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111 rows where devstage_curation_coarse = "Juvenile" and technology = "10x"

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tissue_curation 10

experiment.library_selection 3

experiment.library_source 2

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technology 1

  • 10x · 111 ✖

experiment.platform 1

experiment.library_strategy 1

devstage_curation_coarse 1

  • Juvenile · 111 ✖

devstage_curation 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
25326 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.   pubmed:38497789   vaccinated+SVCV scRNAseq Kidney leukocyte GSM7749529   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   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 μm 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 μg/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 3’ 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.   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 μm 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 μg/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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP457977     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     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   China 2023-09-01 Juvenile Juvenile Kidney Renal System
25327 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.   pubmed:38497789   SVCV scRNAseq Kidney leukocyte GSM7749528   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   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 μm 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 μg/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 3’ 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.   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 μm 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 μg/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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP457977     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     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   China 2023-09-01 Juvenile Juvenile Kidney Renal System
25328 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.   pubmed:38497789   PBS scRNAseq Kidney leukocyte GSM7749527   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   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 μm 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 μg/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 3’ 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.   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 μm 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 μg/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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP457977     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     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   China 2023-09-01 Juvenile Juvenile Kidney Renal System
29188 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   pubmed:38529407   Nadia 30dpf ZZ Gonad Single Cell RNA Seq Nadia 30dpf ZZ Gonad Single Cell RNA Seq   strain:Nadia|age:30 dpf provider:John H. Postlethwait University of Oregon|genotype:ZZ|BioSampleModel:Model organism or animal                 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.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   SRP480945   loader:fastq load.py     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     6732844252 4934497997 5685086026 6219863789 14881374 SRX4996870 SRS4031878 SRA807619 University of Oregon|Institute of Neuroscience University of Oregon                       T B sc-like readlen illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   United States 2018-11-08 Juvenile Juvenile Gonad Reproductive System
29189 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   pubmed:38529407   Nadia 30dpf ZW Gonad Single Cell RNA Seq Nadia 30dpf ZW Gonad Single Cell RNA Seq   strain:Nadia|age:30 dpf provider:John H. Postlethwait University of Oregon|genotype:ZW|BioSampleModel:Model organism or animal                 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.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   SRP480945   loader:fastq load.py     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     12290612367 8880655083 10261318751 11898771792 27450487 SRX4996869 SRS4031877 SRA807619 University of Oregon|Institute of Neuroscience University of Oregon                       T B sc-like readlen illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   United States 2018-11-08 Juvenile Juvenile Gonad Reproductive System
30738 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/ß catenin signaling activated cardiomyocytes ß 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/ß catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß 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 µM 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   AVC IWR1 scRNAseq GSM8147318   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 μM MTZ dissolved in fish water for 48 h in the dark. Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM 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 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC 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’reagent 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.   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 TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM 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 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP495277   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                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Japan 2024-03-14 Juvenile Juvenile Heart Cardiovascular System
30739 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/ß catenin signaling activated cardiomyocytes ß 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/ß catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß 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 µM 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   AVC IWR1 scRNAseq GSM8147318   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 μM MTZ dissolved in fish water for 48 h in the dark. Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM 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 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC 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’reagent 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.   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 TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM 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 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP495277   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                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Japan 2024-03-14 Juvenile Juvenile Heart Cardiovascular System
30740 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/ß catenin signaling activated cardiomyocytes ß 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/ß catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß 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 µM 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   AVC IWR1 scRNAseq GSM8147318   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 μM MTZ dissolved in fish water for 48 h in the dark. Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM 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 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC 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’reagent 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.   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 TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM 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 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP495277   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                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Japan 2024-03-14 Juvenile Juvenile Heart Cardiovascular System
30741 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/ß catenin signaling activated cardiomyocytes ß 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/ß catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß 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 µM 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   AVC IWR1 scRNAseq GSM8147318   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 μM MTZ dissolved in fish water for 48 h in the dark. Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM 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 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC 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’reagent 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.   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 TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM 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 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP495277   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                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Japan 2024-03-14 Juvenile Juvenile Heart Cardiovascular System
30742 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/ß catenin signaling activated cardiomyocytes ß 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/ß catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß 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 µM 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   AVC DMSO scRNAseq GSM8147317   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 μM MTZ dissolved in fish water for 48 h in the dark. Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM 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 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC 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’reagent 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.   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 TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM 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 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP495277   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                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Japan 2024-03-14 Juvenile Juvenile Heart Cardiovascular System
30743 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/ß catenin signaling activated cardiomyocytes ß 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/ß catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß 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 µM 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   AVC DMSO scRNAseq GSM8147317   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 μM MTZ dissolved in fish water for 48 h in the dark. Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM 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 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC 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’reagent 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.   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 TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM 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 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP495277   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                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Japan 2024-03-14 Juvenile Juvenile Heart Cardiovascular System
30744 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/ß catenin signaling activated cardiomyocytes ß 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/ß catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß 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 µM 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   AVC DMSO scRNAseq GSM8147317   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 μM MTZ dissolved in fish water for 48 h in the dark. Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM 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 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC 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’reagent 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.   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 TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM 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 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP495277   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                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Japan 2024-03-14 Juvenile Juvenile Heart Cardiovascular System
30745 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/ß catenin signaling activated cardiomyocytes ß 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/ß catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß 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 µM 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   AVC DMSO scRNAseq GSM8147317   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 μM MTZ dissolved in fish water for 48 h in the dark. Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM 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 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC 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’reagent 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.   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 TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM 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 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP495277   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                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Japan 2024-03-14 Juvenile Juvenile Heart Cardiovascular System
50847 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 –attribute=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.   pubmed:32694805   2mpf Pancreas GSM3509161   tissue:pancreatic cells|age:2mpf|strain:Tgins:BB1.0L|disease state:Normal 2mpf Pancreas 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 –attribute=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. Genome build: Zebrafish GRCz10 Supplementary files format and content: csv format with rows as genes and columns as cells pancreatic cells   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 – was performed based on the manufacturer’s protocol.   age:2mpf|strain:Tgins:BB1.0L|disease state:Normal GSM3509161 GSM3509161: 2mpf Pancreas; Danio rerio; RNA Seq GSM3509161   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 – was performed based on the manufacturer's protocol. GEO Accession:GSM3509161 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP173304     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     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   Belgium 2018-12-11 Juvenile Juvenile Pancreas Endocrine System
52954 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: ' …       2mpf Thyroid GSM3909771   tissue:thyroid gland|treatment:2mpf|strain:Tgtg:mVenus T2A NTR|tag:Normal 2mpf Thyroid 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 –attribute=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. Genome build: Zebrafish GRCz10 Supplementary files format and content: Matrix with rows as genes and columns as cells. thyroid gland   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 – was performed based on the manufacturer’s protocol.   treatment:2mpf|strain:Tgtg:mVenus T2A NTR|tag:Normal GSM3909771 GSM3909771: 2mpf Thyroid; Danio rerio; RNA Seq GSM3909771   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 – was performed based on the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP212225     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     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   Belgium 2019-06-27 Juvenile Juvenile Thyroid Endocrine System
54727 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       whole organism single cell RNA seq of juvenile zebrafish SC2S3   strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP222654     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     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   China 2019-09-20 Juvenile Juvenile Whole Organism All anatomical structures
54728 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       whole organism single cell RNA seq of juvenile zebrafish SC2S3   strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP222654     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     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   China 2019-09-20 Juvenile Juvenile Whole Organism All anatomical structures
54729 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       whole organism single cell RNA seq of juvenile zebrafish SC2S3   strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP222654     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     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   China 2019-09-20 Juvenile Juvenile Whole Organism All anatomical structures
54730 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       whole organism single cell RNA seq of juvenile zebrafish SC2S3   strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP222654     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     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   China 2019-09-20 Juvenile Juvenile Whole Organism All anatomical structures
54731 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       whole organism single cell RNA seq of juvenile zebrafish SC2S3   strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP222654     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     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   China 2019-09-20 Juvenile Juvenile Whole Organism All anatomical structures
54732 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       whole organism single cell RNA seq of juvenile zebrafish SC2S3   strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP222654     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     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   China 2019-09-20 Juvenile Juvenile Whole Organism All anatomical structures
54733 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       whole organism single cell RNA seq of juvenile zebrafish SC2S3   strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP222654     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     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   China 2019-09-20 Juvenile Juvenile Whole Organism All anatomical structures
54734 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       whole organism single cell RNA seq of juvenile zebrafish SC2S3   strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP222654     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     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   China 2019-09-20 Juvenile Juvenile Whole Organism All anatomical structures
65060 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.   pubmed:35013168   scRNAseq Sox10 Cre bact BtR 60dpf rep 2 GSM5402440   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 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To  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 component… Cranial neural crest derived cells   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°C 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 °C 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 µl 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 chroma… 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°C. 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   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°C 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 °C 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 µl 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 chroma… GEO Accession:GSM5402440 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP325759     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     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   United States 2021-06-27 Juvenile Juvenile Brain Nervous System
65061 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.   pubmed:35013168   scRNAseq Sox10 Cre bact BtR 60dpf rep 2 GSM5402440   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 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To  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 component… Cranial neural crest derived cells   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°C 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 °C 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 µl 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 chroma… 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°C. 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   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°C 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 °C 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 µl 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 chroma… GEO Accession:GSM5402440 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP325759     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     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   United States 2021-06-27 Juvenile Juvenile Brain Nervous System
65062 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.   pubmed:35013168   scRNAseq Sox10 Cre bact BtR 60dpf rep 2 GSM5402440   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 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To  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 component… Cranial neural crest derived cells   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°C 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 °C 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 µl 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 chroma… 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°C. 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   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°C 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 °C 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 µl 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 chroma… GEO Accession:GSM5402440 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP325759     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     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   United States 2021-06-27 Juvenile Juvenile Brain Nervous System
65063 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.   pubmed:35013168   scRNAseq Sox10 Cre bact BtR 60dpf rep 2 GSM5402440   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 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To  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 component… Cranial neural crest derived cells   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°C 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 °C 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 µl 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 chroma… 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°C. 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   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°C 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 °C 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 µl 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 chroma… GEO Accession:GSM5402440 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP325759     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     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   United States 2021-06-27 Juvenile Juvenile Brain Nervous System
65064 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.   pubmed:35013168   scRNAseq Sox10 Cre bact BtR 60dpf rep 1 GSM5402439   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 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To  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 component… Cranial neural crest derived cells   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°C 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 °C 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 µl 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 chroma… 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°C. 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   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°C 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 °C 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 µl 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 chroma… GEO Accession:GSM5402439 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP325759     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     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   United States 2021-06-27 Juvenile Juvenile Brain Nervous System
65065 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.   pubmed:35013168   scRNAseq Sox10 Cre bact BtR 60dpf rep 1 GSM5402439   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 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To  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 component… Cranial neural crest derived cells   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°C 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 °C 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 µl 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 chroma… 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°C. 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   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°C 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 °C 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 µl 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 chroma… GEO Accession:GSM5402439 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP325759     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     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   United States 2021-06-27 Juvenile Juvenile Brain Nervous System
65066 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.   pubmed:35013168   scRNAseq Sox10 Cre bact BtR 60dpf rep 1 GSM5402439   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 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To  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 component… Cranial neural crest derived cells   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°C 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 °C 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 µl 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 chroma… 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°C. 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   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°C 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 °C 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 µl 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 chroma… GEO Accession:GSM5402439 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP325759     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     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   United States 2021-06-27 Juvenile Juvenile Brain Nervous System
65067 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.   pubmed:35013168   scRNAseq Sox10 Cre bact BtR 60dpf rep 1 GSM5402439   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 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To  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 component… Cranial neural crest derived cells   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°C 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 °C 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 µl 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 chroma… 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°C. 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   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°C 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 °C 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 µl 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 chroma… GEO Accession:GSM5402439 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP325759     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     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   United States 2021-06-27 Juvenile Juvenile Brain Nervous System
66846 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™ 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–PCR 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 w…   pubmed:39741296   runx2b / scRNA seq GSM5664293   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’s 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   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.   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   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   SRP344071   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     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   China 2021-11-01 Juvenile Juvenile Muscle Muscular System
66847 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™ 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–PCR 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 w…   pubmed:39741296   runx2b+/+ scRNA seq GSM5664292   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’s 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   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.   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   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   SRP344071   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     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   China 2021-11-01 Juvenile Juvenile Muscle Muscular System
66848 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™ 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–PCR 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 w…   pubmed:39741296   runx2b / bulk RNA seq rep3 GSM5664299   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’s 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   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.   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   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   SRP344071   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     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   China 2021-11-01 Juvenile Juvenile Muscle Muscular System
66849 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™ 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–PCR 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 w…   pubmed:39741296   runx2b / bulk RNA seq rep2 GSM5664298   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’s 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   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.   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   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   SRP344071   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     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   China 2021-11-01 Juvenile Juvenile Muscle Muscular System
66850 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™ 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–PCR 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 w…   pubmed:39741296   runx2b / bulk RNA seq rep1 GSM5664297   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’s 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   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.   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   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   SRP344071   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     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   China 2021-11-01 Juvenile Juvenile Muscle Muscular System
66851 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™ 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–PCR 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 w…   pubmed:39741296   runx2b+/+ bulk RNA seq rep3 GSM5664296   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’s 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   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.   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   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   SRP344071   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     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   China 2021-11-01 Juvenile Juvenile Muscle Muscular System
66852 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™ 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–PCR 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 w…   pubmed:39741296   runx2b+/+ bulk RNA seq rep2 GSM5664295   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’s 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   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.   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   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   SRP344071   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     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   China 2021-11-01 Juvenile Juvenile Muscle Muscular System
66853 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™ 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–PCR 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 w…   pubmed:39741296   runx2b+/+ bulk RNA seq rep1 GSM5664294   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’s 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   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.   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   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   SRP344071   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     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   China 2021-11-01 Juvenile Juvenile Muscle Muscular System
67758 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   pubmed:35588359   40 dpf zebrafish ovaries cells zx4 GSM5739896   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 “mkgtf” 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’s “mkref” 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 “count” function in Cell Ranger v3.0.2; 10x Genomic. “expect cells” was setted to 10000 based on estimated cell recovery.  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   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 µL 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’ single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell 3’ 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 … 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 µL 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 …   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP351377     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     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   United States 2021-12-17 Juvenile Juvenile Gonad Reproductive System
67759 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   pubmed:35588359   40 dpf zebrafish ovaries cells zx2 GSM5739895   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 “mkgtf” 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’s “mkref” 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 “count” function in Cell Ranger v3.0.2; 10x Genomic. “expect cells” was setted to 10000 based on estimated cell recovery.  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   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 µL 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’ single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell 3’ 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 … 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 µL 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 …   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP351377     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     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   0.54454 151 151 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-12-17 Juvenile Juvenile Gonad Reproductive System
67760 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   pubmed:35588359   40 dpf zebrafish ovaries cells sorted germ cells GSM5739894   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 “mkgtf” 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’s “mkref” 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 “count” function in Cell Ranger v3.0.2; 10x Genomic. “expect cells” was setted to 10000 based on estimated cell recovery.  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   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 µL of 20 mg/mL of type 2 collagenase in L15 Cat.No. NC9870009; Worthington were added and incubated on an orbital rotator at 28°C for 35 min. The cell suspension was then gently passed through a 23g needle five times to break up large cell clumps. 200 µL 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 µL 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 µm nylon filter Cat.No. 431752; Corning and then through a 40 µm 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 µm 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… 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 µL of 20 mg/mL of type 2 collagenase in L15 Cat.No. NC9870009; Worthington were added and incubated on an orbital rotator at 28°C for 35 min. The cell suspension was then gently passed through a 23g needle five times to break up large cell clumps. 200 µL 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 µL 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 µm nylon filter Cat.No. 431752; Corning and then through a 40 µm 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 µm 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…   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP351377     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     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   United States 2021-12-17 Juvenile Juvenile Gonad Reproductive System
68139 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.   pubmed:35615540;pubmed:35799832   scRNA seq TCDD testes rep 2 GSM5820556   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP355202   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   2329833844 1736580490 2028746154 1974513391 435168 SRX13799339 SRS11681628 SRA1357269 University of Florida University of Florida 1 0.89663   0.23137   0.75166   0.55299   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68140 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.   pubmed:35615540;pubmed:35799832   scRNA seq TCDD testes rep 2 GSM5820556   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP355202   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   2351124750 1758531934 2054452297 1992620872 535263 SRX13799339 SRS11681628 SRA1357269 University of Florida University of Florida 1 0.89836   0.23263   0.7543   0.55738   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68141 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.   pubmed:35615540;pubmed:35799832   scRNA seq TCDD testes rep 1 GSM5820555   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP355202   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   2363149906 1616901304 1945888469 1940298056 439174 SRX13799338 SRS11681627 SRA1357269 University of Florida University of Florida 1 0.87562   0.208   0.75511   0.5329   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68142 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.   pubmed:35615540;pubmed:35799832   scRNA seq TCDD testes rep 1 GSM5820555   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP355202   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   2382115862 1635424114 1968060449 1956671635 516066 SRX13799338 SRS11681627 SRA1357269 University of Florida University of Florida 1 0.8745   0.20808   0.7585   0.52692   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68143 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.   pubmed:35615540;pubmed:35799832   scRNA seq control testes rep 3 GSM5820554   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP355202   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   2491182657 1749727321 2001921423 2166620469 464918 SRX13799337 SRS11681626 SRA1357269 University of Florida University of Florida 1 0.89927   0.17983   0.71601   0.52261   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68144 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.   pubmed:35615540;pubmed:35799832   scRNA seq control testes rep 3 GSM5820554   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP355202   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   2515246562 1770645118 2026263526 2187182415 549866 SRX13799337 SRS11681626 SRA1357269 University of Florida University of Florida 1 0.89922   0.1803   0.71419   0.52093   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68145 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.   pubmed:35615540;pubmed:35799832   scRNA seq control testes rep 2 GSM5820553   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP355202   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   2441188567 1731265684 2062239362 2074648513 460375 SRX13799336 SRS11681625 SRA1357269 University of Florida University of Florida 1 0.87524   0.22302   0.75893   0.55047   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68146 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.   pubmed:35615540;pubmed:35799832   scRNA seq control testes rep 2 GSM5820553   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP355202   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   2464546352 1753014248 2088164317 2094592155 565782 SRX13799336 SRS11681625 SRA1357269 University of Florida University of Florida 1 0.87809   0.22205   0.75272   0.55306   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68147 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.   pubmed:35615540;pubmed:35799832   scRNA seq control testes rep 1 GSM5820552   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP355202   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   2554285232 1757437977 2060709302 2114543968 474857 SRX13799335 SRS11681624 SRA1357269 University of Florida University of Florida 1 0.89006   0.16375   0.74714   0.51816   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68148 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.   pubmed:35615540;pubmed:35799832   scRNA seq control testes rep 1 GSM5820552   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP355202   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   2577816465 1779883368 2086781140 2134925822 569974 SRX13799335 SRS11681624 SRA1357269 University of Florida University of Florida 1 0.89007   0.16458   0.74986   0.52005   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68149 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.   pubmed:35615540;pubmed:35799832   dissociated bulk seq control testes rep 3 compared to intact control testes GSM5820567   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     535632392 366862698 429979337 514873991 23205 SRX13799350 SRS11681639 SRA1357269 University of Florida University of Florida 1 0.87212   0.1857   0.69372   0.56886   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68150 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.   pubmed:35615540;pubmed:35799832   dissociated bulk seq control testes rep 3 compared to intact control testes GSM5820567   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     529009592 361883074 424030274 508289743 18141 SRX13799350 SRS11681639 SRA1357269 University of Florida University of Florida 1 0.8708   0.18714   0.6955   0.5716   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68151 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.   pubmed:35615540;pubmed:35799832   dissociated bulk seq control testes rep 2 compared to intact control testes GSM5820566   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     163430759 106016694 122059136 145048023 6596 SRX13799349 SRS11681638 SRA1357269 University of Florida University of Florida 1 0.83573   0.2005   0.71056   0.52825   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68152 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.   pubmed:35615540;pubmed:35799832   dissociated bulk seq control testes rep 2 compared to intact control testes GSM5820566   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     161875304 104815309 120705456 143576873 5296 SRX13799349 SRS11681638 SRA1357269 University of Florida University of Florida 1 0.83663   0.19964   0.71104   0.54143   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68153 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.   pubmed:35615540;pubmed:35799832   dissociated bulk seq control testes rep 1 compared to intact control testes GSM5820565   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     155891194 103400919 120028554 144451616 6999 SRX13799348 SRS11681637 SRA1357269 University of Florida University of Florida 1 0.85957   0.19557   0.69501   0.56637   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68154 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.   pubmed:35615540;pubmed:35799832   dissociated bulk seq control testes rep 1 compared to intact control testes GSM5820565   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     153923180 101966413 118359254 142647450 5686 SRX13799348 SRS11681637 SRA1357269 University of Florida University of Florida 1 0.85795   0.19403   0.69627   0.57159   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68155 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.   pubmed:35615540;pubmed:35799832   bulk seq intact control testes rep 3 GSM5820564   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     496655744 334242155 387205466 455330132 23383 SRX13799347 SRS11681636 SRA1357269 University of Florida University of Florida 1 0.8707   0.22045   0.71078   0.60605   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68156 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.   pubmed:35615540;pubmed:35799832   bulk seq intact control testes rep 3 GSM5820564   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     489182217 328774657 380849646 448358863 19204 SRX13799347 SRS11681636 SRA1357269 University of Florida University of Florida 1 0.87032   0.22081   0.71261   0.60917   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68157 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.   pubmed:35615540;pubmed:35799832   bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes GSM5820561   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     447529477 312467507 374130013 449667219 21392 SRX13799346 SRS11681635 SRA1357269 University of Florida University of Florida 1 0.86982   0.25275   0.70774   0.5721   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68158 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.   pubmed:35615540;pubmed:35799832   bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes GSM5820561   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     442209708 308400147 369229792 444230646 17648 SRX13799346 SRS11681635 SRA1357269 University of Florida University of Florida 1 0.87035   0.2527   0.70682   0.57673   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68159 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.   pubmed:35615540;pubmed:35799832   bulk seq intact control testes rep 2 GSM5820563   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     445588125 289131502 340459665 418525850 19527 SRX13799345 SRS11681634 SRA1357269 University of Florida University of Florida 1 0.85779   0.20343   0.69887   0.56808   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68160 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.   pubmed:35615540;pubmed:35799832   bulk seq intact control testes rep 2 GSM5820563   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     440339743 285301590 335922618 413432380 16234 SRX13799345 SRS11681634 SRA1357269 University of Florida University of Florida 1 0.85783   0.20221   0.70102   0.57116   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68161 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.   pubmed:35615540;pubmed:35799832   bulk seq intact control testes rep 1 GSM5820562   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     503613569 361648917 420357217 497872153 23840 SRX13799344 SRS11681633 SRA1357269 University of Florida University of Florida 1 0.88797   0.22692   0.69522   0.57676   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68162 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.   pubmed:35615540;pubmed:35799832   bulk seq intact control testes rep 1 GSM5820562   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     496669418 356271536 414028881 491077933 19795 SRX13799344 SRS11681633 SRA1357269 University of Florida University of Florida 1 0.88843   0.22792   0.69619   0.57488   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68163 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.   pubmed:35615540;pubmed:35799832   bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes GSM5820560   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     1025376436 691776192 829134506 979443851 49057 SRX13799343 SRS11681632 SRA1357269 University of Florida University of Florida 1 0.86505   0.30929   0.72074   0.6373   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68164 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.   pubmed:35615540;pubmed:35799832   bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes GSM5820560   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     1012622841 682305804 817948602 966881210 40699 SRX13799343 SRS11681632 SRA1357269 University of Florida University of Florida 1 0.86392   0.30933   0.71863   0.63706   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68165 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.   pubmed:35615540;pubmed:35799832   bulk seq control testes rep 2 to be compared to scRNA seq control testes GSM5820558   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     361072135 254984535 302043978 346569617 16872 SRX13799342 SRS11681631 SRA1357269 University of Florida University of Florida 1 0.86972   0.31888   0.71561   0.6242   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68166 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.   pubmed:35615540;pubmed:35799832   bulk seq control testes rep 2 to be compared to scRNA seq control testes GSM5820558   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     356333809 251264657 297639103 341883185 13866 SRX13799342 SRS11681631 SRA1357269 University of Florida University of Florida 1 0.8683   0.31544   0.71332   0.62605   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68167 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.   pubmed:35615540;pubmed:35799832   bulk seq control testes rep 3 to be compared to scRNA seq control testes GSM5820559   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     370125548 258465981 307735443 362125609 17976 SRX13799341 SRS11681630 SRA1357269 University of Florida University of Florida 1 0.87017   0.23168   0.7049   0.43404   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68168 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.   pubmed:35615540;pubmed:35799832   bulk seq control testes rep 3 to be compared to scRNA seq control testes GSM5820559   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     365706822 255117242 303741803 357696714 14864 SRX13799341 SRS11681630 SRA1357269 University of Florida University of Florida 1 0.86967   0.23412   0.70447   0.60084   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68169 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.   pubmed:35615540;pubmed:35799832   bulk seq control testes rep 1 to be compared to scRNA seq control testes GSM5820557   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     101645255 77359657 89895787 94805817 5135 SRX13799340 SRS11681629 SRA1357269 University of Florida University of Florida 1 0.86049   0.29611   0.72293   0.54071   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
68170 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.   pubmed:35615540;pubmed:35799832   bulk seq control testes rep 1 to be compared to scRNA seq control testes GSM5820557   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.   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°C– 30°C. 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP355202     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     100176173 76199709 88532838 93436578 4162 SRX13799340 SRS11681629 SRA1357269 University of Florida University of Florida 1 0.86034   0.29588   0.72346   0.54277   51   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-01-15 Juvenile Juvenile Gonad Reproductive System
71018 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.   pubmed:37227178;pubmed:40392591   vaccinated+SVCV scRNAseq GSM6469457   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   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 μm 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 μg/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 3’ 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.   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 μm 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 μg/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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP392539     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     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   China 2022-08-16 Juvenile Juvenile Spleen Hematopoietic System
71019 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.   pubmed:37227178;pubmed:40392591   SVCV scRNAseq GSM6469456   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   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 μm 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 μg/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 3’ 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.   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 μm 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 μg/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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP392539     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     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   China 2022-08-16 Juvenile Juvenile Spleen Hematopoietic System
71020 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.   pubmed:37227178;pubmed:40392591   PBS scRNAseq GSM6469455   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   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 μm 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 μg/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 3’ 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.   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 μm 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 μg/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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP392539     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     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   China 2022-08-16 Juvenile Juvenile Spleen Hematopoietic System
71807 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   hapln1a+ development scRNAseq GSM6685234   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   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 3’ v3.1 protocol 10x Genomics   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP404721   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   339791226 243552181 266423271 301107277 140546 SRX18039091 SRS15545647 SRA1528482 Emory University Emory University 1 0.92176   0.1499   0.81781   0.50927   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-10-26 Juvenile Juvenile Heart Cardiovascular System
71808 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   hapln1a+ development scRNAseq GSM6685234   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   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 3’ v3.1 protocol 10x Genomics   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP404721   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   281795062 202126091 221122322 249574256 112773 SRX18039091 SRS15545647 SRA1528482 Emory University Emory University 1 0.92141   0.14909   0.81714   0.50543   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-10-26 Juvenile Juvenile Heart Cardiovascular System
71809 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   hapln1a+ development scRNAseq GSM6685234   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   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 3’ v3.1 protocol 10x Genomics   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP404721   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   251072030 180002392 196984629 222418470 101754 SRX18039091 SRS15545647 SRA1528482 Emory University Emory University 1 0.92231   0.15014   0.8174   0.50735   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-10-26 Juvenile Juvenile Heart Cardiovascular System
71810 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   hapln1a+ development scRNAseq GSM6685234   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   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 3’ v3.1 protocol 10x Genomics   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP404721   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   288451488 206540819 226008729 255442217 119152 SRX18039091 SRS15545647 SRA1528482 Emory University Emory University 1 0.92215   0.15108   0.81706   0.51589   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-10-26 Juvenile Juvenile Heart Cardiovascular System
71811 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   tcf21+ development scRNAseq GSM6685266   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   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 3’ v3.1 protocol 10x Genomics   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP404726     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     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   United States 2022-10-26 Juvenile Juvenile Heart Cardiovascular System
72748 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   pubmed:39138165   9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg GSM6940303   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 “Integration and Label Transfer” 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   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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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. 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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP418118     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     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   United States 2023-01-18 Juvenile Juvenile Embryo Imprecise All anatomical structures
72749 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   pubmed:39138165   9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg GSM6940303   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 “Integration and Label Transfer” 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   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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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. 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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP418118     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     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   United States 2023-01-18 Juvenile Juvenile Embryo Imprecise All anatomical structures
72750 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   pubmed:39138165   9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg GSM6940303   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 “Integration and Label Transfer” 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   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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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. 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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP418118     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     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   United States 2023-01-18 Juvenile Juvenile Embryo Imprecise All anatomical structures
72751 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   pubmed:39138165   9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg GSM6940303   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 “Integration and Label Transfer” 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   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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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. 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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP418118     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     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   United States 2023-01-18 Juvenile Juvenile Embryo Imprecise All anatomical structures
72752 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   pubmed:39138165   9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg GSM6940302   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 “Integration and Label Transfer” 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   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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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. 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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP418118     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     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   United States 2023-01-18 Juvenile Juvenile Embryo Imprecise All anatomical structures
72753 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   pubmed:39138165   9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg GSM6940302   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 “Integration and Label Transfer” 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   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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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. 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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP418118     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     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   United States 2023-01-18 Juvenile Juvenile Embryo Imprecise All anatomical structures
72754 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   pubmed:39138165   9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg GSM6940302   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 “Integration and Label Transfer” 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   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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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. 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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP418118     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     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   United States 2023-01-18 Juvenile Juvenile Embryo Imprecise All anatomical structures
72755 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   pubmed:39138165   9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg GSM6940302   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 “Integration and Label Transfer” 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   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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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. 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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP418118     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     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   United States 2023-01-18 Juvenile Juvenile Embryo Imprecise All anatomical structures
74187 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.   pubmed:38518783   Replicate3 GSM7058866   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   Library was performed according to the manufacter’s instructions single cell 3’ 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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA HiSeq X Ten   SRP424004   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   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   0.25806   0.75777   0.51359   98   B   usable mapping rate illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   France 2023-02-22 Juvenile Juvenile Brain Nervous System
74188 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.   pubmed:38518783   Replicate3 GSM7058866   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   Library was performed according to the manufacter’s instructions single cell 3’ 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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA HiSeq X Ten   SRP424004   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   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   0.25527   0.76077   0.5112   98   B   usable mapping rate illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   France 2023-02-22 Juvenile Juvenile Brain Nervous System
74189 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.   pubmed:38518783   Replicate3 GSM7058866   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   Library was performed according to the manufacter’s instructions single cell 3’ 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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA HiSeq X Ten   SRP424004   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   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   0.2551   0.76256   0.50337   98   B   usable mapping rate illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   France 2023-02-22 Juvenile Juvenile Brain Nervous System
74190 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.   pubmed:38518783   Replicate3 GSM7058866   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   Library was performed according to the manufacter’s instructions single cell 3’ 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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA HiSeq X Ten   SRP424004   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   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   0.25596   0.7626   0.5081   98   B   usable mapping rate illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   France 2023-02-22 Juvenile Juvenile Brain Nervous System
74191 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.   pubmed:38518783   Replicate3 GSM7058866   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   Library was performed according to the manufacter’s instructions single cell 3’ 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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA HiSeq X Ten   SRP424004   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   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   0.25581   0.75996   0.51556   98   B   usable mapping rate illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   France 2023-02-22 Juvenile Juvenile Brain Nervous System
74192 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. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.   pubmed:38518783   Replicate3 GSM7058866   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   Library was performed according to the manufacter’s instructions single cell 3’ 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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA HiSeq X Ten   SRP424004   loader:fastq load.py Replicate3_S6_L007_I1_001.fastq.gz Replicate3_S6_L007_R1_001.fastq.gz Replicate3_S6_L007_R2_001.fastq.gz fastq fastq fastq 10691125368.0 80993374.0 GSM7058866 r6 0:8 1:26 2:98 A:2364908014;C:1503792848;G:1627924254;T:2438606668;N:2118868 8 26 98   2364908014 1503792848 1627924254 2438606668 2118868 SRX19477372 SRS16868715 SRA1594515 Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur 1 0.88503   0.2597   0.76088   0.49989   98   B   usable mapping rate illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   France 2023-02-22 Juvenile Juvenile Brain Nervous System
74193 74193 SRR23592275 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.   pubmed:38518783   Replicate3 GSM7058866   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   Library was performed according to the manufacter’s instructions single cell 3’ 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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA HiSeq X Ten   SRP424004   loader:fastq load.py Replicate3_S6_L008_I1_001.fastq.gz Replicate3_S6_L008_R1_001.fastq.gz Replicate3_S6_L008_R2_001.fastq.gz fastq fastq fastq 10670015664.0 80833452.0 GSM7058866 r7 0:8 1:26 2:98 A:2360988524;C:1500040180;G:1624712352;T:2433842237;N:2095003 8 26 98   2360988524 1500040180 1624712352 2433842237 2095003 SRX19477372 SRS16868715 SRA1594515 Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur 1 0.8827   0.25599   0.76404   0.51295   98   B   usable mapping rate illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   France 2023-02-22 Juvenile Juvenile Brain Nervous System
74194 74194 SRR23592276 SRX19477371 SRS16868714 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.   pubmed:38518783   Replicate2 GSM7058865   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   Library was performed according to the manufacter’s instructions single cell 3’ 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.   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. 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA HiSeq X Ten   SRP424004   loader:fastq load.py Replicate2_S4_L002_I1_001.fastq.gz Replicate2_S4_L002_R1_001.fastq.gz Replicate2_S4_L002_R2_001.fastq.gz fastq fastq fastq 9701122992.0 73493356.0 GSM7058865 r1 0:8 1:26 2:98 A:2156760689;C:1368071124;G:1455967716;T:2219399616;N:2149743 8 26 98   2156760689 1368071124 1455967716 2219399616 2149743 SRX19477371 SRS16868714 SRA1594515 Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur 1 0.88255   0.29986   0.76455   0.51063   98   B   usable mapping rate illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   France 2023-02-22 Juvenile Juvenile Brain Nervous System
74195 74195 SRR23592277 SRX19477371 SRS16868714 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.   pubmed:38518783   Replicate2 GSM7058865   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   Library was performed according to the manufacter’s instructions single cell 3’ 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.   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. 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA HiSeq X Ten   SRP424004   loader:fastq load.py Replicate2_S4_L003_I1_001.fastq.gz Replicate2_S4_L003_R1_001.fastq.gz Replicate2_S4_L003_R2_001.fastq.gz fastq fastq fastq 9709605840.0 73557620.0 GSM7058865 r2 0:8 1:26 2:98 A:2158945438;C:1367438603;G:1458088740;T:2222002830;N:2171149 8 26 98   2158945438 1367438603 1458088740 2222002830 2171149 SRX19477371 SRS16868714 SRA1594515 Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur 1 0.87759   0.2985   0.76684   0.5129   98   B   usable mapping rate illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   France 2023-02-22 Juvenile Juvenile Brain Nervous System
74196 74196 SRR23592278 SRX19477371 SRS16868714 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.   pubmed:38518783   Replicate2 GSM7058865   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   Library was performed according to the manufacter’s instructions single cell 3’ 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.   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. 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA HiSeq X Ten   SRP424004   loader:fastq load.py Replicate2_S4_L004_I1_001.fastq.gz Replicate2_S4_L004_R1_001.fastq.gz Replicate2_S4_L004_R2_001.fastq.gz fastq fastq fastq 9708008508.0 73545519.0 GSM7058865 r3 0:8 1:26 2:98 A:2159475104;C:1367156483;G:1455925675;T:2222489574;N:2414026 8 26 98   2159475104 1367156483 1455925675 2222489574 2414026 SRX19477371 SRS16868714 SRA1594515 Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur 1 0.88227   0.30004   0.76564   0.50693   98   B   usable mapping rate illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   France 2023-02-22 Juvenile Juvenile Brain Nervous System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;