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 30626,SRR27907720,SRX23567476,SRS20412967,SRP488787,PRJNA1074408,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [scRNA seq],GSE255303,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: intestine leukocyte WT and KO Ctla 4 deficiency of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.,,pubmed:40392591,,KO scRNAseq,GSM8068833,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO|geo loc name:missing|collection date:missing,KO 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: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine 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.,,tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO,GSM8068833,GSM8068833: KO scRNAseq; Danio rerio; RNA Seq,GSM8068833 r1,GSM8068833,1,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine 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,,SRP488787,,loader:fastq load.py,KO_S1_L001_R2_001.fastq.gz KO_S1_L001_R1_001.fastq.gz,fastq fastq,40958285011.0,344187269.0,GSM8068833 r1,0:28 1:91,A:11614416767;C:9247684357;G:9480911439;T:10614469263;N:803185,28,91,,,11614416767,9247684357,9480911439,10614469263,803185,SRX23567476,SRS20412967,SRA1799569,zhejiang university,zhejiang university,2,0.00982,0.9431,0.00356,0.10625,0.99277,0.8187,0.41297,0.63838,28,91,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System 30627,SRR27907721,SRX23567475,SRS20412966,SRP488787,PRJNA1074408,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [scRNA seq],GSE255303,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: intestine leukocyte WT and KO Ctla 4 deficiency of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.,,pubmed:40392591,,WT scRNAseq,GSM8068832,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Wildtype|geo loc name:missing|collection date:missing,WT 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: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine 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.,,tissue:intestine|cell type:leukocyte|genotype:Wildtype,GSM8068832,GSM8068832: WT scRNAseq; Danio rerio; RNA Seq,GSM8068832 r1,GSM8068832,1,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine 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,,SRP488787,,loader:fastq load.py,WT_S1_L001_R1_001.fastq.gz WT_S1_L001_R2_001.fastq.gz,fastq fastq,36724066995.0,308605605.0,GSM8068832 r1,0:28 1:91,A:10425178276;C:8399183780;G:8411777361;T:9487202777;N:724801,28,91,,,10425178276,8399183780,8411777361,9487202777,724801,SRX23567475,SRS20412966,SRA1799569,zhejiang university,zhejiang university,2,0.01141,0.94944,0.0039,0.1092,0.99324,0.841,0.43558,0.73314,28,91,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System 30694,SRR28272066,SRX23882001,SRS20705714,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122775 HuNoV infected replicate 2 scRNAseq,GSM8136771,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing,GC122775 HuNoV infected replicate 2 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected,GSM8136771,GSM8136771: GC122775 HuNoV infected replicate 2 scRNAseq; Danio rerio; RNA Seq,GSM8136771 r1,GSM8136771,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122775_SI-GA-D7_S4_L001_R1_001.fastq.gz GC122775_SI-GA-D7_S4_L001_R2_001.fastq.gz,fastq fastq,6487168261.0,54514019.0,GSM8136771 r1,0:28 1:91,A:1754199332;C:1533792234;G:1687916105;T:1511168304;N:92286,28,91,,,1754199332,1533792234,1687916105,1511168304,92286,SRX23882001,SRS20705714,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System 30695,SRR28272067,SRX23882001,SRS20705714,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122775 HuNoV infected replicate 2 scRNAseq,GSM8136771,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing,GC122775 HuNoV infected replicate 2 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected,GSM8136771,GSM8136771: GC122775 HuNoV infected replicate 2 scRNAseq; Danio rerio; RNA Seq,GSM8136771 r1,GSM8136771,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122775_SI-GA-D7_S4_L002_R1_001.fastq.gz GC122775_SI-GA-D7_S4_L002_R2_001.fastq.gz,fastq fastq,6313572727.0,53055233.0,GSM8136771 r2,0:28 1:91,A:1709609257;C:1491468410;G:1640296277;T:1472111501;N:87282,28,91,,,1709609257,1491468410,1640296277,1472111501,87282,SRX23882001,SRS20705714,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System 30696,SRR28272068,SRX23882000,SRS20705713,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122774 HuNoV infected replicate 1 scRNAseq,GSM8136770,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing,GC122774 HuNoV infected replicate 1 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected,GSM8136770,GSM8136770: GC122774 HuNoV infected replicate 1 scRNAseq; Danio rerio; RNA Seq,GSM8136770 r1,GSM8136770,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122774_SI-GA-C7_S3_L001_R1_001.fastq.gz GC122774_SI-GA-C7_S3_L001_R2_001.fastq.gz,fastq fastq,15738518978.0,132256462.0,GSM8136770 r1,0:28 1:91,A:4181691582;C:3761213961;G:4083789142;T:3711597081;N:227212,28,91,,,4181691582,3761213961,4083789142,3711597081,227212,SRX23882000,SRS20705713,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System 30697,SRR28272069,SRX23882000,SRS20705713,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122774 HuNoV infected replicate 1 scRNAseq,GSM8136770,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing,GC122774 HuNoV infected replicate 1 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected,GSM8136770,GSM8136770: GC122774 HuNoV infected replicate 1 scRNAseq; Danio rerio; RNA Seq,GSM8136770 r1,GSM8136770,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122774_SI-GA-C7_S3_L002_R1_001.fastq.gz GC122774_SI-GA-C7_S3_L002_R2_001.fastq.gz,fastq fastq,15261653253.0,128249187.0,GSM8136770 r2,0:28 1:91,A:4059552936;C:3644406570;G:3954261902;T:3603216152;N:215693,28,91,,,4059552936,3644406570,3954261902,3603216152,215693,SRX23882000,SRS20705713,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System 30698,SRR28272070,SRX23881999,SRS20705712,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122773 uninfected replicate 2 scRNAseq,GSM8136769,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing,GC122773 uninfected replicate 2 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected,GSM8136769,GSM8136769: GC122773 uninfected replicate 2 scRNAseq; Danio rerio; RNA Seq,GSM8136769 r1,GSM8136769,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122773_SI-GA-B7_S2_L001_R1_001.fastq.gz GC122773_SI-GA-B7_S2_L001_R2_001.fastq.gz,fastq fastq,15150656598.0,127316442.0,GSM8136769 r1,0:28 1:91,A:4100783574;C:3526779401;G:3845684506;T:3677189004;N:220113,28,91,,,4100783574,3526779401,3845684506,3677189004,220113,SRX23881999,SRS20705712,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System 30699,SRR28272071,SRX23881999,SRS20705712,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122773 uninfected replicate 2 scRNAseq,GSM8136769,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing,GC122773 uninfected replicate 2 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected,GSM8136769,GSM8136769: GC122773 uninfected replicate 2 scRNAseq; Danio rerio; RNA Seq,GSM8136769 r1,GSM8136769,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122773_SI-GA-B7_S2_L002_R1_001.fastq.gz GC122773_SI-GA-B7_S2_L002_R2_001.fastq.gz,fastq fastq,14942015326.0,125563154.0,GSM8136769 r2,0:28 1:91,A:4048600218;C:3475105088;G:3787275869;T:3630822343;N:211808,28,91,,,4048600218,3475105088,3787275869,3630822343,211808,SRX23881999,SRS20705712,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System 30700,SRR28272072,SRX23881998,SRS20705711,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122772 uninfected replicate 1 scRNAseq,GSM8136768,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing,GC122772 uninfected replicate 1 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected,GSM8136768,GSM8136768: GC122772 uninfected replicate 1 scRNAseq; Danio rerio; RNA Seq,GSM8136768 r1,GSM8136768,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122772_SI-GA-A7_S1_L001_R1_001.fastq.gz GC122772_SI-GA-A7_S1_L001_R2_001.fastq.gz,fastq fastq,7397061301.0,62160179.0,GSM8136768 r1,0:28 1:91,A:2023651844;C:1711760729;G:1860691426;T:1800850496;N:106806,28,91,,,2023651844,1711760729,1860691426,1800850496,106806,SRX23881998,SRS20705711,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System 30701,SRR28272073,SRX23881998,SRS20705711,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122772 uninfected replicate 1 scRNAseq,GSM8136768,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing,GC122772 uninfected replicate 1 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected,GSM8136768,GSM8136768: GC122772 uninfected replicate 1 scRNAseq; Danio rerio; RNA Seq,GSM8136768 r1,GSM8136768,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122772_SI-GA-A7_S1_L002_R1_001.fastq.gz GC122772_SI-GA-A7_S1_L002_R2_001.fastq.gz,fastq fastq,7290496444.0,61264676.0,GSM8136768 r2,0:28 1:91,A:1996736343;C:1685693360;G:1830823892;T:1777138653;N:104196,28,91,,,1996736343,1685693360,1830823892,1777138653,104196,SRX23881998,SRS20705711,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System 33014,SRR29633212,SRX25139207,SRS21831220,SRP516661,PRJNA1129181,A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing,GSE271002,Transcriptome Analysis,To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation and DAPI live cells were sorted by FACS.,,pubmed:40252728,,Mtz 5dpf,GSM8366963,,source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole|geo loc name:missing|collection date:missing,Mtz 5dpf,Demultiplexing of raw Illumina sequencing files barcoding processing gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files,Dissected larval intestines,,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole,GSM8366963,GSM8366963: Mtz 5dpf; Danio rerio; RNA Seq,GSM8366963 r1,GSM8366963,1,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP516661,,loader:fastq load.py,NTR-Mtz-d5_R1.fastq.gz NTR-Mtz-d5_R2.fastq.gz,fastq fastq,105173263361.0,348971465.0,GSM8366963 r1,0:150.76 1:150.62,A:29260313483;C:18342577741;G:20471735616;T:37097033318;N:1603203,150,150,,,29260313483,18342577741,20471735616,37097033318,1603203,SRX25139207,SRS21831220,SRA1911905,Karolinska Institutet,Karolinska Institutet,2,0.56019,0.89517,0.13273,0.11945,0.9795,0.82258,0.63676,0.6161,151,150,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-06-27,Larval,Larval,Gut,Digestive System 33015,SRR29633213,SRX25139206,SRS21831219,SRP516661,PRJNA1129181,A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing,GSE271002,Transcriptome Analysis,To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation and DAPI live cells were sorted by FACS.,,pubmed:40252728,,Control 5dpf,GSM8366962,,source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control|geo loc name:missing|collection date:missing,Control 5dpf,Demultiplexing of raw Illumina sequencing files barcoding processing gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files,Dissected larval intestines,,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control,GSM8366962,GSM8366962: Control 5dpf; Danio rerio; RNA Seq,GSM8366962 r1,GSM8366962,1,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP516661,,loader:fastq load.py,NTR-Control-d5_R1.fastq.gz NTR-Control-d5_R2.fastq.gz,fastq fastq,139967773505.0,464402100.0,GSM8366962 r1,0:150.76 1:150.63,A:39202616731;C:24289494719;G:27175225437;T:49298534102;N:1902516,150,150,,,39202616731,24289494719,27175225437,49298534102,1902516,SRX25139206,SRS21831219,SRA1911905,Karolinska Institutet,Karolinska Institutet,2,0.54902,0.89315,0.13449,0.13341,0.97954,0.80553,0.69256,0.59244,151,151,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-06-27,Larval,Larval,Gut,Digestive System 33016,SRR29633214,SRX25139205,SRS21831218,SRP516661,PRJNA1129181,A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing,GSE271002,Transcriptome Analysis,To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation and DAPI live cells were sorted by FACS.,,pubmed:40252728,,Mtz ablation 4dpf,GSM8366961,,source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole|geo loc name:missing|collection date:missing,Mtz ablation 4dpf,Demultiplexing of raw Illumina sequencing files barcoding processing gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files,Dissected larval intestines,,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole,GSM8366961,GSM8366961: Mtz ablation 4dpf; Danio rerio; RNA Seq,GSM8366961 r1,GSM8366961,1,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP516661,,loader:fastq load.py|options: readTypes=BBTT read1PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 R1 001.fastq.gz read2PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 R2 001.fastq.gz read3PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 I1 001.fastq.gz read4PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 I2 001.fastq.gz,Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_R2_001.fastq.gz Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_R1_001.fastq.gz Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_I2_001.fastq.gz Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_I1_001.fastq.gz,fastq fastq fastq fastq,33049837760.0,103280743.0,GSM8366961 r1,0:150 1:150 2:10 3:10,A:9739096160;C:6338831532;G:6106096444;T:8799858219;N:340545,150,150,10,10,9739096160,6338831532,6106096444,8799858219,340545,SRX25139205,SRS21831218,SRA1911905,Karolinska Institutet,Karolinska Institutet,2,0.0,0.91169,0.0,0.19328,1.0,0.81722,,0.64993,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-06-27,Larval,Larval,Gut,Digestive System 33017,SRR29633215,SRX25139204,SRS21831217,SRP516661,PRJNA1129181,A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing,GSE271002,Transcriptome Analysis,To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation and DAPI live cells were sorted by FACS.,,pubmed:40252728,,Control ablation 4dpf,GSM8366960,,source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control|geo loc name:missing|collection date:missing,Control ablation 4dpf,Demultiplexing of raw Illumina sequencing files barcoding processing gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files,Dissected larval intestines,,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control,GSM8366960,GSM8366960: Control ablation 4dpf; Danio rerio; RNA Seq,GSM8366960 r1,GSM8366960,1,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP516661,,loader:fastq load.py|options: readTypes=BBTT read1PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 R1 001.fastq.gz read2PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 R2 001.fastq.gz read3PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 I1 001.fastq.gz read4PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 I2 001.fastq.gz,Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_R2_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_R1_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_I2_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_I1_001.fastq.gz,fastq fastq fastq fastq,115286504000.0,360270325.0,GSM8366960 r1,0:150 1:150 2:10 3:10,A:32679027944;C:17748865933;G:17885040590;T:39764959491;N:3203542,150,150,10,10,32679027944,17748865933,17885040590,39764959491,3203542,SRX25139204,SRS21831217,SRA1911905,Karolinska Institutet,Karolinska Institutet,2,0.39015,0.90036,0.10989,0.19421,0.97845,0.79401,0.69547,0.6103,150,150,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-06-27,Larval,Larval,Gut,Digestive System 33417,SRR30186672,SRX25652379,SRS22295184,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS6dpf,GSM8448586,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf|geo loc name:missing|collection date:missing,ENS6dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf,GSM8448586,GSM8448586: ENS6dpf; Danio rerio; RNA Seq,GSM8448586 r1,GSM8448586,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26637_S5_L005_I1_001.fastq.gz FT-SA26637_S5_L005_R1_001.fastq.gz FT-SA26637_S5_L005_R2_001.fastq.gz,fastq fastq fastq,40502433410.0,130653011.0,GSM8448586 r1,0:8 1:151 2:151,A:10014178947;C:5704376875;G:6596271508;T:17137143949;N:5238043,8,151,151,,10014178947,5704376875,6596271508,17137143949,5238043,SRX25652379,SRS22295184,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System 33418,SRR30186673,SRX25652379,SRS22295184,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS6dpf,GSM8448586,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf|geo loc name:missing|collection date:missing,ENS6dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf,GSM8448586,GSM8448586: ENS6dpf; Danio rerio; RNA Seq,GSM8448586 r1,GSM8448586,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26637_S5_L006_I1_001.fastq.gz FT-SA26637_S5_L006_R1_001.fastq.gz FT-SA26637_S5_L006_R2_001.fastq.gz,fastq fastq fastq,41972742020.0,135395942.0,GSM8448586 r2,0:8 1:151 2:151,A:10346550415;C:6105559893;G:6757897068;T:17672755179;N:6811929,8,151,151,,10346550415,6105559893,6757897068,17672755179,6811929,SRX25652379,SRS22295184,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System 33419,SRR30186674,SRX25652378,SRS22295179,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS5dpf,GSM8448585,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf|geo loc name:missing|collection date:missing,ENS5dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf,GSM8448585,GSM8448585: ENS5dpf; Danio rerio; RNA Seq,GSM8448585 r1,GSM8448585,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26636_S4_L005_I1_001.fastq.gz FT-SA26636_S4_L005_R1_001.fastq.gz FT-SA26636_S4_L005_R2_001.fastq.gz,fastq fastq fastq,21590505830.0,69646793.0,GSM8448585 r1,0:8 1:151 2:151,A:5324745627;C:3047288539;G:3517496789;T:9140955618;N:2844913,8,151,151,,5324745627,3047288539,3517496789,9140955618,2844913,SRX25652378,SRS22295179,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System 33420,SRR30186675,SRX25652378,SRS22295179,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS5dpf,GSM8448585,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf|geo loc name:missing|collection date:missing,ENS5dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf,GSM8448585,GSM8448585: ENS5dpf; Danio rerio; RNA Seq,GSM8448585 r1,GSM8448585,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26636_S4_L006_I1_001.fastq.gz FT-SA26636_S4_L006_R1_001.fastq.gz FT-SA26636_S4_L006_R2_001.fastq.gz,fastq fastq fastq,22493595040.0,72559984.0,GSM8448585 r2,0:8 1:151 2:151,A:5532271824;C:3275587569;G:3623404196;T:9478183540;N:3668039,8,151,151,,5532271824,3275587569,3623404196,9478183540,3668039,SRX25652378,SRS22295179,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System 33421,SRR30186676,SRX25652377,SRS22295180,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS4dpf,GSM8448584,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:4dpf|geo loc name:missing|collection date:missing,ENS4dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:4dpf,GSM8448584,GSM8448584: ENS4dpf; Danio rerio; RNA Seq,GSM8448584 r1,GSM8448584,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26635_S3_L005_I1_001.fastq.gz FT-SA26635_S3_L005_R1_001.fastq.gz FT-SA26635_S3_L005_R2_001.fastq.gz,fastq fastq fastq,29011782450.0,93586395.0,GSM8448584 r1,0:8 1:151 2:151,A:7041483148;C:4220842692;G:4903817651;T:12093250712;N:3697087,8,151,151,,7041483148,4220842692,4903817651,12093250712,3697087,SRX25652377,SRS22295180,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System 33422,SRR30186677,SRX25652377,SRS22295180,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS4dpf,GSM8448584,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:4dpf|geo loc name:missing|collection date:missing,ENS4dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:4dpf,GSM8448584,GSM8448584: ENS4dpf; Danio rerio; RNA Seq,GSM8448584 r1,GSM8448584,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26635_S3_L006_I1_001.fastq.gz FT-SA26635_S3_L006_R1_001.fastq.gz FT-SA26635_S3_L006_R2_001.fastq.gz,fastq fastq fastq,30061975960.0,96974116.0,GSM8448584 r2,0:8 1:151 2:151,A:7272472037;C:4518131790;G:5023942263;T:12466801069;N:4835873,8,151,151,,7272472037,4518131790,5023942263,12466801069,4835873,SRX25652377,SRS22295180,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System 33423,SRR30186678,SRX25652376,SRS22295175,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS3dpf,GSM8448583,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:3dpf|geo loc name:missing|collection date:missing,ENS3dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:3dpf,GSM8448583,GSM8448583: ENS3dpf; Danio rerio; RNA Seq,GSM8448583 r1,GSM8448583,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26634_S2_L005_I1_001.fastq.gz FT-SA26634_S2_L005_R1_001.fastq.gz FT-SA26634_S2_L005_R2_001.fastq.gz,fastq fastq fastq,28701845380.0,92586598.0,GSM8448583 r1,0:8 1:151 2:151,A:6898569356;C:4281479855;G:4993869601;T:11783488306;N:3745478,8,151,151,,6898569356,4281479855,4993869601,11783488306,3745478,SRX25652376,SRS22295175,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System 33424,SRR30186679,SRX25652376,SRS22295175,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS3dpf,GSM8448583,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:3dpf|geo loc name:missing|collection date:missing,ENS3dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:3dpf,GSM8448583,GSM8448583: ENS3dpf; Danio rerio; RNA Seq,GSM8448583 r1,GSM8448583,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26634_S2_L006_I1_001.fastq.gz FT-SA26634_S2_L006_R1_001.fastq.gz FT-SA26634_S2_L006_R2_001.fastq.gz,fastq fastq fastq,29814490250.0,96175775.0,GSM8448583 r2,0:8 1:151 2:151,A:7143218463;C:4592538828;G:5130593993;T:12173956857;N:4775909,8,151,151,,7143218463,4592538828,5130593993,12173956857,4775909,SRX25652376,SRS22295175,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System 33425,SRR30186680,SRX25652375,SRS22295177,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS2dpf,GSM8448582,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:2dpf|geo loc name:missing|collection date:missing,ENS2dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:2dpf,GSM8448582,GSM8448582: ENS2dpf; Danio rerio; RNA Seq,GSM8448582 r1,GSM8448582,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26633_S1_L005_I1_001.fastq.gz FT-SA26633_S1_L005_R1_001.fastq.gz FT-SA26633_S1_L005_R2_001.fastq.gz,fastq fastq fastq,16641390240.0,53681904.0,GSM8448582 r1,0:8 1:151 2:151,A:3957785280;C:2573469243;G:2993166279;T:6685407270;N:2106936,8,151,151,,3957785280,2573469243,2993166279,6685407270,2106936,SRX25652375,SRS22295177,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Hatching,Embryo,Gut,Digestive System 33426,SRR30186681,SRX25652375,SRS22295177,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS2dpf,GSM8448582,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:2dpf|geo loc name:missing|collection date:missing,ENS2dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:2dpf,GSM8448582,GSM8448582: ENS2dpf; Danio rerio; RNA Seq,GSM8448582 r1,GSM8448582,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26633_S1_L006_I1_001.fastq.gz FT-SA26633_S1_L006_R1_001.fastq.gz FT-SA26633_S1_L006_R2_001.fastq.gz,fastq fastq fastq,17304656010.0,55821471.0,GSM8448582 r2,0:8 1:151 2:151,A:4101777717;C:2763806899;G:3078134302;T:6911601509;N:2763815,8,151,151,,4101777717,2763806899,3078134302,6911601509,2763815,SRX25652375,SRS22295177,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Hatching,Embryo,Gut,Digestive System 74121,SRR23507771,SRX19401042,SRS16795999,SRP423151,PRJNA936083,Gene expression profile at single cell level of the enteric nervous system ENS of 5 dpf dpf zebrafish,GSE225510,Other,We used single cell RNA sequencing scRNA seq to characterize the ENS in the zebrafish intestine. Overall design: Zebrafish intestines were manually isolated at 5dpf and dissociated into a single cell suspension. Live single cells were sorted by Fluorescence activated cell sorting FACS according to the presence or absence of DAPI signal. Sorted cells were processed and analyzed using 10X scRNAseq.,,pubmed:37426341,,LK1 Gut ZF,GSM7049686,,source name:Whole gut|cell type:Enteric nervous system cells|tissue:Whole gut|line:wt tgphox2bb:GFP|age:5 dpf loc name:missing|collection date:missing,LK1 Gut ZF,Cellranger count v 4.0.0 was employed for barcode processing gene counting and aggregation of the samples Downstream analysis was performed in Seurat v 4.1.1 Assembly: GRCz10 Supplementary files format and content: Tab separated values files and matrix files,Whole gut,N/A N/A,In total 244 intestines of 5 dpf dpf larvae were isolated cells were dissociated using 2.17mg/mL papain and the live cells were sorted using FACS. Cells were then loaded onto the 10X platform for single cell RNA sequencing. Libraries were made according to the manufacter’s instructions Single Cell three prime v3 chemistry 10x Genomics,Zebrafish were kept on a 14/10h light/dark cycle. Embryos and larvae were kept in an incubator at 28.5°C in HEPES buffered E3 medium.,cell type:Enteric nervous system cells|tissue:Whole gut|line:wt tgphox2bb:GFP|age:5 dpf,GSM7049686,GSM7049686: LK1 Gut ZF; Danio rerio; RNA Seq,GSM7049686 r1,GSM7049686,1,In total 244 intestines of 5 dpf dpf larvae were isolated cells were dissociated using 2.17mg/mL papain and the live cells were sorted using FACS. Cells were then loaded onto the 10X platform for single cell RNA sequencing. Libraries were made according to the manufacter's instructions Single Cell three prime v3 chemistry 10x Genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP423151,,loader:fastq load.py|options: readTypes=TTB read1PairFiles=LK1 Gut ZF run2 S8 L001 I1 001.fastq.gz read2PairFiles=LK1 Gut ZF run2 S8 L001 R1 001.fastq.gz read3PairFiles=LK1 Gut ZF run2 S8 L001 R2 001.fastq.gz,LK1_Gut_ZF_run2_S8_L001_I1_001.fastq.gz LK1_Gut_ZF_run2_S8_L001_R1_001.fastq.gz LK1_Gut_ZF_run2_S8_L001_R2_001.fastq.gz,fastq fastq fastq,11881203187.0,93552781.0,GSM7049686 r1,0:8 1:28 2:91,A:2429036172;C:1882931305;G:2017284406;T:2183658347;N:392841,8,28,91,,2429036172,1882931305,2017284406,2183658347,392841,SRX19401042,SRS16795999,SRA1591972,"Clinical, Erasmus MC","Clinical Genetics, Erasmus MC",1,0.94131,,0.11964,,0.75694,,0.51218,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Netherlands,2023-02-17,Larval,Larval,Gut,Digestive System 74122,SRR23507772,SRX19401042,SRS16795999,SRP423151,PRJNA936083,Gene expression profile at single cell level of the enteric nervous system ENS of 5 dpf dpf zebrafish,GSE225510,Other,We used single cell RNA sequencing scRNA seq to characterize the ENS in the zebrafish intestine. Overall design: Zebrafish intestines were manually isolated at 5dpf and dissociated into a single cell suspension. Live single cells were sorted by Fluorescence activated cell sorting FACS according to the presence or absence of DAPI signal. Sorted cells were processed and analyzed using 10X scRNAseq.,,pubmed:37426341,,LK1 Gut ZF,GSM7049686,,source name:Whole gut|cell type:Enteric nervous system cells|tissue:Whole gut|line:wt tgphox2bb:GFP|age:5 dpf loc name:missing|collection date:missing,LK1 Gut ZF,Cellranger count v 4.0.0 was employed for barcode processing gene counting and aggregation of the samples Downstream analysis was performed in Seurat v 4.1.1 Assembly: GRCz10 Supplementary files format and content: Tab separated values files and matrix files,Whole gut,N/A N/A,In total 244 intestines of 5 dpf dpf larvae were isolated cells were dissociated using 2.17mg/mL papain and the live cells were sorted using FACS. Cells were then loaded onto the 10X platform for single cell RNA sequencing. Libraries were made according to the manufacter’s instructions Single Cell three prime v3 chemistry 10x Genomics,Zebrafish were kept on a 14/10h light/dark cycle. Embryos and larvae were kept in an incubator at 28.5°C in HEPES buffered E3 medium.,cell type:Enteric nervous system cells|tissue:Whole gut|line:wt tgphox2bb:GFP|age:5 dpf,GSM7049686,GSM7049686: LK1 Gut ZF; Danio rerio; RNA Seq,GSM7049686 r1,GSM7049686,1,In total 244 intestines of 5 dpf dpf larvae were isolated cells were dissociated using 2.17mg/mL papain and the live cells were sorted using FACS. Cells were then loaded onto the 10X platform for single cell RNA sequencing. Libraries were made according to the manufacter's instructions Single Cell three prime v3 chemistry 10x Genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP423151,,loader:fastq load.py|options: readTypes=TTB read1PairFiles=LK1 Gut ZF run2 S8 L002 I1 001.fastq.gz read2PairFiles=LK1 Gut ZF run2 S8 L002 R1 001.fastq.gz read3PairFiles=LK1 Gut ZF run2 S8 L002 R2 001.fastq.gz,LK1_Gut_ZF_run2_S8_L002_I1_001.fastq.gz LK1_Gut_ZF_run2_S8_L002_R1_001.fastq.gz LK1_Gut_ZF_run2_S8_L002_R2_001.fastq.gz,fastq fastq fastq,11851111426.0,93315838.0,GSM7049686 r2,0:8 1:28 2:91,A:2423220506;C:1877745404;G:2011423380;T:2178841059;N:510909,8,28,91,,2423220506,1877745404,2011423380,2178841059,510909,SRX19401042,SRS16795999,SRA1591972,"Clinical, Erasmus MC","Clinical Genetics, Erasmus MC",1,0.94177,,0.12005,,0.75592,,0.50957,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Netherlands,2023-02-17,Larval,Larval,Gut,Digestive System 74123,SRR23507773,SRX19401042,SRS16795999,SRP423151,PRJNA936083,Gene expression profile at single cell level of the enteric nervous system ENS of 5 dpf dpf zebrafish,GSE225510,Other,We used single cell RNA sequencing scRNA seq to characterize the ENS in the zebrafish intestine. Overall design: Zebrafish intestines were manually isolated at 5dpf and dissociated into a single cell suspension. Live single cells were sorted by Fluorescence activated cell sorting FACS according to the presence or absence of DAPI signal. Sorted cells were processed and analyzed using 10X scRNAseq.,,pubmed:37426341,,LK1 Gut ZF,GSM7049686,,source name:Whole gut|cell type:Enteric nervous system cells|tissue:Whole gut|line:wt tgphox2bb:GFP|age:5 dpf loc name:missing|collection date:missing,LK1 Gut ZF,Cellranger count v 4.0.0 was employed for barcode processing gene counting and aggregation of the samples Downstream analysis was performed in Seurat v 4.1.1 Assembly: GRCz10 Supplementary files format and content: Tab separated values files and matrix files,Whole gut,N/A N/A,In total 244 intestines of 5 dpf dpf larvae were isolated cells were dissociated using 2.17mg/mL papain and the live cells were sorted using FACS. Cells were then loaded onto the 10X platform for single cell RNA sequencing. Libraries were made according to the manufacter’s instructions Single Cell three prime v3 chemistry 10x Genomics,Zebrafish were kept on a 14/10h light/dark cycle. Embryos and larvae were kept in an incubator at 28.5°C in HEPES buffered E3 medium.,cell type:Enteric nervous system cells|tissue:Whole gut|line:wt tgphox2bb:GFP|age:5 dpf,GSM7049686,GSM7049686: LK1 Gut ZF; Danio rerio; RNA Seq,GSM7049686 r1,GSM7049686,1,In total 244 intestines of 5 dpf dpf larvae were isolated cells were dissociated using 2.17mg/mL papain and the live cells were sorted using FACS. Cells were then loaded onto the 10X platform for single cell RNA sequencing. Libraries were made according to the manufacter's instructions Single Cell three prime v3 chemistry 10x Genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP423151,,loader:fastq load.py|options: readTypes=TTB read1PairFiles=LK1 Gut ZF S17 L001 I1 001.fastq.gz read2PairFiles=LK1 Gut ZF S17 L001 R1 001.fastq.gz read3PairFiles=LK1 Gut ZF S17 L001 R2 001.fastq.gz,LK1_Gut_ZF_S17_L001_I1_001.fastq.gz LK1_Gut_ZF_S17_L001_R1_001.fastq.gz LK1_Gut_ZF_S17_L001_R2_001.fastq.gz,fastq fastq fastq,1348909164.0,10621332.0,GSM7049686 r3,0:8 1:28 2:91,A:277752540;C:212054476;G:226444772;T:250181229;N:108195,8,28,91,,277752540,212054476,226444772,250181229,108195,SRX19401042,SRS16795999,SRA1591972,"Clinical, Erasmus MC","Clinical Genetics, Erasmus MC",1,0.92509,,0.12318,,0.76002,,0.52069,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Netherlands,2023-02-17,Larval,Larval,Gut,Digestive System 74124,SRR23507774,SRX19401042,SRS16795999,SRP423151,PRJNA936083,Gene expression profile at single cell level of the enteric nervous system ENS of 5 dpf dpf zebrafish,GSE225510,Other,We used single cell RNA sequencing scRNA seq to characterize the ENS in the zebrafish intestine. Overall design: Zebrafish intestines were manually isolated at 5dpf and dissociated into a single cell suspension. Live single cells were sorted by Fluorescence activated cell sorting FACS according to the presence or absence of DAPI signal. Sorted cells were processed and analyzed using 10X scRNAseq.,,pubmed:37426341,,LK1 Gut ZF,GSM7049686,,source name:Whole gut|cell type:Enteric nervous system cells|tissue:Whole gut|line:wt tgphox2bb:GFP|age:5 dpf loc name:missing|collection date:missing,LK1 Gut ZF,Cellranger count v 4.0.0 was employed for barcode processing gene counting and aggregation of the samples Downstream analysis was performed in Seurat v 4.1.1 Assembly: GRCz10 Supplementary files format and content: Tab separated values files and matrix files,Whole gut,N/A N/A,In total 244 intestines of 5 dpf dpf larvae were isolated cells were dissociated using 2.17mg/mL papain and the live cells were sorted using FACS. Cells were then loaded onto the 10X platform for single cell RNA sequencing. Libraries were made according to the manufacter’s instructions Single Cell three prime v3 chemistry 10x Genomics,Zebrafish were kept on a 14/10h light/dark cycle. Embryos and larvae were kept in an incubator at 28.5°C in HEPES buffered E3 medium.,cell type:Enteric nervous system cells|tissue:Whole gut|line:wt tgphox2bb:GFP|age:5 dpf,GSM7049686,GSM7049686: LK1 Gut ZF; Danio rerio; RNA Seq,GSM7049686 r1,GSM7049686,1,In total 244 intestines of 5 dpf dpf larvae were isolated cells were dissociated using 2.17mg/mL papain and the live cells were sorted using FACS. Cells were then loaded onto the 10X platform for single cell RNA sequencing. Libraries were made according to the manufacter's instructions Single Cell three prime v3 chemistry 10x Genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP423151,,loader:fastq load.py|options: readTypes=TTB read1PairFiles=LK1 Gut ZF S17 L002 I1 001.fastq.gz read2PairFiles=LK1 Gut ZF S17 L002 R1 001.fastq.gz read3PairFiles=LK1 Gut ZF S17 L002 R2 001.fastq.gz,LK1_Gut_ZF_S17_L002_I1_001.fastq.gz LK1_Gut_ZF_S17_L002_R1_001.fastq.gz LK1_Gut_ZF_S17_L002_R2_001.fastq.gz,fastq fastq fastq,1342784716.0,10573108.0,GSM7049686 r4,0:8 1:28 2:91,A:276367810;C:211254670;G:225486422;T:248888442;N:155484,8,28,91,,276367810,211254670,225486422,248888442,155484,SRX19401042,SRS16795999,SRA1591972,"Clinical, Erasmus MC","Clinical Genetics, Erasmus MC",1,0.92536,,0.12213,,0.75668,,0.51878,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Netherlands,2023-02-17,Larval,Larval,Gut,Digestive System 74856,SRR24049045,SRX19850770,SRS17208527,SRP430632,PRJNA951670,Single cell transcriptome profiling reveals macrophage and dendritic cell heterogeneity across six zebrafish organs,GSE228806,Transcriptome Analysis,Tissue resident macrophages TRMs and dendritic cells DCs are highly diverse and play essential roles in immunity tissue regeneration and homeostasis maintenance. To systematically assess the heterogeneity of TRM and DC in adult zebrafish we performed droplet based scRNA seq on mpeg1.1+ cells sorted from six different organs epidermis gill intestine liver heart and brain of 6 mpf Tgmpeg1.1:DsRedx fish a widely used myeloid cell reporter line. We identified two macrophage subpopulations with pro inflammatory and pro remodeling signatures respectively as well as one conventional dendritic cell population with prominent antigen presentation capacity and plasmacytoid dendritic cells featuring anti viral properties. Our study provides a comprehensive landscape of TRMs and DCs in zebrafish and offers valuable tools for future in depth investigations of these cell types. Overall design: scRNA seq 10X genomics three prime V3.1 of FACS sorted mpeg1.1+ cells isolated from six different organs epidermis gill intestine liver heart and brain of 6 mpf Tgmpeg1.1:DsRedx fish,,pubmed:37453064,,intestine,GSM7139011,,source name:intestine|tissue:intestine|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT|geo loc name:missing|collection date:missing,intestine,Raw reads were aligned to zebrafish reference genome genome reference: GRCz11; annotation reference: GRCz11.103 combined with the sequences for DsRedx using the Cell Ranger pipelines v6.0. Downstream analysis of unique molecular identifiers UMI count matrix was conducted in R using the Seurat pipeline v4.0.5. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,For each organ six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief post the cell sorting single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.,,tissue:intestine|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT,GSM7139011,GSM7139011: intestine; Danio rerio; RNA Seq,GSM7139011 r1,GSM7139011,1,For each organ six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief post the cell sorting single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430632,,,intestine_S1_L001_R1_001.fastq.gz intestine_S1_L001_R2_001.fastq.gz,fastq fastq,53695349700.0,178984499.0,GSM7139011 r1,0:150 1:150,A:22274483622;C:9253547657;G:8722944861;T:13443840236;N:533324,150,150,,,22274483622,9253547657,8722944861,13443840236,533324,SRX19850770,SRS17208527,SRA1615101,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology","Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.0,0.88637,0.0,0.17744,1.0,0.82098,,0.57997,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-04-03,Adult,Adult,Gut,Digestive System 74857,SRR24049046,SRX19850770,SRS17208527,SRP430632,PRJNA951670,Single cell transcriptome profiling reveals macrophage and dendritic cell heterogeneity across six zebrafish organs,GSE228806,Transcriptome Analysis,Tissue resident macrophages TRMs and dendritic cells DCs are highly diverse and play essential roles in immunity tissue regeneration and homeostasis maintenance. To systematically assess the heterogeneity of TRM and DC in adult zebrafish we performed droplet based scRNA seq on mpeg1.1+ cells sorted from six different organs epidermis gill intestine liver heart and brain of 6 mpf Tgmpeg1.1:DsRedx fish a widely used myeloid cell reporter line. We identified two macrophage subpopulations with pro inflammatory and pro remodeling signatures respectively as well as one conventional dendritic cell population with prominent antigen presentation capacity and plasmacytoid dendritic cells featuring anti viral properties. Our study provides a comprehensive landscape of TRMs and DCs in zebrafish and offers valuable tools for future in depth investigations of these cell types. Overall design: scRNA seq 10X genomics three prime V3.1 of FACS sorted mpeg1.1+ cells isolated from six different organs epidermis gill intestine liver heart and brain of 6 mpf Tgmpeg1.1:DsRedx fish,,pubmed:37453064,,intestine,GSM7139011,,source name:intestine|tissue:intestine|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT|geo loc name:missing|collection date:missing,intestine,Raw reads were aligned to zebrafish reference genome genome reference: GRCz11; annotation reference: GRCz11.103 combined with the sequences for DsRedx using the Cell Ranger pipelines v6.0. Downstream analysis of unique molecular identifiers UMI count matrix was conducted in R using the Seurat pipeline v4.0.5. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,For each organ six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief post the cell sorting single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.,,tissue:intestine|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT,GSM7139011,GSM7139011: intestine; Danio rerio; RNA Seq,GSM7139011 r1,GSM7139011,1,For each organ six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief post the cell sorting single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430632,,,intestine_S1_L002_R1_001.fastq.gz intestine_S1_L002_R2_001.fastq.gz,fastq fastq,46067247000.0,153557490.0,GSM7139011 r2,0:150 1:150,A:19102400130;C:7943678450;G:7491880778;T:11528828007;N:459635,150,150,,,19102400130,7943678450,7491880778,11528828007,459635,SRX19850770,SRS17208527,SRA1615101,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology","Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.0,0.88694,0.0,0.17686,1.0,0.81966,,0.57354,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-04-03,Adult,Adult,Gut,Digestive System 74858,SRR24049047,SRX19850770,SRS17208527,SRP430632,PRJNA951670,Single cell transcriptome profiling reveals macrophage and dendritic cell heterogeneity across six zebrafish organs,GSE228806,Transcriptome Analysis,Tissue resident macrophages TRMs and dendritic cells DCs are highly diverse and play essential roles in immunity tissue regeneration and homeostasis maintenance. To systematically assess the heterogeneity of TRM and DC in adult zebrafish we performed droplet based scRNA seq on mpeg1.1+ cells sorted from six different organs epidermis gill intestine liver heart and brain of 6 mpf Tgmpeg1.1:DsRedx fish a widely used myeloid cell reporter line. We identified two macrophage subpopulations with pro inflammatory and pro remodeling signatures respectively as well as one conventional dendritic cell population with prominent antigen presentation capacity and plasmacytoid dendritic cells featuring anti viral properties. Our study provides a comprehensive landscape of TRMs and DCs in zebrafish and offers valuable tools for future in depth investigations of these cell types. Overall design: scRNA seq 10X genomics three prime V3.1 of FACS sorted mpeg1.1+ cells isolated from six different organs epidermis gill intestine liver heart and brain of 6 mpf Tgmpeg1.1:DsRedx fish,,pubmed:37453064,,intestine,GSM7139011,,source name:intestine|tissue:intestine|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT|geo loc name:missing|collection date:missing,intestine,Raw reads were aligned to zebrafish reference genome genome reference: GRCz11; annotation reference: GRCz11.103 combined with the sequences for DsRedx using the Cell Ranger pipelines v6.0. Downstream analysis of unique molecular identifiers UMI count matrix was conducted in R using the Seurat pipeline v4.0.5. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,For each organ six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief post the cell sorting single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.,,tissue:intestine|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT,GSM7139011,GSM7139011: intestine; Danio rerio; RNA Seq,GSM7139011 r1,GSM7139011,1,For each organ six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief post the cell sorting single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430632,,,intestine_S1_L003_R1_001.fastq.gz intestine_S1_L003_R2_001.fastq.gz,fastq fastq,49271357100.0,164237857.0,GSM7139011 r3,0:150 1:150,A:20458940951;C:8499435678;G:8005932501;T:12306559916;N:488054,150,150,,,20458940951,8499435678,8005932501,12306559916,488054,SRX19850770,SRS17208527,SRA1615101,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology","Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.0,0.88663,0.0,0.17771,1.0,0.8214,,0.57864,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-04-03,Adult,Adult,Gut,Digestive System 74859,SRR24049048,SRX19850770,SRS17208527,SRP430632,PRJNA951670,Single cell transcriptome profiling reveals macrophage and dendritic cell heterogeneity across six zebrafish organs,GSE228806,Transcriptome Analysis,Tissue resident macrophages TRMs and dendritic cells DCs are highly diverse and play essential roles in immunity tissue regeneration and homeostasis maintenance. To systematically assess the heterogeneity of TRM and DC in adult zebrafish we performed droplet based scRNA seq on mpeg1.1+ cells sorted from six different organs epidermis gill intestine liver heart and brain of 6 mpf Tgmpeg1.1:DsRedx fish a widely used myeloid cell reporter line. We identified two macrophage subpopulations with pro inflammatory and pro remodeling signatures respectively as well as one conventional dendritic cell population with prominent antigen presentation capacity and plasmacytoid dendritic cells featuring anti viral properties. Our study provides a comprehensive landscape of TRMs and DCs in zebrafish and offers valuable tools for future in depth investigations of these cell types. Overall design: scRNA seq 10X genomics three prime V3.1 of FACS sorted mpeg1.1+ cells isolated from six different organs epidermis gill intestine liver heart and brain of 6 mpf Tgmpeg1.1:DsRedx fish,,pubmed:37453064,,intestine,GSM7139011,,source name:intestine|tissue:intestine|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT|geo loc name:missing|collection date:missing,intestine,Raw reads were aligned to zebrafish reference genome genome reference: GRCz11; annotation reference: GRCz11.103 combined with the sequences for DsRedx using the Cell Ranger pipelines v6.0. Downstream analysis of unique molecular identifiers UMI count matrix was conducted in R using the Seurat pipeline v4.0.5. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,For each organ six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief post the cell sorting single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.,,tissue:intestine|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT,GSM7139011,GSM7139011: intestine; Danio rerio; RNA Seq,GSM7139011 r1,GSM7139011,1,For each organ six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief post the cell sorting single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430632,,,intestine_S1_L004_R1_001.fastq.gz intestine_S1_L004_R2_001.fastq.gz,fastq fastq,54717610800.0,182392036.0,GSM7139011 r4,0:150 1:150,A:22673425061;C:9440232860;G:8902374859;T:13701032682;N:545338,150,150,,,22673425061,9440232860,8902374859,13701032682,545338,SRX19850770,SRS17208527,SRA1615101,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology","Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.0,0.88623,0.0,0.17703,1.0,0.82004,,0.57688,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-04-03,Adult,Adult,Gut,Digestive System 74987,SRR24211926,SRX20008465,SRS17352368,SRP433358,PRJNA957280,Single cell resolution of the adult zebrafish intestine under conventional conditions and in response to an acute natural infection,GSE230044,Transcriptome Analysis,We used single cell RNA sequencing to analyze the diversity of intestinal cells under conventional conditions and the effect of an acute natural Vibrio cholerae infection on the intestinal transcriptome. Overall design: Adult zebrafish were infected with Vibrio cholerae for 16h then intestines dissected and dissociated into a single cell suspension and processed for single cell RNA sequencing.,,pubmed:37948182,,Intestine Vibrio cholerae V52,GSM7184373,,source name:Intestine|tissue:Intestine|age:9 mpf type:dissociated intestine|genotype:TL|treatment:Vibrio cholerae V52|indices:SI GA B8 AAAGTGCT GCTACCTG TGCTGTAA CTGCAAGC|geo loc name:missing|collection date:missing,Intestine Vibrio cholerae V52,Raw base call files were demultiplexed and reads aligned to the Zebrafish reference genome Ensemble GRCz11 using Cell Ranger v3.0.2 Supplementary files format and content: barcodes and features as TSV files Supplementary files format and content: feature matrix as MTX file,Intestine,,Intestinal tissue was dissociated enzymatically and mechanically followed by removal of debris and dead cells using OptiPrep™ Density Gradient Medium Sigma. single cell RNA libraries from freshly collected cells were prepared and barcoded with a 10X genomics Chromium Next GEM Single Cell three prime Reagents Kit v3.,,tissue:Intestine|age:9 mpf type:dissociated intestine|genotype:TL|treatment:Vibrio cholerae V52|indices:SI GA B8 AAAGTGCT GCTACCTG TGCTGTAA CTGCAAGC,GSM7184373,GSM7184373: Intestine Vibrio cholerae V52; Danio rerio; RNA Seq,GSM7184373 r1,GSM7184373,1,Intestinal tissue was dissociated enzymatically and mechanically followed by removal of debris and dead cells using OptiPrep™ Density Gradient Medium Sigma. single cell RNA libraries from freshly collected cells were prepared and barcoded with a 10X genomics Chromium Next GEM Single Cell three prime Reagents Kit v3.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP433358,,loader:fastq load.py|options: readTypes=TTB read1PairFiles=V52 S1 L003 I1 001.fastq.gz read2PairFiles=V52 S1 L003 R1 001.fastq.gz read3PairFiles=V52 S1 L003 R2 001.fastq.gz,V52_S1_L003_I1_001.fastq.gz V52_S1_L003_R1_001.fastq.gz V52_S1_L003_R2_001.fastq.gz,fastq fastq fastq,64666701484.0,209956823.0,GSM7184373 r1,0:8 1:150 2:150,A:9345326821;C:6803352407;G:7411059663;T:7922973497;N:10811062,8,150,150,,9345326821,6803352407,7411059663,7922973497,10811062,SRX20008465,SRS17352368,SRA1623886,"6-59 HMRC, Medical Microbiology and Immunology, University of Alberta","6-59 HMRC, Medical Microbiology and Immunology, University of Alberta",1,0.85334,,0.14056,,0.84484,,0.63794,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Canada,2023-04-19,Adult,Adult,Gut,Digestive System 74988,SRR24211927,SRX20008464,SRS17352369,SRP433358,PRJNA957280,Single cell resolution of the adult zebrafish intestine under conventional conditions and in response to an acute natural infection,GSE230044,Transcriptome Analysis,We used single cell RNA sequencing to analyze the diversity of intestinal cells under conventional conditions and the effect of an acute natural Vibrio cholerae infection on the intestinal transcriptome. Overall design: Adult zebrafish were infected with Vibrio cholerae for 16h then intestines dissected and dissociated into a single cell suspension and processed for single cell RNA sequencing.,,pubmed:37948182,,Intestine uninfected Mock,GSM7184372,,source name:Intestine|tissue:Intestine|age:9 mpf type:dissociated intestine|genotype:TL|treatment:PBS|indices:SI GA B7 AAACCTCA GCCTTGGT CTGGACTC TGTAGAAG|geo loc name:missing|collection date:missing,Intestine uninfected Mock,Raw base call files were demultiplexed and reads aligned to the Zebrafish reference genome Ensemble GRCz11 using Cell Ranger v3.0.2 Supplementary files format and content: barcodes and features as TSV files Supplementary files format and content: feature matrix as MTX file,Intestine,,Intestinal tissue was dissociated enzymatically and mechanically followed by removal of debris and dead cells using OptiPrep™ Density Gradient Medium Sigma. single cell RNA libraries from freshly collected cells were prepared and barcoded with a 10X genomics Chromium Next GEM Single Cell three prime Reagents Kit v3.,,tissue:Intestine|age:9 mpf type:dissociated intestine|genotype:TL|treatment:PBS|indices:SI GA B7 AAACCTCA GCCTTGGT CTGGACTC TGTAGAAG,GSM7184372,GSM7184372: Intestine uninfected Mock; Danio rerio; RNA Seq,GSM7184372 r1,GSM7184372,1,Intestinal tissue was dissociated enzymatically and mechanically followed by removal of debris and dead cells using OptiPrep™ Density Gradient Medium Sigma. single cell RNA libraries from freshly collected cells were prepared and barcoded with a 10X genomics Chromium Next GEM Single Cell three prime Reagents Kit v3.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP433358,,loader:fastq load.py|options: readTypes=TTB read1PairFiles=PBS S2 L003 I1 001.fastq.gz read2PairFiles=PBS S2 L003 R1 001.fastq.gz read3PairFiles=PBS S2 L003 R2 001.fastq.gz,PBS_S2_L003_I1_001.fastq.gz PBS_S2_L003_R1_001.fastq.gz PBS_S2_L003_R2_001.fastq.gz,fastq fastq fastq,69578406744.0,225903918.0,GSM7184372 r1,0:8 1:150 2:150,A:10024486429;C:7291509191;G:7957841546;T:8600067541;N:11682993,8,150,150,,10024486429,7291509191,7957841546,8600067541,11682993,SRX20008464,SRS17352369,SRA1623886,"6-59 HMRC, Medical Microbiology and Immunology, University of Alberta","6-59 HMRC, Medical Microbiology and Immunology, University of Alberta",1,0.84019,,0.15791,,0.83021,,0.6357,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Canada,2023-04-19,Adult,Adult,Gut,Digestive System