject:PRJNA894685", "pubmed:37311876", null, "hapln1a+ development scRNAseq", "GSM6685234", null, "source name:heart|strain:EK|tissue:heart|cell type:epicardial cells|age:7 weeks|geo loc name:missing|collection date:missing", "hapln1a+ development scRNAseq", "All processing was performed in 10X Genomics CellRanger v3.1.0 using default parameters Assembly: Danio rerio GRCz11 Supplementary files format and content: Cell Ranger outputs a .mtx file with the feature barcode matrix. This matrix contains the counts of molecules per cell UMI/cell as determined post filtering and counting by Cell Ranger. The matrix is in market exchange format while the row gene or feature and columns cell barcodes are provided as TSV files. File formats are documented in the Cell Ranger software manual", "heart", null, "Hearts were dissected from juvenile zebrafish and ventricles were digested with Liberase TM 0.26 U/ml . Dissociated cells were spun down and live EGFP+ cells were sorted by flow cytometry. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v3.1 protocol 10x Genomics ", null, "strain:EK|tissue:heart|cell type:epicardial cells|cell type sorted:hapln1a+|age:7 weeks", "GSM6685234", "GSM6685234: hapln1a+ development scRNAseq; Danio rerio; RNA Seq", "GSM6685234 r1", "GSM6685234", "1", "Hearts were dissected from juvenile zebrafish and ventricles were digested with Liberase TM 0.26 U/ml . Dissociated cells were spun down and live EGFP+ cells were sorted by flow cytometry. Library was performed according to the manufacter's instructions single cell three prime v3.1 protocol 10x Genomics ", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP404721", null, "loader:fastq load.py", "1_S4_L001_I1_001.fastq.gz 1_S4_L001_R1_001.fastq.gz 1_S4_L001_R2_001.fastq.gz", "fastq fastq fastq", 1362894785.0, 10731455.0, "GSM6685234 r4", "0:8 1:28 2:91", "A:288451488;C:206540819;G:226008729;T:255442217;N:119152", 8, 28, 91, null, 288451488, 206540819, 226008729, 255442217, 119152, "SRX18039091", "SRS15545647", "SRA1528482", "Emory University", "Emory University", 1, 0.92215, null, 0.15108, null, 0.81706, null, 0.51589, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-10-26", "Juvenile", "Juvenile", "Heart", "Cardiovascular System"], [71811, "SRR22058440", "SRX18039491", "SRS15546048", "SRP404726", "PRJNA894687", "hapln1a+ cells guide coronary growth during heart morphogenesis and regeneration [Dev tcf21+ cells]", "GSE216648", "Other", "As cardiac regeneration requires new coronary vessels exploring the underlying mechanisms behind revascularization will facilitate the development of regenerative therapies for heart failure. Although multiple tissues and chemokines likely orchestrate coronary formation the interaction between coronary growth and guidance cues remains unclear. Here by applying single cell RNA sequencing scRNA seq analysis we examined gene expression in zebrafish epicardial cells during coronary vascularization and identified hapln1a expressing epicardial cells enriched with vascular regulating genes. Fluorescence reporter assays indicated hapln1a+ cells not only envelop coronary vessels but also form cellular shear structures in ahead of coronary tips. Live imaging analyses demonstrated coronary growth along the pre formed shears with depletion of hapln1a+ cells blocking this growth. Further we found hapln1a+ cells also pre lead coronary tips in the regenerating area and hapln1a+ cell loss inhibits coronary revascularization. To characterize the molecular nature of hapln1a+ cells during coronary growth we profiled hapln1a+ cells in juvenile and regenerating hearts and detected expression of the cell adhesion and migration regulator serpine1 in hapln1a+ cells adjacent to coronary tips. Pharmacological inhibition of serpine1 function blocked coronary vascularization and revascularization. Altogether our studies reveal that hapln1a+ cells are required for coronary production during heart morphogenesis and regeneration by establishing a microenvironment to facilitate guided coronary growth. Overall design: Epicardial cells of zebrafish heart were isolated by Fluorescence activated cell sorting FACS according to the presence or absence of eGFP signal and analyzed using scRNAseq.", "parent bioproject:PRJNA894685", "pubmed:37311876", null, "tcf21+ development scRNAseq", "GSM6685266", null, "source name:heart|strain:EK|tissue:heart|cell type:epicardial cells|age:7 weeks|geo loc name:missing|collection date:missing", "tcf21+ development scRNAseq", "All processing was performed in 10X Genomics CellRanger v3.1.0 using default parameters Assembly: Danio rerio GRCz11 Supplementary files format and content: Cell Ranger outputs a .mtx file with the feature barcode matrix. This matrix contains the counts of molecules per cell UMI/cell as determined post filtering and counting by Cell Ranger. The matrix is in market exchange format while the row gene or feature and columns cell barcodes are provided as TSV files. File formats are documented in the Cell Ranger software manual", "heart", null, "Hearts were dissected from juvenile zebrafish and ventricles were digested with Liberase TM 0.26 U/ml . Dissociated cells were spun down and live EGFP+ cells were sorted by flow cytometry. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v3.1 protocol 10x Genomics ", null, "strain:EK|tissue:heart|cell type:epicardial cells|cell type sorted:tcf21+|age:7 weeks", "GSM6685266", "GSM6685266: tcf21+ development scRNAseq; Danio rerio; RNA Seq", "GSM6685266 r1", "GSM6685266", "1", "Hearts were dissected from juvenile zebrafish and ventricles were digested with Liberase TM 0.26 U/ml . Dissociated cells were spun down and live EGFP+ cells were sorted by flow cytometry. Library was performed according to the manufacter's instructions single cell three prime v3.1 protocol 10x Genomics ", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP404726", null, null, "TCF_21_S1_L001_R1_001.fastq.gz TCF_21_S1_L001_R2_001.fastq.gz", "fastq fastq", 19362384447.0, 162709113.0, "GSM6685266 r1", "0:28 1:91", "A:5391284818;C:4382019183;G:4643235756;T:4943804153;N:2040537", 28, 91, null, null, 5391284818, 4382019183, 4643235756, 4943804153, 2040537, "SRX18039491", "SRS15546048", "SRA1528514", "Emory University", "Emory University", 2, 0.00432, 0.90419, 0.00171, 0.10489, 0.9947, 0.84737, 0.31827, 0.50898, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-10-26", "Juvenile", "Juvenile", "Heart", "Cardiovascular System"], [72748, "SRR23110580", "SRX19061956", "SRS16477631", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics in vivo expression validation photoconversion based lineage tracing and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish a model for the coronal synostosis of Saethre Chotzen Syndrome reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture misregulated bone formation and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg", "GSM6940303", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg", "Data analysis was performed with Seurat version 4.1.1 and datasets were filtered by nFeature RNA > 200 nFeature RNA < 2500 and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1\u2009mM EDTA and 400\u2009mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C rinsed in suspension media 1% FBS 0.8\u2009mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940303", "GSM6940303: 9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg; Danio rerio; RNA Seq", "GSM6940303 r1", "GSM6940303", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1\u2009mM EDTA and 400\u2009mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C rinsed in suspension media 1% FBS 0.8\u2009mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-1_S21_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-1_S21_L001_R2_001.fastq.gz", "fastq fastq", 26193525700.0, 177672099.0, "GSM6940303 r1", "0:27 1:120.43", "A:7719827835;C:5410495858;G:5661676554;T:7386218620;N:15306833", 27, 120, null, null, 7719827835, 5410495858, 5661676554, 7386218620, 15306833, "SRX19061956", "SRS16477631", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00368, 0.88598, 0.00112, 0.18215, 0.99168, 0.77757, 0.47975, 0.51393, 27, 120, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72749, "SRR23110581", "SRX19061956", "SRS16477631", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics in vivo expression validation photoconversion based lineage tracing and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish a model for the coronal synostosis of Saethre Chotzen Syndrome reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture misregulated bone formation and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg", "GSM6940303", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg", "Data analysis was performed with Seurat version 4.1.1 and datasets were filtered by nFeature RNA > 200 nFeature RNA < 2500 and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1\u2009mM EDTA and 400\u2009mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C rinsed in suspension media 1% FBS 0.8\u2009mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940303", "GSM6940303: 9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg; Danio rerio; RNA Seq", "GSM6940303 r1", "GSM6940303", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1\u2009mM EDTA and 400\u2009mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C rinsed in suspension media 1% FBS 0.8\u2009mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-2_S22_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-2_S22_L001_R2_001.fastq.gz", "fastq fastq", 20405308570.0, 138407397.0, "GSM6940303 r2", "0:27 1:120.43", "A:6066761212;C:4188427284;G:4382899879;T:5755324838;N:11895357", 27, 120, null, null, 6066761212, 4188427284, 4382899879, 5755324838, 11895357, "SRX19061956", "SRS16477631", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00368, 0.88942, 0.00119, 0.18885, 0.99184, 0.78693, 0.44927, 0.51797, 27, 121, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72750, "SRR23110582", "SRX19061956", "SRS16477631", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics in vivo expression validation photoconversion based lineage tracing and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish a model for the coronal synostosis of Saethre Chotzen Syndrome reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture misregulated bone formation and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg", "GSM6940303", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg", "Data analysis was performed with Seurat version 4.1.1 and datasets were filtered by nFeature RNA > 200 nFeature RNA < 2500 and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1\u2009mM EDTA and 400\u2009mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C rinsed in suspension media 1% FBS 0.8\u2009mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940303", "GSM6940303: 9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg; Danio rerio; RNA Seq", "GSM6940303 r1", "GSM6940303", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1\u2009mM EDTA and 400\u2009mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C rinsed in suspension media 1% FBS 0.8\u2009mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-3_S23_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-3_S23_L001_R2_001.fastq.gz", "fastq fastq", 12307572438.0, 83482484.0, "GSM6940303 r3", "0:27 1:120.43", "A:3633520237;C:2534467756;G:2656045405;T:3476373726;N:7165314", 27, 120, null, null, 3633520237, 2534467756, 2656045405, 3476373726, 7165314, "SRX19061956", "SRS16477631", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.0038, 0.8858, 0.00113, 0.18267, 0.99101, 0.77699, 0.46833, 0.52027, 27, 121, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72751, "SRR23110583", "SRX19061956", "SRS16477631", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics in vivo expression validation photoconversion based lineage tracing and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish a model for the coronal synostosis of Saethre Chotzen Syndrome reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture misregulated bone formation and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg", "GSM6940303", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg", "Data analysis was performed with Seurat version 4.1.1 and datasets were filtered by nFeature RNA > 200 nFeature RNA < 2500 and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1\u2009mM EDTA and 400\u2009mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C rinsed in suspension media 1% FBS 0.8\u2009mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940303", "GSM6940303: 9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg; Danio rerio; RNA Seq", "GSM6940303 r1", "GSM6940303", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1\u2009mM EDTA and 400\u2009mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C rinsed in suspension media 1% FBS 0.8\u2009mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-4_S24_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-4_S24_L001_R2_001.fastq.gz", "fastq fastq", 18938094183.0, 128455057.0, "GSM6940303 r4", "0:27 1:120.43", "A:5600343426;C:3891577388;G:4069279675;T:5365803260;N:11090434", 27, 120, null, null, 5600343426, 3891577388, 4069279675, 5365803260, 11090434, "SRX19061956", "SRS16477631", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00359, 0.88634, 0.00128, 0.18783, 0.99212, 0.77893, 0.48997, 0.50684, 27, 120, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72752, "SRR23110584", "SRX19061955", "SRS16477630", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics in vivo expression validation photoconversion based lineage tracing and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish a model for the coronal synostosis of Saethre Chotzen Syndrome reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture misregulated bone formation and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg", "GSM6940302", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg", "Data analysis was performed with Seurat version 4.1.1 and datasets were filtered by nFeature RNA > 200 nFeature RNA < 2500 and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1\u2009mM EDTA and 400\u2009mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C rinsed in suspension media 1% FBS 0.8\u2009mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940302", "GSM6940302: 9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg; Danio rerio; RNA Seq", "GSM6940302 r1", "GSM6940302", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1\u2009mM EDTA and 400\u2009mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C rinsed in suspension media 1% FBS 0.8\u2009mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-1_S1_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-1_S1_L001_R2_001.fastq.gz", "fastq fastq", 11012858533.0, 74696398.0, "GSM6940302 r1", "0:27 1:120.43", "A:3253931864;C:2230032555;G:2516883171;T:3003935990;N:8074953", 27, 120, null, null, 3253931864, 2230032555, 2516883171, 3003935990, 8074953, "SRX19061955", "SRS16477630", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00603, 0.89151, 0.00212, 0.18091, 0.98849, 0.79634, 0.5277, 0.52269, 27, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72753, "SRR23110585", "SRX19061955", "SRS16477630", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics in vivo expression validation photoconversion based lineage tracing and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish a model for the coronal synostosis of Saethre Chotzen Syndrome reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture misregulated bone formation and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg", "GSM6940302", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg", "Data analysis was performed with Seurat version 4.1.1 and datasets were filtered by nFeature RNA > 200 nFeature RNA < 2500 and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1\u2009mM EDTA and 400\u2009mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C rinsed in suspension media 1% FBS 0.8\u2009mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940302", "GSM6940302: 9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg; Danio rerio; RNA Seq", "GSM6940302 r1", "GSM6940302", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1\u2009mM EDTA and 400\u2009mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C rinsed in suspension media 1% FBS 0.8\u2009mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-2_S2_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-2_S2_L001_R2_001.fastq.gz", "fastq fastq", 10212715196.0, 69269302.0, "GSM6940302 r2", "0:27 1:120.43", "A:3014265330;C:2070878830;G:2341755898;T:2778343711;N:7471427", 27, 120, null, null, 3014265330, 2070878830, 2341755898, 2778343711, 7471427, "SRX19061955", "SRS16477630", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00554, 0.89174, 0.00191, 0.1793, 0.98884, 0.79732, 0.51857, 0.52305, 27, 121, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72754, "SRR23110586", "SRX19061955", "SRS16477630", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics in vivo expression validation photoconversion based lineage tracing and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish a model for the coronal synostosis of Saethre Chotzen Syndrome reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture misregulated bone formation and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg", "GSM6940302", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg", "Data analysis was performed with Seurat version 4.1.1 and datasets were filtered by nFeature RNA > 200 nFeature RNA < 2500 and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1\u2009mM EDTA and 400\u2009mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C rinsed in suspension media 1% FBS 0.8\u2009mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940302", "GSM6940302: 9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg; Danio rerio; RNA Seq", "GSM6940302 r1", "GSM6940302", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1\u2009mM EDTA and 400\u2009mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C rinsed in suspension media 1% FBS 0.8\u2009mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-3_S3_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-3_S3_L001_R2_001.fastq.gz", "fastq fastq", 7996112551.0, 54234020.0, "GSM6940302 r3", "0:27 1:120.44", "A:2359724282;C:1611743954;G:1830950721;T:2187871443;N:5822151", 27, 120, null, null, 2359724282, 1611743954, 1830950721, 2187871443, 5822151, "SRX19061955", "SRS16477630", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00614, 0.88908, 0.00216, 0.1836, 0.98821, 0.79547, 0.52232, 0.51954, 27, 121, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72755, "SRR23110587", "SRX19061955", "SRS16477630", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics in vivo expression validation photoconversion based lineage tracing and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish a model for the coronal synostosis of Saethre Chotzen Syndrome reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture misregulated bone formation and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg", "GSM6940302", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg", "Data analysis was performed with Seurat version 4.1.1 and datasets were filtered by nFeature RNA > 200 nFeature RNA < 2500 and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1\u2009mM EDTA and 400\u2009mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C rinsed in suspension media 1% FBS 0.8\u2009mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940302", "GSM6940302: 9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg; Danio rerio; RNA Seq", "GSM6940302 r1", "GSM6940302", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1\u2009mM EDTA and 400\u2009mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C rinsed in suspension media 1% FBS 0.8\u2009mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-4_S4_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-4_S4_L001_R2_001.fastq.gz", "fastq fastq", 11056657034.0, 74991022.0, "GSM6940302 r4", "0:27 1:120.44", "A:3246337136;C:2242556246;G:2556848463;T:3002783409;N:8131780", 27, 120, null, null, 3246337136, 2242556246, 2556848463, 3002783409, 8131780, "SRX19061955", "SRS16477630", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00621, 0.8906, 0.00194, 0.17648, 0.98762, 0.80133, 0.48802, 0.52225, 27, 121, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [74187, "SRR23592269", "SRX19477372", "SRS16868715", "SRP424004", "PRJNA937732", "Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution", "GSE225863", "Transcriptome Analysis", "The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.", null, "pubmed:38518783", null, "Replicate3", "GSM7058866", null, "source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks", "Replicate3", "The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Telencephalon", null, "Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks", "GSM7058866", "GSM7058866: Replicate3; Danio rerio; RNA Seq", "GSM7058866 r1", "GSM7058866", "1", "Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP424004", null, "loader:fastq load.py", "Replicate3_S6_L002_I1_001.fastq.gz Replicate3_S6_L002_R1_001.fastq.gz Replicate3_S6_L002_R2_001.fastq.gz", "fastq fastq fastq", 10975505112.0, 83147766.0, "GSM7058866 r1", "0:8 1:26 2:98", "A:2426282254;C:1547059106;G:1673155133;T:2499529455;N:2455120", 8, 26, 98, null, 2426282254, 1547059106, 1673155133, 2499529455, 2455120, "SRX19477372", "SRS16868715", "SRA1594515", "Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur", "Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur", 1, 0.88458, null, 0.25806, null, 0.75777, null, 0.51359, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "France", "2023-02-22", "Juvenile", "Juvenile", "Brain", "Nervous System"], [74188, "SRR23592270", "SRX19477372", "SRS16868715", "SRP424004", "PRJNA937732", "Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution", "GSE225863", "Transcriptome Analysis", "The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.", null, "pubmed:38518783", null, "Replicate3", "GSM7058866", null, "source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks", "Replicate3", "The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Telencephalon", null, "Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks", "GSM7058866", "GSM7058866: Replicate3; Danio rerio; RNA Seq", "GSM7058866 r1", "GSM7058866", "1", "Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP424004", null, "loader:fastq load.py", "Replicate3_S6_L003_I1_001.fastq.gz Replicate3_S6_L003_R1_001.fastq.gz Replicate3_S6_L003_R2_001.fastq.gz", "fastq fastq fastq", 10997748828.0, 83316279.0, "GSM7058866 r2", "0:8 1:26 2:98", "A:2431471247;C:1548269509;G:1677317277;T:2505450138;N:2487171", 8, 26, 98, null, 2431471247, 1548269509, 1677317277, 2505450138, 2487171, "SRX19477372", "SRS16868715", "SRA1594515", "Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur", "Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur", 1, 0.87918, null, 0.25527, null, 0.76077, null, 0.5112, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "France", "2023-02-22", "Juvenile", "Juvenile", "Brain", "Nervous System"], [74189, "SRR23592271", "SRX19477372", "SRS16868715", "SRP424004", "PRJNA937732", "Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution", "GSE225863", "Transcriptome Analysis", "The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.", null, "pubmed:38518783", null, "Replicate3", "GSM7058866", null, "source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks", "Replicate3", "The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Telencephalon", null, "Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks", "GSM7058866", "GSM7058866: Replicate3; Danio rerio; RNA Seq", "GSM7058866 r1", "GSM7058866", "1", "Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP424004", null, "loader:fastq load.py", "Replicate3_S6_L004_I1_001.fastq.gz Replicate3_S6_L004_R1_001.fastq.gz Replicate3_S6_L004_R2_001.fastq.gz", "fastq fastq fastq", 10983946644.0, 83211717.0, "GSM7058866 r3", "0:8 1:26 2:98", "A:2429637202;C:1546068983;G:1673189416;T:2503083588;N:2769077", 8, 26, 98, null, 2429637202, 1546068983, 1673189416, 2503083588, 2769077, "SRX19477372", "SRS16868715", "SRA1594515", "Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur", "Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur", 1, 0.88521, null, 0.2551, null, 0.76256, null, 0.50337, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "France", "2023-02-22", "Juvenile", "Juvenile", "Brain", "Nervous System"], [74190, "SRR23592272", "SRX19477372", "SRS16868715", "SRP424004", "PRJNA937732", "Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution", "GSE225863", "Transcriptome Analysis", "The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.", null, "pubmed:38518783", null, "Replicate3", "GSM7058866", null, "source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks", "Replicate3", "The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Telencephalon", null, "Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks", "GSM7058866", "GSM7058866: Replicate3; Danio rerio; RNA Seq", "GSM7058866 r1", "GSM7058866", "1", "Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP424004", null, "loader:fastq load.py", "Replicate3_S6_L005_I1_001.fastq.gz Replicate3_S6_L005_R1_001.fastq.gz Replicate3_S6_L005_R2_001.fastq.gz", "fastq fastq fastq", 10968968604.0, 83098247.0, "GSM7058866 r4", "0:8 1:26 2:98", "A:2426652777;C:1543610186;G:1671298649;T:2499458002;N:2608592", 8, 26, 98, null, 2426652777, 1543610186, 1671298649, 2499458002, 2608592, "SRX19477372", "SRS16868715", "SRA1594515", "Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur", "Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur", 1, 0.88307, null, 0.25596, null, 0.7626, null, 0.5081, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "France", "2023-02-22", "Juvenile", "Juvenile", "Brain", "Nervous System"], [74191, "SRR23592273", "SRX19477372", "SRS16868715", "SRP424004", "PRJNA937732", "Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution", "GSE225863", "Transcriptome Analysis", "The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.", null, "pubmed:38518783", null, "Replicate3", "GSM7058866", null, "source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks", "Replicate3", "The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Telencephalon", null, "Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks", "GSM7058866", "GSM7058866: Replicate3; Danio rerio; RNA Seq", "GSM7058866 r1", "GSM7058866", "1", "Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP424004", null, "loader:fastq load.py", "Replicate3_S6_L006_I1_001.fastq.gz Replicate3_S6_L006_R1_001.fastq.gz Replicate3_S6_L006_R2_001.fastq.gz", "fastq fastq fastq", 11010714792.0, 83414506.0, "GSM7058866 r5", "0:8 1:26 2:98", "A:2435577632;C:1549348379;G:1677580141;T:2508999458;N:3115978", 8, 26, 98, null, 2435577632, 1549348379, 1677580141, 2508999458, 3115978, "SRX19477372", "SRS16868715", "SRA1594515", "Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur", "Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur", 1, 0.88298, null, 0.25581, null, 0.75996, null, 0.51556, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "France", "2023-02-22", "Juvenile", "Juvenile", "Brain", "Nervous System"], [74192, "SRR23592274", "SRX19477372", "SRS16868715", "SRP424004", "PRJNA937732", "Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution", "GSE225863", "Transcriptome Analysis", "The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. 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Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.", null, "pubmed:38518783", null, "Replicate2", "GSM7058865", null, "source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks", "Replicate2", "The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Telencephalon", null, "Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks", "GSM7058865", "GSM7058865: Replicate2; Danio rerio; RNA Seq", "GSM7058865 r1", "GSM7058865", "1", "Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. 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GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.", null, "pubmed:38518783", null, "Replicate2", "GSM7058865", null, "source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks", "Replicate2", "The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Telencephalon", null, "Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks", "GSM7058865", "GSM7058865: Replicate2; Danio rerio; RNA Seq", "GSM7058865 r1", "GSM7058865", "1", "Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. 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Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. 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The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.", null, "tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks", "GSM7058865", "GSM7058865: Replicate2; Danio rerio; RNA Seq", "GSM7058865 r1", "GSM7058865", "1", "Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. 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