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
31525,SRR28419473,SRX24023800,SRS20818155,SRP497235,PRJNA1090867,Single cell RNA seq of zebrafish endothelial cells,GSE262232,Transcriptome Analysis,We performed single cell RNA sequencing scRNA seq for isolated endothelial cells Overall design: Tgkdrl:EGFP zebrafish embryos were digested into single cell suspension  EGFP positive cells were isolated using FACS and subjected to 10X Genomics Chromium scRNAseq.,,pubmed:39977018,,Zebrafish endothelial cells 3 dpf 2,GSM8160887,,source name:Whole body|tissue:Whole body|age:embryo|geo loc name:missing|collection date:missing,Zebrafish endothelial cells 3 dpf 2,Cell Ranger v2.1 was used to de multiplex raw base call BCL files generated by Illumina sequencers into FASTQ files  perform the alignment  barcode counting  and UMI counting. Assembly: GRCz11 Supplementary files format and content: Tab seprated values files,Whole body,,Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions  EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM  Library and Gel Bead Kit v2 10X Genomics according to manufacturer’s protocol.,,tissue:Whole body|age:embryo,GSM8160887,GSM8160887: Zebrafish endothelial cells 3 dpf 2; Danio rerio; RNA Seq,GSM8160887 r1,GSM8160887,1,Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions  EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM  Library and Gel Bead Kit v2 10X Genomics according to manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP497235,,assembly:GRCz11|intentional duplicate|dangling references:treat as unmapped|dangling references:skip reference resolution,3dpf_2_possorted_genome_bam.bam,10X Genomics bam file,8478190406.0,86512147.0,GSM8160887 r1,0:98,A:2448546566;C:1819820402;G:2005413327;T:2187171703;N:17238408,98,,,,2448546566,1819820402,2005413327,2187171703,17238408,SRX24023800,SRS20818155,SRA1835509,Uppsala University,Uppsala University,1,0.91631,,0.11199,,0.82106,,0.54746,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-03-22,Larval,Larval,Trunk,Surface Structure
31526,SRR28419474,SRX24023799,SRS20818156,SRP497235,PRJNA1090867,Single cell RNA seq of zebrafish endothelial cells,GSE262232,Transcriptome Analysis,We performed single cell RNA sequencing scRNA seq for isolated endothelial cells Overall design: Tgkdrl:EGFP zebrafish embryos were digested into single cell suspension  EGFP positive cells were isolated using FACS and subjected to 10X Genomics Chromium scRNAseq.,,pubmed:39977018,,Zebrafish endothelial cells 3 dpf 1,GSM8160886,,source name:Whole body|tissue:Whole body|age:embryo|geo loc name:missing|collection date:missing,Zebrafish endothelial cells 3 dpf 1,Cell Ranger v2.1 was used to de multiplex raw base call BCL files generated by Illumina sequencers into FASTQ files  perform the alignment  barcode counting  and UMI counting. Assembly: GRCz11 Supplementary files format and content: Tab seprated values files,Whole body,,Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions  EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM  Library and Gel Bead Kit v2 10X Genomics according to manufacturer’s protocol.,,tissue:Whole body|age:embryo,GSM8160886,GSM8160886: Zebrafish endothelial cells 3 dpf 1; Danio rerio; RNA Seq,GSM8160886 r1,GSM8160886,1,Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions  EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM  Library and Gel Bead Kit v2 10X Genomics according to manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP497235,,assembly:GRCz11|intentional duplicate|dangling references:treat as unmapped|dangling references:skip reference resolution,3dpf_1_possorted_genome_bam.bam,10X Genomics bam file,2842123088.0,29001256.0,GSM8160886 r1,0:98,A:821846800;C:603425858;G:657525459;T:720690292;N:38634679,98,,,,821846800,603425858,657525459,720690292,38634679,SRX24023799,SRS20818156,SRA1835509,Uppsala University,Uppsala University,1,0.86292,,0.0954,,0.82844,,0.52761,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-03-22,Larval,Larval,Trunk,Surface Structure
31527,SRR28419475,SRX24023798,SRS20818154,SRP497235,PRJNA1090867,Single cell RNA seq of zebrafish endothelial cells,GSE262232,Transcriptome Analysis,We performed single cell RNA sequencing scRNA seq for isolated endothelial cells Overall design: Tgkdrl:EGFP zebrafish embryos were digested into single cell suspension  EGFP positive cells were isolated using FACS and subjected to 10X Genomics Chromium scRNAseq.,,pubmed:39977018,,Zebrafish endothelial cells 34 hpf,GSM8160885,,source name:Whole body|tissue:Whole body|age:embryo|geo loc name:missing|collection date:missing,Zebrafish endothelial cells 34 hpf,Cell Ranger v2.1 was used to de multiplex raw base call BCL files generated by Illumina sequencers into FASTQ files  perform the alignment  barcode counting  and UMI counting. Assembly: GRCz11 Supplementary files format and content: Tab seprated values files,Whole body,,Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions  EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM  Library and Gel Bead Kit v2 10X Genomics according to manufacturer’s protocol.,,tissue:Whole body|age:embryo,GSM8160885,GSM8160885: Zebrafish endothelial cells 34 hpf; Danio rerio; RNA Seq,GSM8160885 r1,GSM8160885,1,Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions  EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM  Library and Gel Bead Kit v2 10X Genomics according to manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP497235,,assembly:GRCz11|intentional duplicate|dangling references:treat as unmapped|dangling references:skip reference resolution,34hpf_possorted_genome_bam.bam,10X Genomics bam file,8518745844.0,86925978.0,GSM8160885 r1,0:98,A:2440648674;C:1828442217;G:2000096456;T:2232243146;N:17315351,98,,,,2440648674,1828442217,2000096456,2232243146,17315351,SRX24023798,SRS20818154,SRA1835509,Uppsala University,Uppsala University,1,0.92268,,0.1011,,0.82235,,0.50276,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-03-22,Pharyngula,Embryo,Trunk,Surface Structure
33615,SRR30272850,SRX25733949,SRS22373737,SRP526812,PRJNA1148907,Single cell RNA sequencing to uncover tissue specific transcriptomic changes induced by perfluorooctanesulfonic acid PFOS in larval zebrafish Danio rerio,PRJNA1148907,Other,The aim is to to apply single cell RNA sequencing of zebrafish larvae to identify novel tissue specific mechanisms and processes following embryonic exposure to perfluorooctanesulfonic acid PFOS,,pubmed:39947082,,PFOS  S2,Sample2,,strain:Tgins:GFP zebrafish on an AB wildtype background|age:72 hpf|dev stage:protruding mouth stage|collection date:2023 01 03|geo loc name:USA: Massachusetts|sex:NA|tissue:whole body cells|treatment:PFOS 16 uM|BioSampleModel:Model organism or animal,,,,,,,,,PFOS,PFOS,PFOS,PFOS  S2  scRNAseq,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PCR,PAIRED,ILLUMINA,NextSeq 500,,SRP526812,,,G194-S2-PFOS_S2_L001_R1_001.fastq.gz G194-S2-PFOS_S2_L001_R2_001.fastq.gz G194-S2-PFOS_S2_L002_R1_001.fastq.gz G194-S2-PFOS_S2_L002_R2_001.fastq.gz G194-S2-PFOS_S2_L003_R1_001.fastq.gz G194-S2-PFOS_S2_L003_R2_001.fastq.gz G194-S2-PFOS_S2_L004_R1_001.fastq.gz G194-S2-PFOS_S2_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,21751958340.0,184338630.0,G194 S2 PFOS S2 L001 R1 001.fastq.gz,0:28 1:90,A:6239773453;C:4634671870;G:5196638658;T:5672561386;N:8312973,28,90,,,6239773453,4634671870,5196638658,5672561386,8312973,SRX25733949,SRS22373737,SRA1949185,University of Massachusetts Amherst|Environmental Health Sciences,University of Massachusetts Amherst,2,0.01021,0.92344,0.00451,0.22962,0.99328,0.79847,0.28896,0.51751,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2024-08-16,Larval,Larval,Trunk,Surface Structure
33616,SRR30272851,SRX25733948,SRS22373736,SRP526812,PRJNA1148907,Single cell RNA sequencing to uncover tissue specific transcriptomic changes induced by perfluorooctanesulfonic acid PFOS in larval zebrafish Danio rerio,PRJNA1148907,Other,The aim is to to apply single cell RNA sequencing of zebrafish larvae to identify novel tissue specific mechanisms and processes following embryonic exposure to perfluorooctanesulfonic acid PFOS,,pubmed:39947082,,DMSO  S1,Sample1,,strain:Tgins:GFP zebrafish on an AB wildtype background|age:72 hpf|dev stage:protruding mouth stage|collection date:2023 01 03|geo loc name:USA: Massachusetts|sex:NA|tissue:whole body cells|treatment:DMSO 0.01%|BioSampleModel:Model organism or animal,,,,,,,,,DMSO,DMSO,DMSO,DMSO  S1  scRNAseq,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PCR,PAIRED,ILLUMINA,NextSeq 500,,SRP526812,,,G194-S1-DMSO_S1_L001_R1_001.fastq.gz G194-S1-DMSO_S1_L001_R2_001.fastq.gz G194-S1-DMSO_S1_L002_R1_001.fastq.gz G194-S1-DMSO_S1_L002_R2_001.fastq.gz G194-S1-DMSO_S1_L003_R1_001.fastq.gz G194-S1-DMSO_S1_L003_R2_001.fastq.gz G194-S1-DMSO_S1_L004_R1_001.fastq.gz G194-S1-DMSO_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,21636838838.0,183363041.0,G194 S1 DMSO S1 L001 R1 001.fastq.gz,0:28 1:90,A:6175214014;C:4647929260;G:5248646646;T:5556827078;N:8221840,28,90,,,6175214014,4647929260,5248646646,5556827078,8221840,SRX25733948,SRS22373736,SRA1949185,University of Massachusetts Amherst|Environmental Health Sciences,University of Massachusetts Amherst,2,0.01048,0.92488,0.00455,0.20966,0.99358,0.81464,0.28056,0.57876,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2024-08-16,Larval,Larval,Trunk,Surface Structure
34500,SRR31853995,SRX27213775,SRS23662882,SRP554457,PRJNA1204318,Spatially structured inflammatory response in the presence of a uniform stimulus: RNAseq screen,GSE285534,Transcriptome Analysis,Inflammatory responses occur within the complex spatial context of tissues and organs  and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here  we used single cell RNA sequencing to screen for genes differentially expressed under LPS lipopolysaccharide and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis. Overall design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS P. Aeuruginosa  Sigma  or E3 alone vehicle control  for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification.,,,,Control 10hr,GSM8703960,,source name:Body|tissue:Body|genotype:AB|age:6 dpf|treatment:control|geo loc name:missing|collection date:missing,Control 10hr,Sequencing data was aligned to the zebrafish reference genome GRCz11 using 10X Genomics Cellranger software 6.1.2. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Body,,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,tissue:Body|genotype:AB|age:6 dpf|treatment:control,GSM8703960,GSM8703960: Control 10hr; Danio rerio; RNA Seq,GSM8703960 r1,GSM8703960,1,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP554457,,loader:fastq load.py,Control_S12_L001_I1_001.fastq.gz Control_S12_L001_R1_001.fastq.gz Control_S12_L001_R2_001.fastq.gz,fastq fastq fastq,54727297835.0,430923605.0,GSM8703960 r1,0:8 1:28 2:91,A:11073804966;C:8703587106;G:9746134722;T:9686959402;N:3561859,8,28,91,,11073804966,8703587106,9746134722,9686959402,3561859,SRX27213775,SRS23662882,SRA2042619,"Jerison, Physics, University of Chicago","Jerison, Physics, University of Chicago",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-30,Larval,Larval,Trunk,Surface Structure
34501,SRR31853996,SRX27213775,SRS23662882,SRP554457,PRJNA1204318,Spatially structured inflammatory response in the presence of a uniform stimulus: RNAseq screen,GSE285534,Transcriptome Analysis,Inflammatory responses occur within the complex spatial context of tissues and organs  and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here  we used single cell RNA sequencing to screen for genes differentially expressed under LPS lipopolysaccharide and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis. Overall design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS P. Aeuruginosa  Sigma  or E3 alone vehicle control  for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification.,,,,Control 10hr,GSM8703960,,source name:Body|tissue:Body|genotype:AB|age:6 dpf|treatment:control|geo loc name:missing|collection date:missing,Control 10hr,Sequencing data was aligned to the zebrafish reference genome GRCz11 using 10X Genomics Cellranger software 6.1.2. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Body,,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,tissue:Body|genotype:AB|age:6 dpf|treatment:control,GSM8703960,GSM8703960: Control 10hr; Danio rerio; RNA Seq,GSM8703960 r1,GSM8703960,1,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP554457,,loader:fastq load.py,Control_S12_L002_I1_001.fastq.gz Control_S12_L002_R1_001.fastq.gz Control_S12_L002_R2_001.fastq.gz,fastq fastq fastq,55269352123.0,435191749.0,GSM8703960 r2,0:8 1:28 2:91,A:11174489058;C:8794319355;G:9857401155;T:9771712847;N:4526744,8,28,91,,11174489058,8794319355,9857401155,9771712847,4526744,SRX27213775,SRS23662882,SRA2042619,"Jerison, Physics, University of Chicago","Jerison, Physics, University of Chicago",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-30,Larval,Larval,Trunk,Surface Structure
34502,SRR31853997,SRX27213775,SRS23662882,SRP554457,PRJNA1204318,Spatially structured inflammatory response in the presence of a uniform stimulus: RNAseq screen,GSE285534,Transcriptome Analysis,Inflammatory responses occur within the complex spatial context of tissues and organs  and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here  we used single cell RNA sequencing to screen for genes differentially expressed under LPS lipopolysaccharide and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis. Overall design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS P. Aeuruginosa  Sigma  or E3 alone vehicle control  for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification.,,,,Control 10hr,GSM8703960,,source name:Body|tissue:Body|genotype:AB|age:6 dpf|treatment:control|geo loc name:missing|collection date:missing,Control 10hr,Sequencing data was aligned to the zebrafish reference genome GRCz11 using 10X Genomics Cellranger software 6.1.2. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Body,,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,tissue:Body|genotype:AB|age:6 dpf|treatment:control,GSM8703960,GSM8703960: Control 10hr; Danio rerio; RNA Seq,GSM8703960 r1,GSM8703960,1,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP554457,,loader:fastq load.py,Control_S12_L003_I1_001.fastq.gz Control_S12_L003_R1_001.fastq.gz Control_S12_L003_R2_001.fastq.gz,fastq fastq fastq,56713746491.0,446564933.0,GSM8703960 r3,0:8 1:28 2:91,A:11445709349;C:9041805308;G:10134400820;T:10010485583;N:5007843,8,28,91,,11445709349,9041805308,10134400820,10010485583,5007843,SRX27213775,SRS23662882,SRA2042619,"Jerison, Physics, University of Chicago","Jerison, Physics, University of Chicago",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-30,Larval,Larval,Trunk,Surface Structure
34503,SRR31853998,SRX27213775,SRS23662882,SRP554457,PRJNA1204318,Spatially structured inflammatory response in the presence of a uniform stimulus: RNAseq screen,GSE285534,Transcriptome Analysis,Inflammatory responses occur within the complex spatial context of tissues and organs  and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here  we used single cell RNA sequencing to screen for genes differentially expressed under LPS lipopolysaccharide and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis. Overall design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS P. Aeuruginosa  Sigma  or E3 alone vehicle control  for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification.,,,,Control 10hr,GSM8703960,,source name:Body|tissue:Body|genotype:AB|age:6 dpf|treatment:control|geo loc name:missing|collection date:missing,Control 10hr,Sequencing data was aligned to the zebrafish reference genome GRCz11 using 10X Genomics Cellranger software 6.1.2. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Body,,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,tissue:Body|genotype:AB|age:6 dpf|treatment:control,GSM8703960,GSM8703960: Control 10hr; Danio rerio; RNA Seq,GSM8703960 r1,GSM8703960,1,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP554457,,loader:fastq load.py,Control_S12_L004_I1_001.fastq.gz Control_S12_L004_R1_001.fastq.gz Control_S12_L004_R2_001.fastq.gz,fastq fastq fastq,55438180589.0,436521107.0,GSM8703960 r4,0:8 1:28 2:91,A:11203472019;C:8826429348;G:9895249162;T:9793520783;N:4749425,8,28,91,,11203472019,8826429348,9895249162,9793520783,4749425,SRX27213775,SRS23662882,SRA2042619,"Jerison, Physics, University of Chicago","Jerison, Physics, University of Chicago",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-30,Larval,Larval,Trunk,Surface Structure
34504,SRR31853999,SRX27213774,SRS23662881,SRP554457,PRJNA1204318,Spatially structured inflammatory response in the presence of a uniform stimulus: RNAseq screen,GSE285534,Transcriptome Analysis,Inflammatory responses occur within the complex spatial context of tissues and organs  and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here  we used single cell RNA sequencing to screen for genes differentially expressed under LPS lipopolysaccharide and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis. Overall design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS P. Aeuruginosa  Sigma  or E3 alone vehicle control  for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification.,,,,LPS 10hr,GSM8703959,,source name:Body|tissue:Body|genotype:AB|age:6 dpf|treatment:LPS|geo loc name:missing|collection date:missing,LPS 10hr,Sequencing data was aligned to the zebrafish reference genome GRCz11 using 10X Genomics Cellranger software 6.1.2. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Body,,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,tissue:Body|genotype:AB|age:6 dpf|treatment:LPS,GSM8703959,GSM8703959: LPS 10hr; Danio rerio; RNA Seq,GSM8703959 r1,GSM8703959,1,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP554457,,loader:fastq load.py,LPS_S11_L001_I1_001.fastq.gz LPS_S11_L001_R1_001.fastq.gz LPS_S11_L001_R2_001.fastq.gz,fastq fastq fastq,27204594943.0,214209409.0,GSM8703959 r1,0:8 1:28 2:91,A:5353386805;C:4418850048;G:5242873068;T:4476300884;N:1645414,8,28,91,,5353386805,4418850048,5242873068,4476300884,1645414,SRX27213774,SRS23662881,SRA2042619,"Jerison, Physics, University of Chicago","Jerison, Physics, University of Chicago",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-30,Larval,Larval,Trunk,Surface Structure
34505,SRR31854000,SRX27213774,SRS23662881,SRP554457,PRJNA1204318,Spatially structured inflammatory response in the presence of a uniform stimulus: RNAseq screen,GSE285534,Transcriptome Analysis,Inflammatory responses occur within the complex spatial context of tissues and organs  and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here  we used single cell RNA sequencing to screen for genes differentially expressed under LPS lipopolysaccharide and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis. Overall design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS P. Aeuruginosa  Sigma  or E3 alone vehicle control  for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification.,,,,LPS 10hr,GSM8703959,,source name:Body|tissue:Body|genotype:AB|age:6 dpf|treatment:LPS|geo loc name:missing|collection date:missing,LPS 10hr,Sequencing data was aligned to the zebrafish reference genome GRCz11 using 10X Genomics Cellranger software 6.1.2. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Body,,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,tissue:Body|genotype:AB|age:6 dpf|treatment:LPS,GSM8703959,GSM8703959: LPS 10hr; Danio rerio; RNA Seq,GSM8703959 r1,GSM8703959,1,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP554457,,loader:fastq load.py,LPS_S11_L002_I1_001.fastq.gz LPS_S11_L002_R1_001.fastq.gz LPS_S11_L002_R2_001.fastq.gz,fastq fastq fastq,27514945859.0,216653117.0,GSM8703959 r2,0:8 1:28 2:91,A:5407507765;C:4472892263;G:5312032344;T:4520956753;N:2044522,8,28,91,,5407507765,4472892263,5312032344,4520956753,2044522,SRX27213774,SRS23662881,SRA2042619,"Jerison, Physics, University of Chicago","Jerison, Physics, University of Chicago",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-30,Larval,Larval,Trunk,Surface Structure
34506,SRR31854001,SRX27213774,SRS23662881,SRP554457,PRJNA1204318,Spatially structured inflammatory response in the presence of a uniform stimulus: RNAseq screen,GSE285534,Transcriptome Analysis,Inflammatory responses occur within the complex spatial context of tissues and organs  and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here  we used single cell RNA sequencing to screen for genes differentially expressed under LPS lipopolysaccharide and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis. Overall design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS P. Aeuruginosa  Sigma  or E3 alone vehicle control  for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification.,,,,LPS 10hr,GSM8703959,,source name:Body|tissue:Body|genotype:AB|age:6 dpf|treatment:LPS|geo loc name:missing|collection date:missing,LPS 10hr,Sequencing data was aligned to the zebrafish reference genome GRCz11 using 10X Genomics Cellranger software 6.1.2. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Body,,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,tissue:Body|genotype:AB|age:6 dpf|treatment:LPS,GSM8703959,GSM8703959: LPS 10hr; Danio rerio; RNA Seq,GSM8703959 r1,GSM8703959,1,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP554457,,loader:fastq load.py,LPS_S11_L003_I1_001.fastq.gz LPS_S11_L003_R1_001.fastq.gz LPS_S11_L003_R2_001.fastq.gz,fastq fastq fastq,28512338962.0,224506606.0,GSM8703959 r3,0:8 1:28 2:91,A:5590192273;C:4644899622;G:5516199030;T:4676442556;N:2367665,8,28,91,,5590192273,4644899622,5516199030,4676442556,2367665,SRX27213774,SRS23662881,SRA2042619,"Jerison, Physics, University of Chicago","Jerison, Physics, University of Chicago",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-30,Larval,Larval,Trunk,Surface Structure
34507,SRR31854002,SRX27213774,SRS23662881,SRP554457,PRJNA1204318,Spatially structured inflammatory response in the presence of a uniform stimulus: RNAseq screen,GSE285534,Transcriptome Analysis,Inflammatory responses occur within the complex spatial context of tissues and organs  and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here  we used single cell RNA sequencing to screen for genes differentially expressed under LPS lipopolysaccharide and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis. Overall design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS P. Aeuruginosa  Sigma  or E3 alone vehicle control  for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification.,,,,LPS 10hr,GSM8703959,,source name:Body|tissue:Body|genotype:AB|age:6 dpf|treatment:LPS|geo loc name:missing|collection date:missing,LPS 10hr,Sequencing data was aligned to the zebrafish reference genome GRCz11 using 10X Genomics Cellranger software 6.1.2. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Body,,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,tissue:Body|genotype:AB|age:6 dpf|treatment:LPS,GSM8703959,GSM8703959: LPS 10hr; Danio rerio; RNA Seq,GSM8703959 r1,GSM8703959,1,Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP554457,,loader:fastq load.py,LPS_S11_L004_I1_001.fastq.gz LPS_S11_L004_R1_001.fastq.gz LPS_S11_L004_R2_001.fastq.gz,fastq fastq fastq,27411098848.0,215835424.0,GSM8703959 r4,0:8 1:28 2:91,A:5383218071;C:4459553243;G:5297438054;T:4498601355;N:2212861,8,28,91,,5383218071,4459553243,5297438054,4498601355,2212861,SRX27213774,SRS23662881,SRA2042619,"Jerison, Physics, University of Chicago","Jerison, Physics, University of Chicago",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-30,Larval,Larval,Trunk,Surface Structure
36242,SRR33873799,SRX29085358,SRS25297146,SRP590547,PRJNA1272846,Organism wide contributions to systemic skeletal muscle repair in larval zebrafish.,GSE299146,Transcriptome Analysis,We developed a systemic muscle injury model in zebrafish. Single cell transcriptomic analysis of muscle and non muscle tissues revealed that systemic and local muscle injuries elicit distinct cellular molecular responses  both quantitatively and qualitatively. These studies suggest that large  and small scale muscle injuries activate different regenerative programs  resulting in either systemic or local repair. Overall design: To characterize the regenerative responses and signaling pathways activated post systemic or local muscle injury  we generated Tgactc1b:NTR mCherry transgenic zebrafish lines.At 4 dpf  transgenic larvae were treated with MTZ overnight to systemically injure all myofibers  or were subjected to local mechanical injury needlestick of 2 3 somites.Uninjured and systemically injured larvae were collected at 1  2  and 4 xxx post injury. Mechanically injured larvae were collected at 2 xxx post injury. Sequencing results were compared between uninjured  systemically injured  and mechanically injured siblings.,,,,larval trunk  2dpi Needle Stick,GSM9034433,,source name:Trunk|tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Needle Stick|batch:4/20/2022|geo loc name:missing|collection date:missing,larval trunk  2dpi Needle Stick,post sequencing  the Illumina output was processed using the CellRanger v8.0.1 pipeline to generate gene barcode count matrices. A custom reference genome was made with the “cellranger mkref” command  using the fasta file of zebrafish reference genome GRCz11 constructed from the Ensemble genome build https://useast.ensembl.org/Danio rerio/Info/Index and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Base call files for each sample from Illumina were demultiplexed into FASTQ reads. Then  the “cellranger count” pipeline was used to align sequencing reads in FASTQ files to the custom reference genome. Both exon and intron sequences were included during the alignment. The filtered gene barcode count matrices generated by “cellranger count” was used for downstream analysis. Datasets were integrated and analyzed using Seurat v4.4.0 package with R v4.4.2Stuart etal.  2019; Team  2024. Each sample count matrix was filtered for genes that were expressed in at least 3 cells and cells expressing at least 200 genes  followed by cell quality assessment usingcommonly used QC matrixes Ilicic et al.  2016. Cells having a unique number of genes between 200 and 6500  mitochondrial gene percentage <5 and total number of reads UMIs between 300and 35000 were used for downstream processing. Each dataset was independently normalizedand scaled using the “SCTransform” function  which is an improved method for normalization  that performs a variance stabilizing transformation using negative binomial regression Hafemeisterand Satija  2019. Standard integration workflow of Seurat was used to identify shared sources of variation across experiments as well as mutual nearest neighbors Butler et al.  2018; Haghverdiet al.  2018. Integration features were selected based on the top 6000 highly variable features using “SelectIntegrationFeatures” function nfeatures = 6000  which was used as input for the“anchor.features” argument of the “FindIntegrationAnchors” function. PCA analysis was performed on the 6000 variable features and the top 50 principal components selected based on the elbow plot heuristic  which measures the contribution of variation in each component. These 50 principal components were used in “FindNeighbors” and “FindClusters” functions to perform graph based clustering on a shared nearest neighbor graph Levine et al.  2015; Xu and Su 2015. Louvain algorithm was used for modularity optimization in cell clustering using “FindClusters” function. The resolution parameter res = 0.3 that determines the granularity of clusteringwas selected by visually inspecting clusters with resolutions ranging between 0.1 and 2.0 as well as clustree graph Zappia and Oshlack  2018. Uniform Manifold Approximation and Reduction UMAP was used for non linear dimensional reduction of the first 50 principal components and visualize the data using “RunUMAP” function Becht et al.  2018. Data was graphed using different plot functions  such as “DimPlot”  “VlnPlot”  “FeaturePlot”  “Dotplot” and “DoHeatmap”  to view the cell cluster identity and marker gene expression. Cell proportions were extracted using the “table” and “prop.table” functions. Differential gene expression for individual clusters was identified using Wilcoxon rank sum test in the “FindAllMarkers” function. Marker genes detected in at least 25% of the clustered cells and had a positive average log2FC were reported. Muscle cells identified from the complete dataset were subclustered using the “subset” function for subcluster analysis. The muscle subset was again normalized and scaled using the “SCTransform” function with glmGamPoi method Ahlmann Eltze and Huber  2021. Fifty principal components were used and the resolution parameter was set to 0.4. Downstream analysis was done as described above for the integrated analysis. We used a zebrafish single atlas Sur et al.  2023 to generate a database of markers for each tissue and cell type Table S1. The differentially expressed markers of each cluster were crossreferenced with our compiled database using our “DE Marker Scoring” algorithm Saraswathy et al.  2024. For every matching marker gene  one point was given to the respective cluster under the column name with matching cell identity. Iteration over every marker gene was performed to generate a scoring matrix with varying points for each cluster against the different cell identities compiled in the database Table S2  sheet: scoring. The “phyper” function in R was then used to calculate one tailed binomial probabilities using hypergeometric distribution for the total score obtained from each cluster against each cell identity in the database Table S2  sheet: Binomial probability. −log10 of probability values were obtained for plotting the heatmap Table S2  sheet:−log10P. The resulting values were scaled from 0 to 100 and plotted as a heatmap using GraphPad prism. Each cluster was given an identity based on the maximum −log10 p score obtained in the heatmap. The top DE markers of clusters with ambiguous scores were manually annotated using the “ident genes” from the zebrafish single atlas Sur et al.  2023 and literature search McKellar et al.  2021. Top DE markers generated for each cluster is given in Table S3  sheet:topDEmarkers.all.clusters “RenameIdents” function was used to assign identity to each cluster. To confirm the assigned cluster identities  enrichment of classical markers of respective cell types were tested using Dot plot. The R package CellChat v2.1.2 was used to evaluate regenerative cell cell interactions post local and systemic muscle injury Jin et al.  2021. CellChat models the probability of cell cell communication by integrating our gene expression data with a database of known interaction between signaling ligands  receptors  and their cofactors CellChatDB. The RNA data was used to create CellChat object using “createCellChat” function  followed by the recommended preprocessing functions with default parameters for the analysis of individual datasets. Truncated mean method with 10% trimmed observation was used to compute average gene expression per cell group for the complete dataset. The default trimean method was used to compute average gene expression for the CellChat analysis. CellChatDB.zebrafish was used to infer cell cell communication. All categories of ligand receptor interactions in the database were used in the analysis. Communications involving less than 10 cells were excluded. The “netAnalysis computeCentrality” function was used to calculate network centrality scores at each time point. Functions such as “netVisual circle”  “netAnalysis contribution”  “netVisual aggregate”  “netVisual bubble”  “netAnalysis signalingRole heatmap”  and “netAnalysis signalingRole scatter” were used to generate different plots used in this paper. Assembly: zebrafish reference genome GRCz11 and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Supplementary files format and content: Compressed Filtered Feature and Barcode files as .tsv file and count matrices in .mtx file format.,Trunk,Fish were treated with 12 hours of metronidazole or were stuck locally with a needle,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell 3’ Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,Larval zebrafish of 4 dpf underwent drug treatments or needle stick injuries for muscle ablation,tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Needle Stick|batch:4/20/2022,GSM9034433,GSM9034433: larval trunk  2dpi Needle Stick; Danio rerio; RNA Seq,GSM9034433 r1,GSM9034433,1,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell three prime Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP590547,,,AJAH-ACTC_NTR_Mcherry-Needlestick-2dpi-NS-2dpi-lib1_S1_L003_R1_001.fastq.gz AJAH-ACTC_NTR_Mcherry-Needlestick-2dpi-NS-2dpi-lib1_S1_L003_R2_001.fastq.gz,fastq fastq,73442728978.0,412599601.0,GSM9034433 r1,0:28 1:150,A:21212027449;C:16424751525;G:17879456991;T:17925559458;N:933555,28,150,,,21212027449,16424751525,17879456991,17925559458,933555,SRX29085358,SRS25297146,SRA2144659,"Johnson Lab, Developmental Biology, Washington University in St.Louis","Johnson Lab, Developmental Biology, Washington University in St.Louis",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-06-06,Larval,Larval,Trunk,Surface Structure
36243,SRR33873800,SRX29085357,SRS25297145,SRP590547,PRJNA1272846,Organism wide contributions to systemic skeletal muscle repair in larval zebrafish.,GSE299146,Transcriptome Analysis,We developed a systemic muscle injury model in zebrafish. Single cell transcriptomic analysis of muscle and non muscle tissues revealed that systemic and local muscle injuries elicit distinct cellular molecular responses  both quantitatively and qualitatively. These studies suggest that large  and small scale muscle injuries activate different regenerative programs  resulting in either systemic or local repair. Overall design: To characterize the regenerative responses and signaling pathways activated post systemic or local muscle injury  we generated Tgactc1b:NTR mCherry transgenic zebrafish lines.At 4 dpf  transgenic larvae were treated with MTZ overnight to systemically injure all myofibers  or were subjected to local mechanical injury needlestick of 2 3 somites.Uninjured and systemically injured larvae were collected at 1  2  and 4 xxx post injury. Mechanically injured larvae were collected at 2 xxx post injury. Sequencing results were compared between uninjured  systemically injured  and mechanically injured siblings.,,,,larval trunk  4dpi mcherry MTZ,GSM9034432,,source name:Trunk|tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water + MTZ|batch:10/28/2022|geo loc name:missing|collection date:missing,larval trunk  4dpi mcherry MTZ,post sequencing  the Illumina output was processed using the CellRanger v8.0.1 pipeline to generate gene barcode count matrices. A custom reference genome was made with the “cellranger mkref” command  using the fasta file of zebrafish reference genome GRCz11 constructed from the Ensemble genome build https://useast.ensembl.org/Danio rerio/Info/Index and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Base call files for each sample from Illumina were demultiplexed into FASTQ reads. Then  the “cellranger count” pipeline was used to align sequencing reads in FASTQ files to the custom reference genome. Both exon and intron sequences were included during the alignment. The filtered gene barcode count matrices generated by “cellranger count” was used for downstream analysis. Datasets were integrated and analyzed using Seurat v4.4.0 package with R v4.4.2Stuart etal.  2019; Team  2024. Each sample count matrix was filtered for genes that were expressed in at least 3 cells and cells expressing at least 200 genes  followed by cell quality assessment usingcommonly used QC matrixes Ilicic et al.  2016. Cells having a unique number of genes between 200 and 6500  mitochondrial gene percentage <5 and total number of reads UMIs between 300and 35000 were used for downstream processing. Each dataset was independently normalizedand scaled using the “SCTransform” function  which is an improved method for normalization  that performs a variance stabilizing transformation using negative binomial regression Hafemeisterand Satija  2019. Standard integration workflow of Seurat was used to identify shared sources of variation across experiments as well as mutual nearest neighbors Butler et al.  2018; Haghverdiet al.  2018. Integration features were selected based on the top 6000 highly variable features using “SelectIntegrationFeatures” function nfeatures = 6000  which was used as input for the“anchor.features” argument of the “FindIntegrationAnchors” function. PCA analysis was performed on the 6000 variable features and the top 50 principal components selected based on the elbow plot heuristic  which measures the contribution of variation in each component. These 50 principal components were used in “FindNeighbors” and “FindClusters” functions to perform graph based clustering on a shared nearest neighbor graph Levine et al.  2015; Xu and Su 2015. Louvain algorithm was used for modularity optimization in cell clustering using “FindClusters” function. The resolution parameter res = 0.3 that determines the granularity of clusteringwas selected by visually inspecting clusters with resolutions ranging between 0.1 and 2.0 as well as clustree graph Zappia and Oshlack  2018. Uniform Manifold Approximation and Reduction UMAP was used for non linear dimensional reduction of the first 50 principal components and visualize the data using “RunUMAP” function Becht et al.  2018. Data was graphed using different plot functions  such as “DimPlot”  “VlnPlot”  “FeaturePlot”  “Dotplot” and “DoHeatmap”  to view the cell cluster identity and marker gene expression. Cell proportions were extracted using the “table” and “prop.table” functions. Differential gene expression for individual clusters was identified using Wilcoxon rank sum test in the “FindAllMarkers” function. Marker genes detected in at least 25% of the clustered cells and had a positive average log2FC were reported. Muscle cells identified from the complete dataset were subclustered using the “subset” function for subcluster analysis. The muscle subset was again normalized and scaled using the “SCTransform” function with glmGamPoi method Ahlmann Eltze and Huber  2021. Fifty principal components were used and the resolution parameter was set to 0.4. Downstream analysis was done as described above for the integrated analysis. We used a zebrafish single atlas Sur et al.  2023 to generate a database of markers for each tissue and cell type Table S1. The differentially expressed markers of each cluster were crossreferenced with our compiled database using our “DE Marker Scoring” algorithm Saraswathy et al.  2024. For every matching marker gene  one point was given to the respective cluster under the column name with matching cell identity. Iteration over every marker gene was performed to generate a scoring matrix with varying points for each cluster against the different cell identities compiled in the database Table S2  sheet: scoring. The “phyper” function in R was then used to calculate one tailed binomial probabilities using hypergeometric distribution for the total score obtained from each cluster against each cell identity in the database Table S2  sheet: Binomial probability. −log10 of probability values were obtained for plotting the heatmap Table S2  sheet:−log10P. The resulting values were scaled from 0 to 100 and plotted as a heatmap using GraphPad prism. Each cluster was given an identity based on the maximum −log10 p score obtained in the heatmap. The top DE markers of clusters with ambiguous scores were manually annotated using the “ident genes” from the zebrafish single atlas Sur et al.  2023 and literature search McKellar et al.  2021. Top DE markers generated for each cluster is given in Table S3  sheet:topDEmarkers.all.clusters “RenameIdents” function was used to assign identity to each cluster. To confirm the assigned cluster identities  enrichment of classical markers of respective cell types were tested using Dot plot. The R package CellChat v2.1.2 was used to evaluate regenerative cell cell interactions post local and systemic muscle injury Jin et al.  2021. CellChat models the probability of cell cell communication by integrating our gene expression data with a database of known interaction between signaling ligands  receptors  and their cofactors CellChatDB. The RNA data was used to create CellChat object using “createCellChat” function  followed by the recommended preprocessing functions with default parameters for the analysis of individual datasets. Truncated mean method with 10% trimmed observation was used to compute average gene expression per cell group for the complete dataset. The default trimean method was used to compute average gene expression for the CellChat analysis. CellChatDB.zebrafish was used to infer cell cell communication. All categories of ligand receptor interactions in the database were used in the analysis. Communications involving less than 10 cells were excluded. The “netAnalysis computeCentrality” function was used to calculate network centrality scores at each time point. Functions such as “netVisual circle”  “netAnalysis contribution”  “netVisual aggregate”  “netVisual bubble”  “netAnalysis signalingRole heatmap”  and “netAnalysis signalingRole scatter” were used to generate different plots used in this paper. Assembly: zebrafish reference genome GRCz11 and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Supplementary files format and content: Compressed Filtered Feature and Barcode files as .tsv file and count matrices in .mtx file format.,Trunk,Fish were treated with 12 hours of metronidazole or were stuck locally with a needle,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell 3’ Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,Larval zebrafish of 4 dpf underwent drug treatments or needle stick injuries for muscle ablation,tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water + MTZ|batch:10/28/2022,GSM9034432,GSM9034432: larval trunk  4dpi mcherry MTZ; Danio rerio; RNA Seq,GSM9034432 r1,GSM9034432,1,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell three prime Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP590547,,,AJAH-18300_Red-18300_mCherry_Positive_4dpi-lib1_S2_L004_R1_001.fastq.gz AJAH-18300_Red-18300_mCherry_Positive_4dpi-lib1_S2_L004_R2_001.fastq.gz,fastq fastq,109491443482.0,615120469.0,GSM9034432 r1,0:28 1:150,A:31642210635;C:24956118743;G:26943821428;T:25945839682;N:3452994,28,150,,,31642210635,24956118743,26943821428,25945839682,3452994,SRX29085357,SRS25297145,SRA2144659,"Johnson Lab, Developmental Biology, Washington University in St.Louis","Johnson Lab, Developmental Biology, Washington University in St.Louis",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-06-06,Larval,Larval,Trunk,Surface Structure
36244,SRR33873801,SRX29085356,SRS25297144,SRP590547,PRJNA1272846,Organism wide contributions to systemic skeletal muscle repair in larval zebrafish.,GSE299146,Transcriptome Analysis,We developed a systemic muscle injury model in zebrafish. Single cell transcriptomic analysis of muscle and non muscle tissues revealed that systemic and local muscle injuries elicit distinct cellular molecular responses  both quantitatively and qualitatively. These studies suggest that large  and small scale muscle injuries activate different regenerative programs  resulting in either systemic or local repair. Overall design: To characterize the regenerative responses and signaling pathways activated post systemic or local muscle injury  we generated Tgactc1b:NTR mCherry transgenic zebrafish lines.At 4 dpf  transgenic larvae were treated with MTZ overnight to systemically injure all myofibers  or were subjected to local mechanical injury needlestick of 2 3 somites.Uninjured and systemically injured larvae were collected at 1  2  and 4 xxx post injury. Mechanically injured larvae were collected at 2 xxx post injury. Sequencing results were compared between uninjured  systemically injured  and mechanically injured siblings.,,,,larval trunk  4dpi Negative Control,GSM9034431,,source name:Trunk|tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water|batch:10/28/2022|geo loc name:missing|collection date:missing,larval trunk  4dpi Negative Control,post sequencing  the Illumina output was processed using the CellRanger v8.0.1 pipeline to generate gene barcode count matrices. A custom reference genome was made with the “cellranger mkref” command  using the fasta file of zebrafish reference genome GRCz11 constructed from the Ensemble genome build https://useast.ensembl.org/Danio rerio/Info/Index and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Base call files for each sample from Illumina were demultiplexed into FASTQ reads. Then  the “cellranger count” pipeline was used to align sequencing reads in FASTQ files to the custom reference genome. Both exon and intron sequences were included during the alignment. The filtered gene barcode count matrices generated by “cellranger count” was used for downstream analysis. Datasets were integrated and analyzed using Seurat v4.4.0 package with R v4.4.2Stuart etal.  2019; Team  2024. Each sample count matrix was filtered for genes that were expressed in at least 3 cells and cells expressing at least 200 genes  followed by cell quality assessment usingcommonly used QC matrixes Ilicic et al.  2016. Cells having a unique number of genes between 200 and 6500  mitochondrial gene percentage <5 and total number of reads UMIs between 300and 35000 were used for downstream processing. Each dataset was independently normalizedand scaled using the “SCTransform” function  which is an improved method for normalization  that performs a variance stabilizing transformation using negative binomial regression Hafemeisterand Satija  2019. Standard integration workflow of Seurat was used to identify shared sources of variation across experiments as well as mutual nearest neighbors Butler et al.  2018; Haghverdiet al.  2018. Integration features were selected based on the top 6000 highly variable features using “SelectIntegrationFeatures” function nfeatures = 6000  which was used as input for the“anchor.features” argument of the “FindIntegrationAnchors” function. PCA analysis was performed on the 6000 variable features and the top 50 principal components selected based on the elbow plot heuristic  which measures the contribution of variation in each component. These 50 principal components were used in “FindNeighbors” and “FindClusters” functions to perform graph based clustering on a shared nearest neighbor graph Levine et al.  2015; Xu and Su 2015. Louvain algorithm was used for modularity optimization in cell clustering using “FindClusters” function. The resolution parameter res = 0.3 that determines the granularity of clusteringwas selected by visually inspecting clusters with resolutions ranging between 0.1 and 2.0 as well as clustree graph Zappia and Oshlack  2018. Uniform Manifold Approximation and Reduction UMAP was used for non linear dimensional reduction of the first 50 principal components and visualize the data using “RunUMAP” function Becht et al.  2018. Data was graphed using different plot functions  such as “DimPlot”  “VlnPlot”  “FeaturePlot”  “Dotplot” and “DoHeatmap”  to view the cell cluster identity and marker gene expression. Cell proportions were extracted using the “table” and “prop.table” functions. Differential gene expression for individual clusters was identified using Wilcoxon rank sum test in the “FindAllMarkers” function. Marker genes detected in at least 25% of the clustered cells and had a positive average log2FC were reported. Muscle cells identified from the complete dataset were subclustered using the “subset” function for subcluster analysis. The muscle subset was again normalized and scaled using the “SCTransform” function with glmGamPoi method Ahlmann Eltze and Huber  2021. Fifty principal components were used and the resolution parameter was set to 0.4. Downstream analysis was done as described above for the integrated analysis. We used a zebrafish single atlas Sur et al.  2023 to generate a database of markers for each tissue and cell type Table S1. The differentially expressed markers of each cluster were crossreferenced with our compiled database using our “DE Marker Scoring” algorithm Saraswathy et al.  2024. For every matching marker gene  one point was given to the respective cluster under the column name with matching cell identity. Iteration over every marker gene was performed to generate a scoring matrix with varying points for each cluster against the different cell identities compiled in the database Table S2  sheet: scoring. The “phyper” function in R was then used to calculate one tailed binomial probabilities using hypergeometric distribution for the total score obtained from each cluster against each cell identity in the database Table S2  sheet: Binomial probability. −log10 of probability values were obtained for plotting the heatmap Table S2  sheet:−log10P. The resulting values were scaled from 0 to 100 and plotted as a heatmap using GraphPad prism. Each cluster was given an identity based on the maximum −log10 p score obtained in the heatmap. The top DE markers of clusters with ambiguous scores were manually annotated using the “ident genes” from the zebrafish single atlas Sur et al.  2023 and literature search McKellar et al.  2021. Top DE markers generated for each cluster is given in Table S3  sheet:topDEmarkers.all.clusters “RenameIdents” function was used to assign identity to each cluster. To confirm the assigned cluster identities  enrichment of classical markers of respective cell types were tested using Dot plot. The R package CellChat v2.1.2 was used to evaluate regenerative cell cell interactions post local and systemic muscle injury Jin et al.  2021. CellChat models the probability of cell cell communication by integrating our gene expression data with a database of known interaction between signaling ligands  receptors  and their cofactors CellChatDB. The RNA data was used to create CellChat object using “createCellChat” function  followed by the recommended preprocessing functions with default parameters for the analysis of individual datasets. Truncated mean method with 10% trimmed observation was used to compute average gene expression per cell group for the complete dataset. The default trimean method was used to compute average gene expression for the CellChat analysis. CellChatDB.zebrafish was used to infer cell cell communication. All categories of ligand receptor interactions in the database were used in the analysis. Communications involving less than 10 cells were excluded. The “netAnalysis computeCentrality” function was used to calculate network centrality scores at each time point. Functions such as “netVisual circle”  “netAnalysis contribution”  “netVisual aggregate”  “netVisual bubble”  “netAnalysis signalingRole heatmap”  and “netAnalysis signalingRole scatter” were used to generate different plots used in this paper. Assembly: zebrafish reference genome GRCz11 and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Supplementary files format and content: Compressed Filtered Feature and Barcode files as .tsv file and count matrices in .mtx file format.,Trunk,Fish were treated with 12 hours of metronidazole or were stuck locally with a needle,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell 3’ Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,Larval zebrafish of 4 dpf underwent drug treatments or needle stick injuries for muscle ablation,tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water|batch:10/28/2022,GSM9034431,GSM9034431: larval trunk  4dpi Negative Control; Danio rerio; RNA Seq,GSM9034431 r1,GSM9034431,1,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell three prime Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP590547,,,AJAH-18300_Green-18300_Negative_Control_4dpi-lib1_S1_L004_R1_001.fastq.gz AJAH-18300_Green-18300_Negative_Control_4dpi-lib1_S1_L004_R2_001.fastq.gz,fastq fastq,120050343140.0,674440130.0,GSM9034431 r1,0:28 1:150,A:34219257803;C:27603489363;G:29252474045;T:28971358956;N:3762973,28,150,,,34219257803,27603489363,29252474045,28971358956,3762973,SRX29085356,SRS25297144,SRA2144659,"Johnson Lab, Developmental Biology, Washington University in St.Louis","Johnson Lab, Developmental Biology, Washington University in St.Louis",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-06-06,Larval,Larval,Trunk,Surface Structure
36245,SRR33873802,SRX29085355,SRS25297143,SRP590547,PRJNA1272846,Organism wide contributions to systemic skeletal muscle repair in larval zebrafish.,GSE299146,Transcriptome Analysis,We developed a systemic muscle injury model in zebrafish. Single cell transcriptomic analysis of muscle and non muscle tissues revealed that systemic and local muscle injuries elicit distinct cellular molecular responses  both quantitatively and qualitatively. These studies suggest that large  and small scale muscle injuries activate different regenerative programs  resulting in either systemic or local repair. Overall design: To characterize the regenerative responses and signaling pathways activated post systemic or local muscle injury  we generated Tgactc1b:NTR mCherry transgenic zebrafish lines.At 4 dpf  transgenic larvae were treated with MTZ overnight to systemically injure all myofibers  or were subjected to local mechanical injury needlestick of 2 3 somites.Uninjured and systemically injured larvae were collected at 1  2  and 4 xxx post injury. Mechanically injured larvae were collected at 2 xxx post injury. Sequencing results were compared between uninjured  systemically injured  and mechanically injured siblings.,,,,larval trunk  2dpi mcherry MTZ,GSM9034430,,source name:Trunk|tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water + MTZ|batch:10/26/2022|geo loc name:missing|collection date:missing,larval trunk  2dpi mcherry MTZ,post sequencing  the Illumina output was processed using the CellRanger v8.0.1 pipeline to generate gene barcode count matrices. A custom reference genome was made with the “cellranger mkref” command  using the fasta file of zebrafish reference genome GRCz11 constructed from the Ensemble genome build https://useast.ensembl.org/Danio rerio/Info/Index and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Base call files for each sample from Illumina were demultiplexed into FASTQ reads. Then  the “cellranger count” pipeline was used to align sequencing reads in FASTQ files to the custom reference genome. Both exon and intron sequences were included during the alignment. The filtered gene barcode count matrices generated by “cellranger count” was used for downstream analysis. Datasets were integrated and analyzed using Seurat v4.4.0 package with R v4.4.2Stuart etal.  2019; Team  2024. Each sample count matrix was filtered for genes that were expressed in at least 3 cells and cells expressing at least 200 genes  followed by cell quality assessment usingcommonly used QC matrixes Ilicic et al.  2016. Cells having a unique number of genes between 200 and 6500  mitochondrial gene percentage <5 and total number of reads UMIs between 300and 35000 were used for downstream processing. Each dataset was independently normalizedand scaled using the “SCTransform” function  which is an improved method for normalization  that performs a variance stabilizing transformation using negative binomial regression Hafemeisterand Satija  2019. Standard integration workflow of Seurat was used to identify shared sources of variation across experiments as well as mutual nearest neighbors Butler et al.  2018; Haghverdiet al.  2018. Integration features were selected based on the top 6000 highly variable features using “SelectIntegrationFeatures” function nfeatures = 6000  which was used as input for the“anchor.features” argument of the “FindIntegrationAnchors” function. PCA analysis was performed on the 6000 variable features and the top 50 principal components selected based on the elbow plot heuristic  which measures the contribution of variation in each component. These 50 principal components were used in “FindNeighbors” and “FindClusters” functions to perform graph based clustering on a shared nearest neighbor graph Levine et al.  2015; Xu and Su 2015. Louvain algorithm was used for modularity optimization in cell clustering using “FindClusters” function. The resolution parameter res = 0.3 that determines the granularity of clusteringwas selected by visually inspecting clusters with resolutions ranging between 0.1 and 2.0 as well as clustree graph Zappia and Oshlack  2018. Uniform Manifold Approximation and Reduction UMAP was used for non linear dimensional reduction of the first 50 principal components and visualize the data using “RunUMAP” function Becht et al.  2018. Data was graphed using different plot functions  such as “DimPlot”  “VlnPlot”  “FeaturePlot”  “Dotplot” and “DoHeatmap”  to view the cell cluster identity and marker gene expression. Cell proportions were extracted using the “table” and “prop.table” functions. Differential gene expression for individual clusters was identified using Wilcoxon rank sum test in the “FindAllMarkers” function. Marker genes detected in at least 25% of the clustered cells and had a positive average log2FC were reported. Muscle cells identified from the complete dataset were subclustered using the “subset” function for subcluster analysis. The muscle subset was again normalized and scaled using the “SCTransform” function with glmGamPoi method Ahlmann Eltze and Huber  2021. Fifty principal components were used and the resolution parameter was set to 0.4. Downstream analysis was done as described above for the integrated analysis. We used a zebrafish single atlas Sur et al.  2023 to generate a database of markers for each tissue and cell type Table S1. The differentially expressed markers of each cluster were crossreferenced with our compiled database using our “DE Marker Scoring” algorithm Saraswathy et al.  2024. For every matching marker gene  one point was given to the respective cluster under the column name with matching cell identity. Iteration over every marker gene was performed to generate a scoring matrix with varying points for each cluster against the different cell identities compiled in the database Table S2  sheet: scoring. The “phyper” function in R was then used to calculate one tailed binomial probabilities using hypergeometric distribution for the total score obtained from each cluster against each cell identity in the database Table S2  sheet: Binomial probability. −log10 of probability values were obtained for plotting the heatmap Table S2  sheet:−log10P. The resulting values were scaled from 0 to 100 and plotted as a heatmap using GraphPad prism. Each cluster was given an identity based on the maximum −log10 p score obtained in the heatmap. The top DE markers of clusters with ambiguous scores were manually annotated using the “ident genes” from the zebrafish single atlas Sur et al.  2023 and literature search McKellar et al.  2021. Top DE markers generated for each cluster is given in Table S3  sheet:topDEmarkers.all.clusters “RenameIdents” function was used to assign identity to each cluster. To confirm the assigned cluster identities  enrichment of classical markers of respective cell types were tested using Dot plot. The R package CellChat v2.1.2 was used to evaluate regenerative cell cell interactions post local and systemic muscle injury Jin et al.  2021. CellChat models the probability of cell cell communication by integrating our gene expression data with a database of known interaction between signaling ligands  receptors  and their cofactors CellChatDB. The RNA data was used to create CellChat object using “createCellChat” function  followed by the recommended preprocessing functions with default parameters for the analysis of individual datasets. Truncated mean method with 10% trimmed observation was used to compute average gene expression per cell group for the complete dataset. The default trimean method was used to compute average gene expression for the CellChat analysis. CellChatDB.zebrafish was used to infer cell cell communication. All categories of ligand receptor interactions in the database were used in the analysis. Communications involving less than 10 cells were excluded. The “netAnalysis computeCentrality” function was used to calculate network centrality scores at each time point. Functions such as “netVisual circle”  “netAnalysis contribution”  “netVisual aggregate”  “netVisual bubble”  “netAnalysis signalingRole heatmap”  and “netAnalysis signalingRole scatter” were used to generate different plots used in this paper. Assembly: zebrafish reference genome GRCz11 and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Supplementary files format and content: Compressed Filtered Feature and Barcode files as .tsv file and count matrices in .mtx file format.,Trunk,Fish were treated with 12 hours of metronidazole or were stuck locally with a needle,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell 3’ Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,Larval zebrafish of 4 dpf underwent drug treatments or needle stick injuries for muscle ablation,tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water + MTZ|batch:10/26/2022,GSM9034430,GSM9034430: larval trunk  2dpi mcherry MTZ; Danio rerio; RNA Seq,GSM9034430 r1,GSM9034430,1,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell three prime Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP590547,,,AJAH-18300_Red-18300_mCherry_Positive_2dpi-lib1_S2_L004_R1_001.fastq.gz AJAH-18300_Red-18300_mCherry_Positive_2dpi-lib1_S2_L004_R2_001.fastq.gz,fastq fastq,86534465752.0,486148684.0,GSM9034430 r1,0:28 1:150,A:23591959992;C:20534495856;G:22206815673;T:20199626171;N:1568060,28,150,,,23591959992,20534495856,22206815673,20199626171,1568060,SRX29085355,SRS25297143,SRA2144659,"Johnson Lab, Developmental Biology, Washington University in St.Louis","Johnson Lab, Developmental Biology, Washington University in St.Louis",2,0.01419,0.94664,0.00513,0.17395,0.99504,0.8396,0.29625,0.66798,28,150,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-06-06,Larval,Larval,Trunk,Surface Structure
36246,SRR33873803,SRX29085354,SRS25297142,SRP590547,PRJNA1272846,Organism wide contributions to systemic skeletal muscle repair in larval zebrafish.,GSE299146,Transcriptome Analysis,We developed a systemic muscle injury model in zebrafish. Single cell transcriptomic analysis of muscle and non muscle tissues revealed that systemic and local muscle injuries elicit distinct cellular molecular responses  both quantitatively and qualitatively. These studies suggest that large  and small scale muscle injuries activate different regenerative programs  resulting in either systemic or local repair. Overall design: To characterize the regenerative responses and signaling pathways activated post systemic or local muscle injury  we generated Tgactc1b:NTR mCherry transgenic zebrafish lines.At 4 dpf  transgenic larvae were treated with MTZ overnight to systemically injure all myofibers  or were subjected to local mechanical injury needlestick of 2 3 somites.Uninjured and systemically injured larvae were collected at 1  2  and 4 xxx post injury. Mechanically injured larvae were collected at 2 xxx post injury. Sequencing results were compared between uninjured  systemically injured  and mechanically injured siblings.,,,,larval trunk  2dpi Negative Control,GSM9034429,,source name:Trunk|tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water|batch:10/26/2022|geo loc name:missing|collection date:missing,larval trunk  2dpi Negative Control,post sequencing  the Illumina output was processed using the CellRanger v8.0.1 pipeline to generate gene barcode count matrices. A custom reference genome was made with the “cellranger mkref” command  using the fasta file of zebrafish reference genome GRCz11 constructed from the Ensemble genome build https://useast.ensembl.org/Danio rerio/Info/Index and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Base call files for each sample from Illumina were demultiplexed into FASTQ reads. Then  the “cellranger count” pipeline was used to align sequencing reads in FASTQ files to the custom reference genome. Both exon and intron sequences were included during the alignment. The filtered gene barcode count matrices generated by “cellranger count” was used for downstream analysis. Datasets were integrated and analyzed using Seurat v4.4.0 package with R v4.4.2Stuart etal.  2019; Team  2024. Each sample count matrix was filtered for genes that were expressed in at least 3 cells and cells expressing at least 200 genes  followed by cell quality assessment usingcommonly used QC matrixes Ilicic et al.  2016. Cells having a unique number of genes between 200 and 6500  mitochondrial gene percentage <5 and total number of reads UMIs between 300and 35000 were used for downstream processing. Each dataset was independently normalizedand scaled using the “SCTransform” function  which is an improved method for normalization  that performs a variance stabilizing transformation using negative binomial regression Hafemeisterand Satija  2019. Standard integration workflow of Seurat was used to identify shared sources of variation across experiments as well as mutual nearest neighbors Butler et al.  2018; Haghverdiet al.  2018. Integration features were selected based on the top 6000 highly variable features using “SelectIntegrationFeatures” function nfeatures = 6000  which was used as input for the“anchor.features” argument of the “FindIntegrationAnchors” function. PCA analysis was performed on the 6000 variable features and the top 50 principal components selected based on the elbow plot heuristic  which measures the contribution of variation in each component. These 50 principal components were used in “FindNeighbors” and “FindClusters” functions to perform graph based clustering on a shared nearest neighbor graph Levine et al.  2015; Xu and Su 2015. Louvain algorithm was used for modularity optimization in cell clustering using “FindClusters” function. The resolution parameter res = 0.3 that determines the granularity of clusteringwas selected by visually inspecting clusters with resolutions ranging between 0.1 and 2.0 as well as clustree graph Zappia and Oshlack  2018. Uniform Manifold Approximation and Reduction UMAP was used for non linear dimensional reduction of the first 50 principal components and visualize the data using “RunUMAP” function Becht et al.  2018. Data was graphed using different plot functions  such as “DimPlot”  “VlnPlot”  “FeaturePlot”  “Dotplot” and “DoHeatmap”  to view the cell cluster identity and marker gene expression. Cell proportions were extracted using the “table” and “prop.table” functions. Differential gene expression for individual clusters was identified using Wilcoxon rank sum test in the “FindAllMarkers” function. Marker genes detected in at least 25% of the clustered cells and had a positive average log2FC were reported. Muscle cells identified from the complete dataset were subclustered using the “subset” function for subcluster analysis. The muscle subset was again normalized and scaled using the “SCTransform” function with glmGamPoi method Ahlmann Eltze and Huber  2021. Fifty principal components were used and the resolution parameter was set to 0.4. Downstream analysis was done as described above for the integrated analysis. We used a zebrafish single atlas Sur et al.  2023 to generate a database of markers for each tissue and cell type Table S1. The differentially expressed markers of each cluster were crossreferenced with our compiled database using our “DE Marker Scoring” algorithm Saraswathy et al.  2024. For every matching marker gene  one point was given to the respective cluster under the column name with matching cell identity. Iteration over every marker gene was performed to generate a scoring matrix with varying points for each cluster against the different cell identities compiled in the database Table S2  sheet: scoring. The “phyper” function in R was then used to calculate one tailed binomial probabilities using hypergeometric distribution for the total score obtained from each cluster against each cell identity in the database Table S2  sheet: Binomial probability. −log10 of probability values were obtained for plotting the heatmap Table S2  sheet:−log10P. The resulting values were scaled from 0 to 100 and plotted as a heatmap using GraphPad prism. Each cluster was given an identity based on the maximum −log10 p score obtained in the heatmap. The top DE markers of clusters with ambiguous scores were manually annotated using the “ident genes” from the zebrafish single atlas Sur et al.  2023 and literature search McKellar et al.  2021. Top DE markers generated for each cluster is given in Table S3  sheet:topDEmarkers.all.clusters “RenameIdents” function was used to assign identity to each cluster. To confirm the assigned cluster identities  enrichment of classical markers of respective cell types were tested using Dot plot. The R package CellChat v2.1.2 was used to evaluate regenerative cell cell interactions post local and systemic muscle injury Jin et al.  2021. CellChat models the probability of cell cell communication by integrating our gene expression data with a database of known interaction between signaling ligands  receptors  and their cofactors CellChatDB. The RNA data was used to create CellChat object using “createCellChat” function  followed by the recommended preprocessing functions with default parameters for the analysis of individual datasets. Truncated mean method with 10% trimmed observation was used to compute average gene expression per cell group for the complete dataset. The default trimean method was used to compute average gene expression for the CellChat analysis. CellChatDB.zebrafish was used to infer cell cell communication. All categories of ligand receptor interactions in the database were used in the analysis. Communications involving less than 10 cells were excluded. The “netAnalysis computeCentrality” function was used to calculate network centrality scores at each time point. Functions such as “netVisual circle”  “netAnalysis contribution”  “netVisual aggregate”  “netVisual bubble”  “netAnalysis signalingRole heatmap”  and “netAnalysis signalingRole scatter” were used to generate different plots used in this paper. Assembly: zebrafish reference genome GRCz11 and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Supplementary files format and content: Compressed Filtered Feature and Barcode files as .tsv file and count matrices in .mtx file format.,Trunk,Fish were treated with 12 hours of metronidazole or were stuck locally with a needle,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell 3’ Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,Larval zebrafish of 4 dpf underwent drug treatments or needle stick injuries for muscle ablation,tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water|batch:10/26/2022,GSM9034429,GSM9034429: larval trunk  2dpi Negative Control; Danio rerio; RNA Seq,GSM9034429 r1,GSM9034429,1,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell three prime Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP590547,,,AJAH-18300_Green-18300_Negative_Control-lib1_S1_L004_R1_001.fastq.gz AJAH-18300_Green-18300_Negative_Control-lib1_S1_L004_R2_001.fastq.gz,fastq fastq,81637706044.0,458638798.0,GSM9034429 r1,0:28 1:150,A:23244690048;C:18579650528;G:19634226269;T:20177635070;N:1504129,28,150,,,23244690048,18579650528,19634226269,20177635070,1504129,SRX29085354,SRS25297142,SRA2144659,"Johnson Lab, Developmental Biology, Washington University in St.Louis","Johnson Lab, Developmental Biology, Washington University in St.Louis",2,0.0091,0.93772,0.00313,0.1383,0.99446,0.82698,0.33858,0.5389,28,150,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-06-06,Larval,Larval,Trunk,Surface Structure
36247,SRR33873804,SRX29085353,SRS25297141,SRP590547,PRJNA1272846,Organism wide contributions to systemic skeletal muscle repair in larval zebrafish.,GSE299146,Transcriptome Analysis,We developed a systemic muscle injury model in zebrafish. Single cell transcriptomic analysis of muscle and non muscle tissues revealed that systemic and local muscle injuries elicit distinct cellular molecular responses  both quantitatively and qualitatively. These studies suggest that large  and small scale muscle injuries activate different regenerative programs  resulting in either systemic or local repair. Overall design: To characterize the regenerative responses and signaling pathways activated post systemic or local muscle injury  we generated Tgactc1b:NTR mCherry transgenic zebrafish lines.At 4 dpf  transgenic larvae were treated with MTZ overnight to systemically injure all myofibers  or were subjected to local mechanical injury needlestick of 2 3 somites.Uninjured and systemically injured larvae were collected at 1  2  and 4 xxx post injury. Mechanically injured larvae were collected at 2 xxx post injury. Sequencing results were compared between uninjured  systemically injured  and mechanically injured siblings.,,,,larval trunk  1dpi mcherry MTZ,GSM9034428,,source name:Trunk|tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water + MTZ|batch:10/25/2022|geo loc name:missing|collection date:missing,larval trunk  1dpi mcherry MTZ,post sequencing  the Illumina output was processed using the CellRanger v8.0.1 pipeline to generate gene barcode count matrices. A custom reference genome was made with the “cellranger mkref” command  using the fasta file of zebrafish reference genome GRCz11 constructed from the Ensemble genome build https://useast.ensembl.org/Danio rerio/Info/Index and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Base call files for each sample from Illumina were demultiplexed into FASTQ reads. Then  the “cellranger count” pipeline was used to align sequencing reads in FASTQ files to the custom reference genome. Both exon and intron sequences were included during the alignment. The filtered gene barcode count matrices generated by “cellranger count” was used for downstream analysis. Datasets were integrated and analyzed using Seurat v4.4.0 package with R v4.4.2Stuart etal.  2019; Team  2024. Each sample count matrix was filtered for genes that were expressed in at least 3 cells and cells expressing at least 200 genes  followed by cell quality assessment usingcommonly used QC matrixes Ilicic et al.  2016. Cells having a unique number of genes between 200 and 6500  mitochondrial gene percentage <5 and total number of reads UMIs between 300and 35000 were used for downstream processing. Each dataset was independently normalizedand scaled using the “SCTransform” function  which is an improved method for normalization  that performs a variance stabilizing transformation using negative binomial regression Hafemeisterand Satija  2019. Standard integration workflow of Seurat was used to identify shared sources of variation across experiments as well as mutual nearest neighbors Butler et al.  2018; Haghverdiet al.  2018. Integration features were selected based on the top 6000 highly variable features using “SelectIntegrationFeatures” function nfeatures = 6000  which was used as input for the“anchor.features” argument of the “FindIntegrationAnchors” function. PCA analysis was performed on the 6000 variable features and the top 50 principal components selected based on the elbow plot heuristic  which measures the contribution of variation in each component. These 50 principal components were used in “FindNeighbors” and “FindClusters” functions to perform graph based clustering on a shared nearest neighbor graph Levine et al.  2015; Xu and Su 2015. Louvain algorithm was used for modularity optimization in cell clustering using “FindClusters” function. The resolution parameter res = 0.3 that determines the granularity of clusteringwas selected by visually inspecting clusters with resolutions ranging between 0.1 and 2.0 as well as clustree graph Zappia and Oshlack  2018. Uniform Manifold Approximation and Reduction UMAP was used for non linear dimensional reduction of the first 50 principal components and visualize the data using “RunUMAP” function Becht et al.  2018. Data was graphed using different plot functions  such as “DimPlot”  “VlnPlot”  “FeaturePlot”  “Dotplot” and “DoHeatmap”  to view the cell cluster identity and marker gene expression. Cell proportions were extracted using the “table” and “prop.table” functions. Differential gene expression for individual clusters was identified using Wilcoxon rank sum test in the “FindAllMarkers” function. Marker genes detected in at least 25% of the clustered cells and had a positive average log2FC were reported. Muscle cells identified from the complete dataset were subclustered using the “subset” function for subcluster analysis. The muscle subset was again normalized and scaled using the “SCTransform” function with glmGamPoi method Ahlmann Eltze and Huber  2021. Fifty principal components were used and the resolution parameter was set to 0.4. Downstream analysis was done as described above for the integrated analysis. We used a zebrafish single atlas Sur et al.  2023 to generate a database of markers for each tissue and cell type Table S1. The differentially expressed markers of each cluster were crossreferenced with our compiled database using our “DE Marker Scoring” algorithm Saraswathy et al.  2024. For every matching marker gene  one point was given to the respective cluster under the column name with matching cell identity. Iteration over every marker gene was performed to generate a scoring matrix with varying points for each cluster against the different cell identities compiled in the database Table S2  sheet: scoring. The “phyper” function in R was then used to calculate one tailed binomial probabilities using hypergeometric distribution for the total score obtained from each cluster against each cell identity in the database Table S2  sheet: Binomial probability. −log10 of probability values were obtained for plotting the heatmap Table S2  sheet:−log10P. The resulting values were scaled from 0 to 100 and plotted as a heatmap using GraphPad prism. Each cluster was given an identity based on the maximum −log10 p score obtained in the heatmap. The top DE markers of clusters with ambiguous scores were manually annotated using the “ident genes” from the zebrafish single atlas Sur et al.  2023 and literature search McKellar et al.  2021. Top DE markers generated for each cluster is given in Table S3  sheet:topDEmarkers.all.clusters “RenameIdents” function was used to assign identity to each cluster. To confirm the assigned cluster identities  enrichment of classical markers of respective cell types were tested using Dot plot. The R package CellChat v2.1.2 was used to evaluate regenerative cell cell interactions post local and systemic muscle injury Jin et al.  2021. CellChat models the probability of cell cell communication by integrating our gene expression data with a database of known interaction between signaling ligands  receptors  and their cofactors CellChatDB. The RNA data was used to create CellChat object using “createCellChat” function  followed by the recommended preprocessing functions with default parameters for the analysis of individual datasets. Truncated mean method with 10% trimmed observation was used to compute average gene expression per cell group for the complete dataset. The default trimean method was used to compute average gene expression for the CellChat analysis. CellChatDB.zebrafish was used to infer cell cell communication. All categories of ligand receptor interactions in the database were used in the analysis. Communications involving less than 10 cells were excluded. The “netAnalysis computeCentrality” function was used to calculate network centrality scores at each time point. Functions such as “netVisual circle”  “netAnalysis contribution”  “netVisual aggregate”  “netVisual bubble”  “netAnalysis signalingRole heatmap”  and “netAnalysis signalingRole scatter” were used to generate different plots used in this paper. Assembly: zebrafish reference genome GRCz11 and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Supplementary files format and content: Compressed Filtered Feature and Barcode files as .tsv file and count matrices in .mtx file format.,Trunk,Fish were treated with 12 hours of metronidazole or were stuck locally with a needle,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell 3’ Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,Larval zebrafish of 4 dpf underwent drug treatments or needle stick injuries for muscle ablation,tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water + MTZ|batch:10/25/2022,GSM9034428,GSM9034428: larval trunk  1dpi mcherry MTZ; Danio rerio; RNA Seq,GSM9034428 r1,GSM9034428,1,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell three prime Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP590547,,,AJAH-18300_Red-18300_mCherry_Positive-lib1_S2_L004_R1_001.fastq.gz AJAH-18300_Red-18300_mCherry_Positive-lib1_S2_L004_R2_001.fastq.gz,fastq fastq,84014647022.0,471992399.0,GSM9034428 r1,0:28 1:150,A:24181834463;C:18988262388;G:20195117959;T:20647899177;N:1533035,28,150,,,24181834463,18988262388,20195117959,20647899177,1533035,SRX29085353,SRS25297141,SRA2144659,"Johnson Lab, Developmental Biology, Washington University in St.Louis","Johnson Lab, Developmental Biology, Washington University in St.Louis",2,0.00859,0.93077,0.00306,0.13947,0.99393,0.81807,0.39035,0.66419,28,150,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-06-06,Larval,Larval,Trunk,Surface Structure
36248,SRR33873805,SRX29085352,SRS25297140,SRP590547,PRJNA1272846,Organism wide contributions to systemic skeletal muscle repair in larval zebrafish.,GSE299146,Transcriptome Analysis,We developed a systemic muscle injury model in zebrafish. Single cell transcriptomic analysis of muscle and non muscle tissues revealed that systemic and local muscle injuries elicit distinct cellular molecular responses  both quantitatively and qualitatively. These studies suggest that large  and small scale muscle injuries activate different regenerative programs  resulting in either systemic or local repair. Overall design: To characterize the regenerative responses and signaling pathways activated post systemic or local muscle injury  we generated Tgactc1b:NTR mCherry transgenic zebrafish lines.At 4 dpf  transgenic larvae were treated with MTZ overnight to systemically injure all myofibers  or were subjected to local mechanical injury needlestick of 2 3 somites.Uninjured and systemically injured larvae were collected at 1  2  and 4 xxx post injury. Mechanically injured larvae were collected at 2 xxx post injury. Sequencing results were compared between uninjured  systemically injured  and mechanically injured siblings.,,,,larval trunk  1dpi Negative Control,GSM9034427,,source name:Trunk|tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water|batch:11/4/2024|geo loc name:missing|collection date:missing,larval trunk  1dpi Negative Control,post sequencing  the Illumina output was processed using the CellRanger v8.0.1 pipeline to generate gene barcode count matrices. A custom reference genome was made with the “cellranger mkref” command  using the fasta file of zebrafish reference genome GRCz11 constructed from the Ensemble genome build https://useast.ensembl.org/Danio rerio/Info/Index and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Base call files for each sample from Illumina were demultiplexed into FASTQ reads. Then  the “cellranger count” pipeline was used to align sequencing reads in FASTQ files to the custom reference genome. Both exon and intron sequences were included during the alignment. The filtered gene barcode count matrices generated by “cellranger count” was used for downstream analysis. Datasets were integrated and analyzed using Seurat v4.4.0 package with R v4.4.2Stuart etal.  2019; Team  2024. Each sample count matrix was filtered for genes that were expressed in at least 3 cells and cells expressing at least 200 genes  followed by cell quality assessment usingcommonly used QC matrixes Ilicic et al.  2016. Cells having a unique number of genes between 200 and 6500  mitochondrial gene percentage <5 and total number of reads UMIs between 300and 35000 were used for downstream processing. Each dataset was independently normalizedand scaled using the “SCTransform” function  which is an improved method for normalization  that performs a variance stabilizing transformation using negative binomial regression Hafemeisterand Satija  2019. Standard integration workflow of Seurat was used to identify shared sources of variation across experiments as well as mutual nearest neighbors Butler et al.  2018; Haghverdiet al.  2018. Integration features were selected based on the top 6000 highly variable features using “SelectIntegrationFeatures” function nfeatures = 6000  which was used as input for the“anchor.features” argument of the “FindIntegrationAnchors” function. PCA analysis was performed on the 6000 variable features and the top 50 principal components selected based on the elbow plot heuristic  which measures the contribution of variation in each component. These 50 principal components were used in “FindNeighbors” and “FindClusters” functions to perform graph based clustering on a shared nearest neighbor graph Levine et al.  2015; Xu and Su 2015. Louvain algorithm was used for modularity optimization in cell clustering using “FindClusters” function. The resolution parameter res = 0.3 that determines the granularity of clusteringwas selected by visually inspecting clusters with resolutions ranging between 0.1 and 2.0 as well as clustree graph Zappia and Oshlack  2018. Uniform Manifold Approximation and Reduction UMAP was used for non linear dimensional reduction of the first 50 principal components and visualize the data using “RunUMAP” function Becht et al.  2018. Data was graphed using different plot functions  such as “DimPlot”  “VlnPlot”  “FeaturePlot”  “Dotplot” and “DoHeatmap”  to view the cell cluster identity and marker gene expression. Cell proportions were extracted using the “table” and “prop.table” functions. Differential gene expression for individual clusters was identified using Wilcoxon rank sum test in the “FindAllMarkers” function. Marker genes detected in at least 25% of the clustered cells and had a positive average log2FC were reported. Muscle cells identified from the complete dataset were subclustered using the “subset” function for subcluster analysis. The muscle subset was again normalized and scaled using the “SCTransform” function with glmGamPoi method Ahlmann Eltze and Huber  2021. Fifty principal components were used and the resolution parameter was set to 0.4. Downstream analysis was done as described above for the integrated analysis. We used a zebrafish single atlas Sur et al.  2023 to generate a database of markers for each tissue and cell type Table S1. The differentially expressed markers of each cluster were crossreferenced with our compiled database using our “DE Marker Scoring” algorithm Saraswathy et al.  2024. For every matching marker gene  one point was given to the respective cluster under the column name with matching cell identity. Iteration over every marker gene was performed to generate a scoring matrix with varying points for each cluster against the different cell identities compiled in the database Table S2  sheet: scoring. The “phyper” function in R was then used to calculate one tailed binomial probabilities using hypergeometric distribution for the total score obtained from each cluster against each cell identity in the database Table S2  sheet: Binomial probability. −log10 of probability values were obtained for plotting the heatmap Table S2  sheet:−log10P. The resulting values were scaled from 0 to 100 and plotted as a heatmap using GraphPad prism. Each cluster was given an identity based on the maximum −log10 p score obtained in the heatmap. The top DE markers of clusters with ambiguous scores were manually annotated using the “ident genes” from the zebrafish single atlas Sur et al.  2023 and literature search McKellar et al.  2021. Top DE markers generated for each cluster is given in Table S3  sheet:topDEmarkers.all.clusters “RenameIdents” function was used to assign identity to each cluster. To confirm the assigned cluster identities  enrichment of classical markers of respective cell types were tested using Dot plot. The R package CellChat v2.1.2 was used to evaluate regenerative cell cell interactions post local and systemic muscle injury Jin et al.  2021. CellChat models the probability of cell cell communication by integrating our gene expression data with a database of known interaction between signaling ligands  receptors  and their cofactors CellChatDB. The RNA data was used to create CellChat object using “createCellChat” function  followed by the recommended preprocessing functions with default parameters for the analysis of individual datasets. Truncated mean method with 10% trimmed observation was used to compute average gene expression per cell group for the complete dataset. The default trimean method was used to compute average gene expression for the CellChat analysis. CellChatDB.zebrafish was used to infer cell cell communication. All categories of ligand receptor interactions in the database were used in the analysis. Communications involving less than 10 cells were excluded. The “netAnalysis computeCentrality” function was used to calculate network centrality scores at each time point. Functions such as “netVisual circle”  “netAnalysis contribution”  “netVisual aggregate”  “netVisual bubble”  “netAnalysis signalingRole heatmap”  and “netAnalysis signalingRole scatter” were used to generate different plots used in this paper. Assembly: zebrafish reference genome GRCz11 and the sorted Gene Transfer Format file v4.3.2 from the improved zebrafish transcriptome annotation Lawson et al.  2020. Supplementary files format and content: Compressed Filtered Feature and Barcode files as .tsv file and count matrices in .mtx file format.,Trunk,Fish were treated with 12 hours of metronidazole or were stuck locally with a needle,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell 3’ Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,Larval zebrafish of 4 dpf underwent drug treatments or needle stick injuries for muscle ablation,tissue:Trunk|genotype:Tgactc1b:NTR mCherry|treatment:Fish Water|batch:11/4/2024,GSM9034427,GSM9034427: larval trunk  1dpi Negative Control; Danio rerio; RNA Seq,GSM9034427 r1,GSM9034427,1,15 larvae per cohort were dissected to remove the head  caudal fin  and internal organs and then processed as described Farnsworth DB 459 2020. For tissue lysis  500μL of dissociation buffer 2ug/ul Collagenase P  2mM CaCl2  0.2 ul DNaseI  0.25% Trypsin  in 1X PBS was added to the samples and incubated at 28 °C until samples were visually dissociated 15min. Dissociation was stopped with equal volume of stop buffer 10% FBS  0.001mM EDTA  in 1X PBS. Samples were centrifuged at 750rcf for 7min at 4°C  the supernatant was discarded  and the pellet was resuspended in 100μL of resuspension buffer 1% FBS  2mM CaCl2  1X Penicillin/Streptomycin  in DMEM. The suspension was strained through 20μm cell strainer Pluriselect USA  43 10020  40  centrifuged once 500rcf  1 min  4°C to pass cells through the strainer  and centrifuged a second time 750rcf  7 min  4°C to pellet the cells. The cells were resuspended in 100μL of resuspension buffer  centrifugated 750rcf  7min  4°C  and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst Invitrogen  H3570  incubated for 10min  and transferred to a hemocytometer Bulldogbio  NC1731934 to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue Sigma  T8154 for 5min  transferred to a hemocytometer  and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing. For snRNA seq  30 µl of isolated nuclei at a concentration of 1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared post the GEM generation and barcoding  followed by the GEM RT reaction and bead cleanup steps.  cDNA was amplified for 11 13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry Dual Index with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform  the Chromium Next GEM Single Cell three prime Kit v3.1  16 rxns PN 1000268  Chromium Next GEM Chip G Single Cell Kit  48 rxns PN 1000120  and Dual Index Kit TT Set A  96 rxns PN 1000215 were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol KAPA Biosystems/Roche to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50 000 reads/cell was targeted for each Gene Expression Library.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP590547,,,LIB065814-DIL01_22CNHTLT4_S90_L008_R1_001.fastq.gz LIB065814-DIL01_22CNHTLT4_S90_L008_R2_001.fastq.gz,fastq fastq,96199623993.0,537428067.0,GSM9034427 r1,0:28 1:151,A:26836117761;C:21626512077;G:22419696915;T:25306734573;N:10562667,28,151,,,26836117761,21626512077,22419696915,25306734573,10562667,SRX29085352,SRS25297140,SRA2144659,"Johnson Lab, Developmental Biology, Washington University in St.Louis","Johnson Lab, Developmental Biology, Washington University in St.Louis",2,0.01026,0.90959,0.00375,0.1621,0.99019,0.80945,0.41304,0.54052,28,151,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-06-06,Larval,Larval,Trunk,Surface Structure
70967,SRR21007395,SRX17024129,SRS14609022,SRP390913,PRJNA868351,Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [scRNA seq],GSE210941,Transcriptome Analysis,Investigate the role of miR128 in the EHT process and the formation of nHSPCs Overall design: Comparative gene expression  analysis of RNA seq data for WT and MT samples for miRNA128 in Human and Fish,parent bioproject:PRJNA868347,pubmed:37460694,,gRNA jag1  26HPF  scRNAseq,GSM6443156,,source name:trunk tissue containing the AGM|cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF|geo loc name:missing|collection date:missing,gRNA jag1  26HPF  scRNAseq,The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: Tab separated values files and matrix files,trunk tissue containing the AGM,,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b g3’UTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF,GSM6443156,GSM6443156: gRNA jag1  26HPF  scRNAseq; Danio rerio; RNA Seq,GSM6443156 r1,GSM6443156,1,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b gthree primeUTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP390913,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=jag1b DRT S3 L003 I1 001.fastq.gz   read2PairFiles=jag1b DRT S3 L003 R1 001.fastq.gz   read3PairFiles=jag1b DRT S3 L003 R2 001.fastq.gz,jag1b_DRT_S3_L003_I1_001.fastq.gz jag1b_DRT_S3_L003_R1_001.fastq.gz jag1b_DRT_S3_L003_R2_001.fastq.gz,fastq fastq fastq,16114282986.0,126884118.0,GSM6443156 r1,0:8 1:28 2:91,A:4274223175;C:3328097087;G:3589117645;T:3907323607;N:448528,8,28,91,,4274223175,3328097087,3589117645,3907323607,448528,SRX17024129,SRS14609022,SRA1473366,"Nicoli Lab, Genetics/Internal Medicine, Yale University","Nicoli Lab, Genetics/Internal Medicine, Yale University",2,0.00772,0.88765,0.00298,0.21848,0.98776,0.7934,0.36184,0.53575,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-08-10,Pharyngula,Embryo,Trunk,Surface Structure
70968,SRR21007396,SRX17024129,SRS14609022,SRP390913,PRJNA868351,Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [scRNA seq],GSE210941,Transcriptome Analysis,Investigate the role of miR128 in the EHT process and the formation of nHSPCs Overall design: Comparative gene expression  analysis of RNA seq data for WT and MT samples for miRNA128 in Human and Fish,parent bioproject:PRJNA868347,pubmed:37460694,,gRNA jag1  26HPF  scRNAseq,GSM6443156,,source name:trunk tissue containing the AGM|cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF|geo loc name:missing|collection date:missing,gRNA jag1  26HPF  scRNAseq,The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: Tab separated values files and matrix files,trunk tissue containing the AGM,,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b g3’UTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF,GSM6443156,GSM6443156: gRNA jag1  26HPF  scRNAseq; Danio rerio; RNA Seq,GSM6443156 r1,GSM6443156,1,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b gthree primeUTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP390913,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=jag1b DRT S3 L004 I1 001.fastq.gz   read2PairFiles=jag1b DRT S3 L004 R1 001.fastq.gz   read3PairFiles=jag1b DRT S3 L004 R2 001.fastq.gz,jag1b_DRT_S3_L004_I1_001.fastq.gz jag1b_DRT_S3_L004_R1_001.fastq.gz jag1b_DRT_S3_L004_R2_001.fastq.gz,fastq fastq fastq,16084657188.0,126650844.0,GSM6443156 r2,0:8 1:28 2:91,A:4267990504;C:3319270032;G:3579390545;T:3904256142;N:543213,8,28,91,,4267990504,3319270032,3579390545,3904256142,543213,SRX17024129,SRS14609022,SRA1473366,"Nicoli Lab, Genetics/Internal Medicine, Yale University","Nicoli Lab, Genetics/Internal Medicine, Yale University",2,0.00747,0.8896,0.00283,0.21781,0.98778,0.79263,0.36736,0.53802,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-08-10,Pharyngula,Embryo,Trunk,Surface Structure
70969,SRR21007397,SRX17024128,SRS14609021,SRP390913,PRJNA868351,Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [scRNA seq],GSE210941,Transcriptome Analysis,Investigate the role of miR128 in the EHT process and the formation of nHSPCs Overall design: Comparative gene expression  analysis of RNA seq data for WT and MT samples for miRNA128 in Human and Fish,parent bioproject:PRJNA868347,pubmed:37460694,,gRNA csnk1  26HPF  scRNAseq,GSM6443155,,source name:trunk tissue containing the AGM|cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF|geo loc name:missing|collection date:missing,gRNA csnk1  26HPF  scRNAseq,The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: Tab separated values files and matrix files,trunk tissue containing the AGM,,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b g3’UTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF,GSM6443155,GSM6443155: gRNA csnk1  26HPF  scRNAseq; Danio rerio; RNA Seq,GSM6443155 r1,GSM6443155,1,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b gthree primeUTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP390913,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=csnk1a DRT S2 L003 I1 001.fastq.gz   read2PairFiles=csnk1a DRT S2 L003 R1 001.fastq.gz   read3PairFiles=csnk1a DRT S2 L003 R2 001.fastq.gz,csnk1a_DRT_S2_L003_I1_001.fastq.gz csnk1a_DRT_S2_L003_R1_001.fastq.gz csnk1a_DRT_S2_L003_R2_001.fastq.gz,fastq fastq fastq,17585727973.0,138470299.0,GSM6443155 r1,0:8 1:28 2:91,A:4685099762;C:3662694223;G:3795199750;T:4334481609;N:490237,8,28,91,,4685099762,3662694223,3795199750,4334481609,490237,SRX17024128,SRS14609021,SRA1473366,"Nicoli Lab, Genetics/Internal Medicine, Yale University","Nicoli Lab, Genetics/Internal Medicine, Yale University",2,0.01126,0.9112,0.00402,0.18979,0.98137,0.7838,0.32952,0.50602,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-08-10,Pharyngula,Embryo,Trunk,Surface Structure
70970,SRR21007398,SRX17024128,SRS14609021,SRP390913,PRJNA868351,Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [scRNA seq],GSE210941,Transcriptome Analysis,Investigate the role of miR128 in the EHT process and the formation of nHSPCs Overall design: Comparative gene expression  analysis of RNA seq data for WT and MT samples for miRNA128 in Human and Fish,parent bioproject:PRJNA868347,pubmed:37460694,,gRNA csnk1  26HPF  scRNAseq,GSM6443155,,source name:trunk tissue containing the AGM|cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF|geo loc name:missing|collection date:missing,gRNA csnk1  26HPF  scRNAseq,The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: Tab separated values files and matrix files,trunk tissue containing the AGM,,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b g3’UTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF,GSM6443155,GSM6443155: gRNA csnk1  26HPF  scRNAseq; Danio rerio; RNA Seq,GSM6443155 r1,GSM6443155,1,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b gthree primeUTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP390913,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=csnk1a DRT S2 L004 I1 001.fastq.gz   read2PairFiles=csnk1a DRT S2 L004 R1 001.fastq.gz   read3PairFiles=csnk1a DRT S2 L004 R2 001.fastq.gz,csnk1a_DRT_S2_L004_I1_001.fastq.gz csnk1a_DRT_S2_L004_R1_001.fastq.gz csnk1a_DRT_S2_L004_R2_001.fastq.gz,fastq fastq fastq,17642162328.0,138914664.0,GSM6443155 r2,0:8 1:28 2:91,A:4700864535;C:3672134070;G:3805292893;T:4351958835;N:594683,8,28,91,,4700864535,3672134070,3805292893,4351958835,594683,SRX17024128,SRS14609021,SRA1473366,"Nicoli Lab, Genetics/Internal Medicine, Yale University","Nicoli Lab, Genetics/Internal Medicine, Yale University",2,0.01083,0.91228,0.00389,0.19017,0.98175,0.78413,0.34007,0.51895,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-08-10,Pharyngula,Embryo,Trunk,Surface Structure
70971,SRR21007399,SRX17024127,SRS14609020,SRP390913,PRJNA868351,Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [scRNA seq],GSE210941,Transcriptome Analysis,Investigate the role of miR128 in the EHT process and the formation of nHSPCs Overall design: Comparative gene expression  analysis of RNA seq data for WT and MT samples for miRNA128 in Human and Fish,parent bioproject:PRJNA868347,pubmed:37460694,,MT  26HPF  scRNAseq,GSM6443154,,source name:trunk tissue containing the AGM|cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF|geo loc name:missing|collection date:missing,MT  26HPF  scRNAseq,The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: Tab separated values files and matrix files,trunk tissue containing the AGM,,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b g3’UTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF,GSM6443154,GSM6443154: MT  26HPF  scRNAseq; Danio rerio; RNA Seq,GSM6443154 r1,GSM6443154,1,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b gthree primeUTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP390913,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=MT DRT S2 L004 I1 001.fastq.gz   read2PairFiles=MT DRT S2 L004 R1 001.fastq.gz   read3PairFiles=MT DRT S2 L004 R2 001.fastq.gz,MT_DRT_S2_L004_I1_001.fastq.gz MT_DRT_S2_L004_R1_001.fastq.gz MT_DRT_S2_L004_R2_001.fastq.gz,fastq fastq fastq,44640313691.0,351498533.0,GSM6443154 r1,0:8 1:28 2:91,A:11802470987;C:9130307392;G:9708029949;T:11186763112;N:753987,8,28,91,,11802470987,9130307392,9708029949,11186763112,753987,SRX17024127,SRS14609020,SRA1473366,"Nicoli Lab, Genetics/Internal Medicine, Yale University","Nicoli Lab, Genetics/Internal Medicine, Yale University",2,0.01069,0.92492,0.00314,0.17525,0.98338,0.79586,0.42895,0.5135,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-08-10,Pharyngula,Embryo,Trunk,Surface Structure
70972,SRR21007400,SRX17024126,SRS14609019,SRP390913,PRJNA868351,Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [scRNA seq],GSE210941,Transcriptome Analysis,Investigate the role of miR128 in the EHT process and the formation of nHSPCs Overall design: Comparative gene expression  analysis of RNA seq data for WT and MT samples for miRNA128 in Human and Fish,parent bioproject:PRJNA868347,pubmed:37460694,,WT  26HPF  scRNAseq,GSM6443153,,source name:trunk tissue containing the AGM|cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF|geo loc name:missing|collection date:missing,WT  26HPF  scRNAseq,The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: Tab separated values files and matrix files,trunk tissue containing the AGM,,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b g3’UTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF,GSM6443153,GSM6443153: WT  26HPF  scRNAseq; Danio rerio; RNA Seq,GSM6443153 r1,GSM6443153,1,Wild type  miR 128Δ/Δ  csnk1a1 and jag1b gthree primeUTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP390913,,loader:fastq load.py|options:  readTypes=TBB   read1PairFiles=WT DRT S1 L004 I1 001.fastq.gz   read2PairFiles=WT DRT S1 L004 R1 001.fastq.gz   read3PairFiles=WT DRT S1 L004 R2 001.fastq.gz,WT_DRT_S1_L004_I1_001.fastq.gz WT_DRT_S1_L004_R1_001.fastq.gz WT_DRT_S1_L004_R2_001.fastq.gz,fastq fastq fastq,63333837772.0,498691636.0,GSM6443153 r1,0:8 1:28 2:91,A:16776941902;C:12869180260;G:13716776874;T:15980339022;N:1066626,8,28,91,,16776941902,12869180260,13716776874,15980339022,1066626,SRX17024126,SRS14609019,SRA1473366,"Nicoli Lab, Genetics/Internal Medicine, Yale University","Nicoli Lab, Genetics/Internal Medicine, Yale University",2,0.00896,0.91613,0.0026,0.16276,0.98466,0.79279,0.44896,0.53257,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-08-10,Pharyngula,Embryo,Trunk,Surface Structure
74668,SRR23928776,SRX19738955,SRS17105108,SRP428413,PRJNA947108,Gene expression profile at single cell level of zebrafish trunk from WT or flt1 mutant 3dpf.,GSE227806,Transcriptome Analysis,scRNA seq was used to investigate neurovascular cross talk in zebrafish trunk. Overall design: Zebrafish trunk of WT and flt1 mutant were dissected  dissociated and processed for single cell RNA Seq using 10X Genomics Chromium droplet based system,parent bioproject:PRJNA947103,pubmed:38600061,,flt1mut  replicate 2  scRNAseq trunk,GSM7108419,,source name:Trunk|tissue:Trunk|genotype:flt1ka604|age:3dpf|geo loc name:missing|collection date:missing,flt1mut  replicate 2  scRNAseq trunk,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software  https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCZ11 v107 Supplementary files format and content: matrix files,Trunk,,Zebrafish embryos 3dpf were anesthethised with Tricain prior the dissection of the trunk. Dissected trunks were dissociated using a mix of 0.25% Trypsin and collagenase 4mg/mL  centrifuged to collect the cells  resuspended into DMEM + 10% Fetal Bovine Serum and filtered to remove the debris.  Cells were washed and resuspend in PBS prior 10X genomic experiment Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics,,tissue:Trunk|genotype:flt1ka604|age:3dpf,GSM7108419,GSM7108419: flt1mut  replicate 2  scRNAseq trunk; Danio rerio; RNA Seq,GSM7108419 r1,GSM7108419,1,Zebrafish embryos 3dpf were anesthethised with Tricain prior the dissection of the trunk. Dissected trunks were dissociated using a mix of 0.25% Trypsin and collagenase 4mg/mL  centrifuged to collect the cells  resuspended into DMEM + 10% Fetal Bovine Serum and filtered to remove the debris.  Cells were washed and resuspend in PBS prior 10X genomic experiment Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP428413,,loader:fastq load.py,AAAVLTHHV_trunk_flt1_pool_22s004695-1-1_PREAU_lane1MUT2_1_sequence.txt AAAVLTHHV_trunk_flt1_pool_22s004695-1-1_PREAU_lane1MUT2_2_sequence.txt,fastq fastq,35418985138.0,300160891.0,GSM7108419 r1,0:28 1:90,A:9637251760;C:8083980683;G:8336318307;T:9349259129;N:12175259,28,90,,,9637251760,8083980683,8336318307,9349259129,12175259,SRX19738955,SRS17105108,SRA1608738,Karlsruhe Institute of Technology (KIT),Karlsruhe Institute of Technology (KIT),2,0.00564,0.94991,0.00167,0.10681,0.99088,0.78904,0.41428,0.4583,28,90,T,B,sc-like readlen,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-03-21,Larval,Larval,Trunk,Surface Structure
74669,SRR23928777,SRX19738954,SRS17105107,SRP428413,PRJNA947108,Gene expression profile at single cell level of zebrafish trunk from WT or flt1 mutant 3dpf.,GSE227806,Transcriptome Analysis,scRNA seq was used to investigate neurovascular cross talk in zebrafish trunk. Overall design: Zebrafish trunk of WT and flt1 mutant were dissected  dissociated and processed for single cell RNA Seq using 10X Genomics Chromium droplet based system,parent bioproject:PRJNA947103,pubmed:38600061,,WT  replicate 2  scRNAseq trunk,GSM7108418,,source name:Trunk|tissue:Trunk|genotype:WT|age:3dpf|geo loc name:missing|collection date:missing,WT  replicate 2  scRNAseq trunk,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software  https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCZ11 v107 Supplementary files format and content: matrix files,Trunk,,Zebrafish embryos 3dpf were anesthethised with Tricain prior the dissection of the trunk. Dissected trunks were dissociated using a mix of 0.25% Trypsin and collagenase 4mg/mL  centrifuged to collect the cells  resuspended into DMEM + 10% Fetal Bovine Serum and filtered to remove the debris.  Cells were washed and resuspend in PBS prior 10X genomic experiment Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics,,tissue:Trunk|genotype:WT|age:3dpf,GSM7108418,GSM7108418: WT  replicate 2  scRNAseq trunk; Danio rerio; RNA Seq,GSM7108418 r1,GSM7108418,1,Zebrafish embryos 3dpf were anesthethised with Tricain prior the dissection of the trunk. Dissected trunks were dissociated using a mix of 0.25% Trypsin and collagenase 4mg/mL  centrifuged to collect the cells  resuspended into DMEM + 10% Fetal Bovine Serum and filtered to remove the debris.  Cells were washed and resuspend in PBS prior 10X genomic experiment Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP428413,,loader:fastq load.py,AAAVLTHHV_trunk_flt1_pool_22s004695-1-1_PREAU_lane1WT2_1_sequence.txt AAAVLTHHV_trunk_flt1_pool_22s004695-1-1_PREAU_lane1WT2_2_sequence.txt,fastq fastq,41802904672.0,354261904.0,GSM7108418 r1,0:28 1:90,A:11394356103;C:9573831647;G:9783049319;T:11037144706;N:14522897,28,90,,,11394356103,9573831647,9783049319,11037144706,14522897,SRX19738954,SRS17105107,SRA1608738,Karlsruhe Institute of Technology (KIT),Karlsruhe Institute of Technology (KIT),2,0.00624,0.94184,0.00181,0.10196,0.99003,0.79407,0.40186,0.46338,28,90,T,B,sc-like readlen,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-03-21,Larval,Larval,Trunk,Surface Structure
74670,SRR23928778,SRX19738953,SRS17105385,SRP428413,PRJNA947108,Gene expression profile at single cell level of zebrafish trunk from WT or flt1 mutant 3dpf.,GSE227806,Transcriptome Analysis,scRNA seq was used to investigate neurovascular cross talk in zebrafish trunk. Overall design: Zebrafish trunk of WT and flt1 mutant were dissected  dissociated and processed for single cell RNA Seq using 10X Genomics Chromium droplet based system,parent bioproject:PRJNA947103,pubmed:38600061,,flt1mut  replicate 1  scRNAseq trunk,GSM7108417,,source name:Trunk|tissue:Trunk|genotype:flt1ka604|age:3dpf|geo loc name:missing|collection date:missing,flt1mut  replicate 1  scRNAseq trunk,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software  https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCZ11 v107 Supplementary files format and content: matrix files,Trunk,,Zebrafish embryos 3dpf were anesthethised with Tricain prior the dissection of the trunk. Dissected trunks were dissociated using a mix of 0.25% Trypsin and collagenase 4mg/mL  centrifuged to collect the cells  resuspended into DMEM + 10% Fetal Bovine Serum and filtered to remove the debris.  Cells were washed and resuspend in PBS prior 10X genomic experiment Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics,,tissue:Trunk|genotype:flt1ka604|age:3dpf,GSM7108417,GSM7108417: flt1mut  replicate 1  scRNAseq trunk; Danio rerio; RNA Seq,GSM7108417 r1,GSM7108417,1,Zebrafish embryos 3dpf were anesthethised with Tricain prior the dissection of the trunk. Dissected trunks were dissociated using a mix of 0.25% Trypsin and collagenase 4mg/mL  centrifuged to collect the cells  resuspended into DMEM + 10% Fetal Bovine Serum and filtered to remove the debris.  Cells were washed and resuspend in PBS prior 10X genomic experiment Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP428413,,loader:fastq load.py,AAAVLTHHV_trunk_flt1_pool_22s004695-1-1_PREAU_lane1MUT1_1_sequence.txt AAAVLTHHV_trunk_flt1_pool_22s004695-1-1_PREAU_lane1MUT1_2_sequence.txt,fastq fastq,37702754542.0,319514869.0,GSM7108417 r1,0:28 1:90,A:10209528305;C:8624230061;G:8827524184;T:10028556038;N:12915954,28,90,,,10209528305,8624230061,8827524184,10028556038,12915954,SRX19738953,SRS17105385,SRA1608738,Karlsruhe Institute of Technology (KIT),Karlsruhe Institute of Technology (KIT),2,0.00594,0.95138,0.00188,0.10717,0.9919,0.79058,0.38343,0.46223,28,90,T,B,sc-like readlen,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-03-21,Larval,Larval,Trunk,Surface Structure
74671,SRR23928779,SRX19738952,SRS17105106,SRP428413,PRJNA947108,Gene expression profile at single cell level of zebrafish trunk from WT or flt1 mutant 3dpf.,GSE227806,Transcriptome Analysis,scRNA seq was used to investigate neurovascular cross talk in zebrafish trunk. Overall design: Zebrafish trunk of WT and flt1 mutant were dissected  dissociated and processed for single cell RNA Seq using 10X Genomics Chromium droplet based system,parent bioproject:PRJNA947103,pubmed:38600061,,WT  replicate 1  scRNAseq trunk,GSM7108416,,source name:Trunk|tissue:Trunk|genotype:WT|age:3dpf|geo loc name:missing|collection date:missing,WT  replicate 1  scRNAseq trunk,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software  https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCZ11 v107 Supplementary files format and content: matrix files,Trunk,,Zebrafish embryos 3dpf were anesthethised with Tricain prior the dissection of the trunk. Dissected trunks were dissociated using a mix of 0.25% Trypsin and collagenase 4mg/mL  centrifuged to collect the cells  resuspended into DMEM + 10% Fetal Bovine Serum and filtered to remove the debris.  Cells were washed and resuspend in PBS prior 10X genomic experiment Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics,,tissue:Trunk|genotype:WT|age:3dpf,GSM7108416,GSM7108416: WT  replicate 1  scRNAseq trunk; Danio rerio; RNA Seq,GSM7108416 r1,GSM7108416,1,Zebrafish embryos 3dpf were anesthethised with Tricain prior the dissection of the trunk. Dissected trunks were dissociated using a mix of 0.25% Trypsin and collagenase 4mg/mL  centrifuged to collect the cells  resuspended into DMEM + 10% Fetal Bovine Serum and filtered to remove the debris.  Cells were washed and resuspend in PBS prior 10X genomic experiment Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP428413,,loader:fastq load.py,AAAVLTHHV_trunk_flt1_pool_22s004695-1-1_PREAU_lane1WT1_1_sequence.txt AAAVLTHHV_trunk_flt1_pool_22s004695-1-1_PREAU_lane1WT1_2_sequence.txt,fastq fastq,30416957822.0,257770829.0,GSM7108416 r1,0:28 1:90,A:8231697522;C:6992122503;G:7225363090;T:7957278327;N:10496380,28,90,,,8231697522,6992122503,7225363090,7957278327,10496380,SRX19738952,SRS17105106,SRA1608738,Karlsruhe Institute of Technology (KIT),Karlsruhe Institute of Technology (KIT),2,0.00623,0.94345,0.00214,0.11682,0.99105,0.78033,0.36317,0.48249,28,90,T,B,sc-like readlen,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-03-21,Larval,Larval,Trunk,Surface Structure
74951,SRR24203796,SRX20000418,SRS17345141,SRP433186,PRJNA956844,Gene expression profile at single cell level of sclerotome derived fibroblasts from 52 hpf transgenic zebrafish trunks.,GSE229939,Other,The sclerotome region of the somite labelled by nkx3.1:Gal4 VP16; UAS:NTR mCherry gives rise to numerous fibroblasts populations in the zebrafish trunk. We performed single cell RNA sequencing scRNA seq on sclerotome derived fibroblasts from 52 hpf embryos to determine population heterogeneity and plasticity. Overall design: scRNA seq was performed on mCherry positive cells from trunk regions of 52 hpf Tg BACnkx3.1:Gal4 VP16ca101; TgUAS:NTR mCherryca264 zebrafish isolated by Fluorescence activated cell sorting FACS. The single cell library was prepared using 10X Genomics three prime gene expression profiling droplet based scRNA seq technology v3.1 chemistry according to manufacturer's protocols. Sequencing was performed on the using the Illumina NovaSeq S2 flow cell.,,pubmed:37967180,,52 hpf mCherry positive,GSM7181573,,source name:zebrafish trunks dissected at the beginning of the yolk extension|cell type:Sclerotome derived cells|tissue:zebrafish trunks dissected at the beginning of the yolk extension|strain:Tg BACnkx3.1:Gal4 VP16ca101; TgUAS:NTR mCherryca264|age:52 hpf,52 hpf mCherry positive,A custom zebrafish transcriptome was prepared using V4.3.2 GTFs Lawson et al.  2021 and the GRCz11 Danio rerio reference genome with appended mCherry sequence using standard CellRanger mkgtf and mkref pipelines. FASTQs were then filtered and aligned to the reference using Cellranger count. All pipelines used 10X GEnomics CellRanger v5.0.0 software. Downstream quality control  normalization  dimension reduction  clustering and analysis was performed in R using Seurat v4.0.0. Assembly: GRCz11 Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz,zebrafish trunks dissected at the beginning of the yolk extension,,About 140 hpf 52 hpf nkx3.1NTR mCherry embryos were anesthetized in fish water with 0.4% tricaine and maintained over ice during dissection. Trunks were dissected at the beginning of the yolk extension using a surgical scalpel. Dissected trunk tissues were then 0.25% Trypsin + 1 mM EDTA solution at 28.5°C for 20 minutes with gentle shaking at 300 rpm. Dissociated was then stopped  and dissolved tissue was washed with 1% FBS solution in 1x DPBS Dulbecco’s phosphate buffered saline  ThermoFisher Scientific and strained. Live  mCherry+ cells were collected by fluorescence activated cell sorting FACS. Sorted cells were resuspended in 50 μl HBSS Hank’s Balanced Salt Solution + 2% BSA Bovine Serum Albumin. 15 000 live  mCherry+ cells were loaded into the 10X Genomics Chromium Controller for droplet based cell separation. cDNA libraries were generated using the 10X Genomics 3’ gene expression profiling droplet based scRNA seq kit v3.1 chemistry according to manufacturer’s protocol. cDNA was amplified for 12 cycles and an index primer was added for sequencing using 14 PCR cycles,Zebrafish embryos were raised at 28.5 °C. Embryos older than 24 hours were grown in fish water with added 1 phenyl 2 thiourea PTU to prevent pigmentation.,cell type:Sclerotome derived cells|tissue:zebrafish trunks dissected at the beginning of the yolk extension|strain:Tg BACnkx3.1:Gal4 VP16ca101; TgUAS:NTR mCherryca264|age:52 hpf,GSM7181573,GSM7181573: 52 hpf mCherry positive; Danio rerio; RNA Seq,GSM7181573 r1,GSM7181573,1,About 140 hpf 52 hpf nkx3.1NTR mCherry embryos were anesthetized in fish water with 0.4% tricaine and maintained over ice during dissection. Trunks were dissected at the beginning of the yolk extension using a surgical scalpel. Dissected trunk tissues were then 0.25% Trypsin + 1 mM EDTA solution at 28.5°C for 20 minutes with gentle shaking at 300 rpm. Dissociated was then stopped  and dissolved tissue was washed with 1% FBS solution in 1x DPBS Dulbecco's phosphate buffered saline  ThermoFisher Scientific and strained. Live  mCherry+ cells were collected by fluorescence activated cell sorting FACS. Sorted cells were resuspended in 50 μl HBSS Hank's Balanced Salt Solution + 2% BSA Bovine Serum Albumin. 15 000 live  mCherry+ cells were loaded into the 10X Genomics Chromium Controller for droplet based cell separation. cDNA libraries were generated using the 10X Genomics three prime gene expression profiling droplet based scRNA seq kit v3.1 chemistry according to manufacturer's protocol. cDNA was amplified for 12 cycles and an index primer was added for sequencing using 14 PCR cycles,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP433186,,loader:fastq load.py,AR_2_S5_L002_I1_001.fastq.gz AR_2_S5_L002_R1_001.fastq.gz AR_2_S5_L002_R2_001.fastq.gz,fastq fastq fastq,12097924750.0,95259250.0,GSM7181573 r1,0:8 1:28 2:91,A:2458401542;C:1953802815;G:2304998485;T:1951185638;N:203270,8,28,91,,2458401542,1953802815,2304998485,1951185638,203270,SRX20000418,SRS17345141,SRA1623336,"Department of Biochemistry and Molecular Biology, University of Calgary","Department of Biochemistry and Molecular Biology, University of Calgary",1,0.85356,,0.24065,,0.84705,,0.64618,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Canada,2023-04-18,Hatching,Embryo,Trunk,Surface Structure
74952,SRR24203797,SRX20000418,SRS17345141,SRP433186,PRJNA956844,Gene expression profile at single cell level of sclerotome derived fibroblasts from 52 hpf transgenic zebrafish trunks.,GSE229939,Other,The sclerotome region of the somite labelled by nkx3.1:Gal4 VP16; UAS:NTR mCherry gives rise to numerous fibroblasts populations in the zebrafish trunk. We performed single cell RNA sequencing scRNA seq on sclerotome derived fibroblasts from 52 hpf embryos to determine population heterogeneity and plasticity. Overall design: scRNA seq was performed on mCherry positive cells from trunk regions of 52 hpf Tg BACnkx3.1:Gal4 VP16ca101; TgUAS:NTR mCherryca264 zebrafish isolated by Fluorescence activated cell sorting FACS. The single cell library was prepared using 10X Genomics three prime gene expression profiling droplet based scRNA seq technology v3.1 chemistry according to manufacturer's protocols. Sequencing was performed on the using the Illumina NovaSeq S2 flow cell.,,pubmed:37967180,,52 hpf mCherry positive,GSM7181573,,source name:zebrafish trunks dissected at the beginning of the yolk extension|cell type:Sclerotome derived cells|tissue:zebrafish trunks dissected at the beginning of the yolk extension|strain:Tg BACnkx3.1:Gal4 VP16ca101; TgUAS:NTR mCherryca264|age:52 hpf,52 hpf mCherry positive,A custom zebrafish transcriptome was prepared using V4.3.2 GTFs Lawson et al.  2021 and the GRCz11 Danio rerio reference genome with appended mCherry sequence using standard CellRanger mkgtf and mkref pipelines. FASTQs were then filtered and aligned to the reference using Cellranger count. All pipelines used 10X GEnomics CellRanger v5.0.0 software. Downstream quality control  normalization  dimension reduction  clustering and analysis was performed in R using Seurat v4.0.0. Assembly: GRCz11 Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz,zebrafish trunks dissected at the beginning of the yolk extension,,About 140 hpf 52 hpf nkx3.1NTR mCherry embryos were anesthetized in fish water with 0.4% tricaine and maintained over ice during dissection. Trunks were dissected at the beginning of the yolk extension using a surgical scalpel. Dissected trunk tissues were then 0.25% Trypsin + 1 mM EDTA solution at 28.5°C for 20 minutes with gentle shaking at 300 rpm. Dissociated was then stopped  and dissolved tissue was washed with 1% FBS solution in 1x DPBS Dulbecco’s phosphate buffered saline  ThermoFisher Scientific and strained. Live  mCherry+ cells were collected by fluorescence activated cell sorting FACS. Sorted cells were resuspended in 50 μl HBSS Hank’s Balanced Salt Solution + 2% BSA Bovine Serum Albumin. 15 000 live  mCherry+ cells were loaded into the 10X Genomics Chromium Controller for droplet based cell separation. cDNA libraries were generated using the 10X Genomics 3’ gene expression profiling droplet based scRNA seq kit v3.1 chemistry according to manufacturer’s protocol. cDNA was amplified for 12 cycles and an index primer was added for sequencing using 14 PCR cycles,Zebrafish embryos were raised at 28.5 °C. Embryos older than 24 hours were grown in fish water with added 1 phenyl 2 thiourea PTU to prevent pigmentation.,cell type:Sclerotome derived cells|tissue:zebrafish trunks dissected at the beginning of the yolk extension|strain:Tg BACnkx3.1:Gal4 VP16ca101; TgUAS:NTR mCherryca264|age:52 hpf,GSM7181573,GSM7181573: 52 hpf mCherry positive; Danio rerio; RNA Seq,GSM7181573 r1,GSM7181573,1,About 140 hpf 52 hpf nkx3.1NTR mCherry embryos were anesthetized in fish water with 0.4% tricaine and maintained over ice during dissection. Trunks were dissected at the beginning of the yolk extension using a surgical scalpel. Dissected trunk tissues were then 0.25% Trypsin + 1 mM EDTA solution at 28.5°C for 20 minutes with gentle shaking at 300 rpm. Dissociated was then stopped  and dissolved tissue was washed with 1% FBS solution in 1x DPBS Dulbecco's phosphate buffered saline  ThermoFisher Scientific and strained. Live  mCherry+ cells were collected by fluorescence activated cell sorting FACS. Sorted cells were resuspended in 50 μl HBSS Hank's Balanced Salt Solution + 2% BSA Bovine Serum Albumin. 15 000 live  mCherry+ cells were loaded into the 10X Genomics Chromium Controller for droplet based cell separation. cDNA libraries were generated using the 10X Genomics three prime gene expression profiling droplet based scRNA seq kit v3.1 chemistry according to manufacturer's protocol. cDNA was amplified for 12 cycles and an index primer was added for sequencing using 14 PCR cycles,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP433186,,loader:fastq load.py,AR_2_S5_L001_I1_001.fastq.gz AR_2_S5_L001_R1_001.fastq.gz AR_2_S5_L001_R2_001.fastq.gz,fastq fastq fastq,11926942872.0,93912936.0,GSM7181573 r2,0:8 1:28 2:91,A:2430702466;C:1919825027;G:2264443130;T:1930929426;N:177127,8,28,91,,2430702466,1919825027,2264443130,1930929426,177127,SRX20000418,SRS17345141,SRA1623336,"Department of Biochemistry and Molecular Biology, University of Calgary","Department of Biochemistry and Molecular Biology, University of Calgary",1,0.85561,,0.24037,,0.84678,,0.66835,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Canada,2023-04-18,Hatching,Embryo,Trunk,Surface Structure
74953,SRR24203798,SRX20000418,SRS17345141,SRP433186,PRJNA956844,Gene expression profile at single cell level of sclerotome derived fibroblasts from 52 hpf transgenic zebrafish trunks.,GSE229939,Other,The sclerotome region of the somite labelled by nkx3.1:Gal4 VP16; UAS:NTR mCherry gives rise to numerous fibroblasts populations in the zebrafish trunk. We performed single cell RNA sequencing scRNA seq on sclerotome derived fibroblasts from 52 hpf embryos to determine population heterogeneity and plasticity. Overall design: scRNA seq was performed on mCherry positive cells from trunk regions of 52 hpf Tg BACnkx3.1:Gal4 VP16ca101; TgUAS:NTR mCherryca264 zebrafish isolated by Fluorescence activated cell sorting FACS. The single cell library was prepared using 10X Genomics three prime gene expression profiling droplet based scRNA seq technology v3.1 chemistry according to manufacturer's protocols. Sequencing was performed on the using the Illumina NovaSeq S2 flow cell.,,pubmed:37967180,,52 hpf mCherry positive,GSM7181573,,source name:zebrafish trunks dissected at the beginning of the yolk extension|cell type:Sclerotome derived cells|tissue:zebrafish trunks dissected at the beginning of the yolk extension|strain:Tg BACnkx3.1:Gal4 VP16ca101; TgUAS:NTR mCherryca264|age:52 hpf,52 hpf mCherry positive,A custom zebrafish transcriptome was prepared using V4.3.2 GTFs Lawson et al.  2021 and the GRCz11 Danio rerio reference genome with appended mCherry sequence using standard CellRanger mkgtf and mkref pipelines. FASTQs were then filtered and aligned to the reference using Cellranger count. All pipelines used 10X GEnomics CellRanger v5.0.0 software. Downstream quality control  normalization  dimension reduction  clustering and analysis was performed in R using Seurat v4.0.0. Assembly: GRCz11 Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz,zebrafish trunks dissected at the beginning of the yolk extension,,About 140 hpf 52 hpf nkx3.1NTR mCherry embryos were anesthetized in fish water with 0.4% tricaine and maintained over ice during dissection. Trunks were dissected at the beginning of the yolk extension using a surgical scalpel. Dissected trunk tissues were then 0.25% Trypsin + 1 mM EDTA solution at 28.5°C for 20 minutes with gentle shaking at 300 rpm. Dissociated was then stopped  and dissolved tissue was washed with 1% FBS solution in 1x DPBS Dulbecco’s phosphate buffered saline  ThermoFisher Scientific and strained. Live  mCherry+ cells were collected by fluorescence activated cell sorting FACS. Sorted cells were resuspended in 50 μl HBSS Hank’s Balanced Salt Solution + 2% BSA Bovine Serum Albumin. 15 000 live  mCherry+ cells were loaded into the 10X Genomics Chromium Controller for droplet based cell separation. cDNA libraries were generated using the 10X Genomics 3’ gene expression profiling droplet based scRNA seq kit v3.1 chemistry according to manufacturer’s protocol. cDNA was amplified for 12 cycles and an index primer was added for sequencing using 14 PCR cycles,Zebrafish embryos were raised at 28.5 °C. Embryos older than 24 hours were grown in fish water with added 1 phenyl 2 thiourea PTU to prevent pigmentation.,cell type:Sclerotome derived cells|tissue:zebrafish trunks dissected at the beginning of the yolk extension|strain:Tg BACnkx3.1:Gal4 VP16ca101; TgUAS:NTR mCherryca264|age:52 hpf,GSM7181573,GSM7181573: 52 hpf mCherry positive; Danio rerio; RNA Seq,GSM7181573 r1,GSM7181573,1,About 140 hpf 52 hpf nkx3.1NTR mCherry embryos were anesthetized in fish water with 0.4% tricaine and maintained over ice during dissection. Trunks were dissected at the beginning of the yolk extension using a surgical scalpel. Dissected trunk tissues were then 0.25% Trypsin + 1 mM EDTA solution at 28.5°C for 20 minutes with gentle shaking at 300 rpm. Dissociated was then stopped  and dissolved tissue was washed with 1% FBS solution in 1x DPBS Dulbecco's phosphate buffered saline  ThermoFisher Scientific and strained. Live  mCherry+ cells were collected by fluorescence activated cell sorting FACS. Sorted cells were resuspended in 50 μl HBSS Hank's Balanced Salt Solution + 2% BSA Bovine Serum Albumin. 15 000 live  mCherry+ cells were loaded into the 10X Genomics Chromium Controller for droplet based cell separation. cDNA libraries were generated using the 10X Genomics three prime gene expression profiling droplet based scRNA seq kit v3.1 chemistry according to manufacturer's protocol. cDNA was amplified for 12 cycles and an index primer was added for sequencing using 14 PCR cycles,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP433186,,loader:fastq load.py,AR_2_S4_L002_I1_001.fastq.gz AR_2_S4_L002_R1_001.fastq.gz AR_2_S4_L002_R2_001.fastq.gz,fastq fastq fastq,6129613598.0,48264674.0,GSM7181573 r3,0:8 1:28 2:91,A:1248940274;C:989811597;G:1170220249;T:982937378;N:175836,8,28,91,,1248940274,989811597,1170220249,982937378,175836,SRX20000418,SRS17345141,SRA1623336,"Department of Biochemistry and Molecular Biology, University of Calgary","Department of Biochemistry and Molecular Biology, University of Calgary",1,0.85545,,0.24212,,0.84816,,0.65892,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Canada,2023-04-18,Hatching,Embryo,Trunk,Surface Structure
74954,SRR24203799,SRX20000418,SRS17345141,SRP433186,PRJNA956844,Gene expression profile at single cell level of sclerotome derived fibroblasts from 52 hpf transgenic zebrafish trunks.,GSE229939,Other,The sclerotome region of the somite labelled by nkx3.1:Gal4 VP16; UAS:NTR mCherry gives rise to numerous fibroblasts populations in the zebrafish trunk. We performed single cell RNA sequencing scRNA seq on sclerotome derived fibroblasts from 52 hpf embryos to determine population heterogeneity and plasticity. Overall design: scRNA seq was performed on mCherry positive cells from trunk regions of 52 hpf Tg BACnkx3.1:Gal4 VP16ca101; TgUAS:NTR mCherryca264 zebrafish isolated by Fluorescence activated cell sorting FACS. The single cell library was prepared using 10X Genomics three prime gene expression profiling droplet based scRNA seq technology v3.1 chemistry according to manufacturer's protocols. Sequencing was performed on the using the Illumina NovaSeq S2 flow cell.,,pubmed:37967180,,52 hpf mCherry positive,GSM7181573,,source name:zebrafish trunks dissected at the beginning of the yolk extension|cell type:Sclerotome derived cells|tissue:zebrafish trunks dissected at the beginning of the yolk extension|strain:Tg BACnkx3.1:Gal4 VP16ca101; TgUAS:NTR mCherryca264|age:52 hpf,52 hpf mCherry positive,A custom zebrafish transcriptome was prepared using V4.3.2 GTFs Lawson et al.  2021 and the GRCz11 Danio rerio reference genome with appended mCherry sequence using standard CellRanger mkgtf and mkref pipelines. FASTQs were then filtered and aligned to the reference using Cellranger count. All pipelines used 10X GEnomics CellRanger v5.0.0 software. Downstream quality control  normalization  dimension reduction  clustering and analysis was performed in R using Seurat v4.0.0. Assembly: GRCz11 Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz,zebrafish trunks dissected at the beginning of the yolk extension,,About 140 hpf 52 hpf nkx3.1NTR mCherry embryos were anesthetized in fish water with 0.4% tricaine and maintained over ice during dissection. Trunks were dissected at the beginning of the yolk extension using a surgical scalpel. Dissected trunk tissues were then 0.25% Trypsin + 1 mM EDTA solution at 28.5°C for 20 minutes with gentle shaking at 300 rpm. Dissociated was then stopped  and dissolved tissue was washed with 1% FBS solution in 1x DPBS Dulbecco’s phosphate buffered saline  ThermoFisher Scientific and strained. Live  mCherry+ cells were collected by fluorescence activated cell sorting FACS. Sorted cells were resuspended in 50 μl HBSS Hank’s Balanced Salt Solution + 2% BSA Bovine Serum Albumin. 15 000 live  mCherry+ cells were loaded into the 10X Genomics Chromium Controller for droplet based cell separation. cDNA libraries were generated using the 10X Genomics 3’ gene expression profiling droplet based scRNA seq kit v3.1 chemistry according to manufacturer’s protocol. cDNA was amplified for 12 cycles and an index primer was added for sequencing using 14 PCR cycles,Zebrafish embryos were raised at 28.5 °C. Embryos older than 24 hours were grown in fish water with added 1 phenyl 2 thiourea PTU to prevent pigmentation.,cell type:Sclerotome derived cells|tissue:zebrafish trunks dissected at the beginning of the yolk extension|strain:Tg BACnkx3.1:Gal4 VP16ca101; TgUAS:NTR mCherryca264|age:52 hpf,GSM7181573,GSM7181573: 52 hpf mCherry positive; Danio rerio; RNA Seq,GSM7181573 r1,GSM7181573,1,About 140 hpf 52 hpf nkx3.1NTR mCherry embryos were anesthetized in fish water with 0.4% tricaine and maintained over ice during dissection. Trunks were dissected at the beginning of the yolk extension using a surgical scalpel. Dissected trunk tissues were then 0.25% Trypsin + 1 mM EDTA solution at 28.5°C for 20 minutes with gentle shaking at 300 rpm. Dissociated was then stopped  and dissolved tissue was washed with 1% FBS solution in 1x DPBS Dulbecco's phosphate buffered saline  ThermoFisher Scientific and strained. Live  mCherry+ cells were collected by fluorescence activated cell sorting FACS. Sorted cells were resuspended in 50 μl HBSS Hank's Balanced Salt Solution + 2% BSA Bovine Serum Albumin. 15 000 live  mCherry+ cells were loaded into the 10X Genomics Chromium Controller for droplet based cell separation. cDNA libraries were generated using the 10X Genomics three prime gene expression profiling droplet based scRNA seq kit v3.1 chemistry according to manufacturer's protocol. cDNA was amplified for 12 cycles and an index primer was added for sequencing using 14 PCR cycles,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP433186,,loader:fastq load.py,AR_2_S4_L001_I1_001.fastq.gz AR_2_S4_L001_R1_001.fastq.gz AR_2_S4_L001_R2_001.fastq.gz,fastq fastq fastq,6325004622.0,49803186.0,GSM7181573 r4,0:8 1:28 2:91,A:1283864621;C:1025588666;G:1211968623;T:1010456763;N:211253,8,28,91,,1283864621,1025588666,1211968623,1010456763,211253,SRX20000418,SRS17345141,SRA1623336,"Department of Biochemistry and Molecular Biology, University of Calgary","Department of Biochemistry and Molecular Biology, University of Calgary",1,0.85448,,0.24209,,0.84934,,0.68035,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Canada,2023-04-18,Hatching,Embryo,Trunk,Surface Structure