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 69438,SRR18687231,SRX14788266,SRS12547158,SRP368307,PRJNA824844,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals,GSE200503,Other,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability,,,,Mutant 5mpf scRNAseq,GSM6035264,,source name:wkm|tissue:marrow|age:5mpf|genotype:gata2a / ,Mutant 5mpf scRNAseq,scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11,wkm,cells were not treated,10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf,tissue:marrow|age:5mpf|genotype:gata2a / ,GSM6035264,GSM6035264: Mutant 5mpf scRNAseq; Danio rerio; RNA Seq,GSM6035264 r1,GSM6035264,1,10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP368307,,loader:fastq load.py,MUTANT_S2_L001_I1_001.fastq.gz MUTANT_S2_L001_R1_001.fastq.gz MUTANT_S2_L001_R2_001.fastq.gz,fastq fastq fastq,7173831982.0,56486866.0,GSM6035264 r1,0:8 1:28 2:91,A:1358934535;C:1244254049;G:1282298109;T:1250397550;N:4420563,8,28,91,,1358934535,1244254049,1282298109,1250397550,4420563,SRX14788266,SRS12547158,SRA1400926,"Institute of Cancer and Genomic Sciences, University of Birminhgam","Institute of Cancer and Genomic Sciences, University of Birminhgam",1,0.96273,,0.07511,,0.84861,,0.53711,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-04-08,Adult,Adult,Marrow,Renal System 69439,SRR18687232,SRX14788266,SRS12547158,SRP368307,PRJNA824844,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals,GSE200503,Other,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability,,,,Mutant 5mpf scRNAseq,GSM6035264,,source name:wkm|tissue:marrow|age:5mpf|genotype:gata2a / ,Mutant 5mpf scRNAseq,scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11,wkm,cells were not treated,10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf,tissue:marrow|age:5mpf|genotype:gata2a / ,GSM6035264,GSM6035264: Mutant 5mpf scRNAseq; Danio rerio; RNA Seq,GSM6035264 r1,GSM6035264,1,10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP368307,,loader:fastq load.py,MUTANT_S2_L002_I1_001.fastq.gz MUTANT_S2_L002_R1_001.fastq.gz MUTANT_S2_L002_R2_001.fastq.gz,fastq fastq fastq,7052205352.0,55529176.0,GSM6035264 r2,0:8 1:28 2:91,A:1335427840;C:1223120616;G:1262490348;T:1228023814;N:4092398,8,28,91,,1335427840,1223120616,1262490348,1228023814,4092398,SRX14788266,SRS12547158,SRA1400926,"Institute of Cancer and Genomic Sciences, University of Birminhgam","Institute of Cancer and Genomic Sciences, University of Birminhgam",1,0.96332,,0.07559,,0.84869,,0.53571,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-04-08,Adult,Adult,Marrow,Renal System 69440,SRR18687233,SRX14788266,SRS12547158,SRP368307,PRJNA824844,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals,GSE200503,Other,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability,,,,Mutant 5mpf scRNAseq,GSM6035264,,source name:wkm|tissue:marrow|age:5mpf|genotype:gata2a / ,Mutant 5mpf scRNAseq,scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11,wkm,cells were not treated,10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf,tissue:marrow|age:5mpf|genotype:gata2a / ,GSM6035264,GSM6035264: Mutant 5mpf scRNAseq; Danio rerio; RNA Seq,GSM6035264 r1,GSM6035264,1,10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP368307,,loader:fastq load.py,MUTANT_S2_L003_I1_001.fastq.gz MUTANT_S2_L003_R1_001.fastq.gz MUTANT_S2_L003_R2_001.fastq.gz,fastq fastq fastq,7121271889.0,56073007.0,GSM6035264 r3,0:8 1:28 2:91,A:1348956241;C:1235761797;G:1273552429;T:1240317702;N:4055468,8,28,91,,1348956241,1235761797,1273552429,1240317702,4055468,SRX14788266,SRS12547158,SRA1400926,"Institute of Cancer and Genomic Sciences, University of Birminhgam","Institute of Cancer and Genomic Sciences, University of Birminhgam",1,0.96323,,0.07544,,0.84776,,0.54532,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-04-08,Adult,Adult,Marrow,Renal System 69441,SRR18687234,SRX14788266,SRS12547158,SRP368307,PRJNA824844,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals,GSE200503,Other,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability,,,,Mutant 5mpf scRNAseq,GSM6035264,,source name:wkm|tissue:marrow|age:5mpf|genotype:gata2a / ,Mutant 5mpf scRNAseq,scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11,wkm,cells were not treated,10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf,tissue:marrow|age:5mpf|genotype:gata2a / ,GSM6035264,GSM6035264: Mutant 5mpf scRNAseq; Danio rerio; RNA Seq,GSM6035264 r1,GSM6035264,1,10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP368307,,loader:fastq load.py,MUTANT_S2_L004_I1_001.fastq.gz MUTANT_S2_L004_R1_001.fastq.gz MUTANT_S2_L004_R2_001.fastq.gz,fastq fastq fastq,7060634088.0,55595544.0,GSM6035264 r4,0:8 1:28 2:91,A:1337923427;C:1225128065;G:1262793134;T:1229767092;N:3582786,8,28,91,,1337923427,1225128065,1262793134,1229767092,3582786,SRX14788266,SRS12547158,SRA1400926,"Institute of Cancer and Genomic Sciences, University of Birminhgam","Institute of Cancer and Genomic Sciences, University of Birminhgam",1,0.96323,,0.07552,,0.84626,,0.53808,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-04-08,Adult,Adult,Marrow,Renal System 69442,SRR18687235,SRX14788265,SRS12547159,SRP368307,PRJNA824844,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals,GSE200503,Other,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability,,,,WT 5mpf scRNA seq,GSM6035263,,source name:wkm|tissue:marrow|age:5mpf|genotype:WT,WT 5mpf scRNA seq,scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11,wkm,cells were not treated,10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf,tissue:marrow|age:5mpf|genotype:WT,GSM6035263,GSM6035263: WT 5mpf scRNA seq; Danio rerio; RNA Seq,GSM6035263 r1,GSM6035263,1,10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP368307,,loader:fastq load.py,WT_S1_L001_I1_001.fastq.gz WT_S1_L001_R1_001.fastq.gz WT_S1_L001_R2_001.fastq.gz,fastq fastq fastq,7887658469.0,62107547.0,GSM6035263 r1,0:8 1:28 2:91,A:1686084589;C:1207047546;G:1347307215;T:1406353747;N:4993680,8,28,91,,1686084589,1207047546,1347307215,1406353747,4993680,SRX14788265,SRS12547159,SRA1400926,"Institute of Cancer and Genomic Sciences, University of Birminhgam","Institute of Cancer and Genomic Sciences, University of Birminhgam",1,0.93208,,0.13464,,0.82885,,0.5507,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-04-08,Adult,Adult,Marrow,Renal System 69443,SRR18687236,SRX14788265,SRS12547159,SRP368307,PRJNA824844,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals,GSE200503,Other,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability,,,,WT 5mpf scRNA seq,GSM6035263,,source name:wkm|tissue:marrow|age:5mpf|genotype:WT,WT 5mpf scRNA seq,scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11,wkm,cells were not treated,10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf,tissue:marrow|age:5mpf|genotype:WT,GSM6035263,GSM6035263: WT 5mpf scRNA seq; Danio rerio; RNA Seq,GSM6035263 r1,GSM6035263,1,10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP368307,,loader:fastq load.py,WT_S1_L002_I1_001.fastq.gz WT_S1_L002_R1_001.fastq.gz WT_S1_L002_R2_001.fastq.gz,fastq fastq fastq,7726846751.0,60841313.0,GSM6035263 r2,0:8 1:28 2:91,A:1651285269;C:1182541074;G:1321442374;T:1376689852;N:4600914,8,28,91,,1651285269,1182541074,1321442374,1376689852,4600914,SRX14788265,SRS12547159,SRA1400926,"Institute of Cancer and Genomic Sciences, University of Birminhgam","Institute of Cancer and Genomic Sciences, University of Birminhgam",1,0.93139,,0.13512,,0.83157,,0.54659,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-04-08,Adult,Adult,Marrow,Renal System 69444,SRR18687237,SRX14788265,SRS12547159,SRP368307,PRJNA824844,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals,GSE200503,Other,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability,,,,WT 5mpf scRNA seq,GSM6035263,,source name:wkm|tissue:marrow|age:5mpf|genotype:WT,WT 5mpf scRNA seq,scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11,wkm,cells were not treated,10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf,tissue:marrow|age:5mpf|genotype:WT,GSM6035263,GSM6035263: WT 5mpf scRNA seq; Danio rerio; RNA Seq,GSM6035263 r1,GSM6035263,1,10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP368307,,loader:fastq load.py,WT_S1_L003_I1_001.fastq.gz WT_S1_L003_R1_001.fastq.gz WT_S1_L003_R2_001.fastq.gz,fastq fastq fastq,7809746382.0,61494066.0,GSM6035263 r3,0:8 1:28 2:91,A:1669649704;C:1195820935;G:1334457445;T:1391506607;N:4525315,8,28,91,,1669649704,1195820935,1334457445,1391506607,4525315,SRX14788265,SRS12547159,SRA1400926,"Institute of Cancer and Genomic Sciences, University of Birminhgam","Institute of Cancer and Genomic Sciences, University of Birminhgam",1,0.9319,,0.13521,,0.83039,,0.54131,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-04-08,Adult,Adult,Marrow,Renal System 69445,SRR18687238,SRX14788265,SRS12547159,SRP368307,PRJNA824844,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals,GSE200503,Other,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability,,,,WT 5mpf scRNA seq,GSM6035263,,source name:wkm|tissue:marrow|age:5mpf|genotype:WT,WT 5mpf scRNA seq,scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11,wkm,cells were not treated,10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf,tissue:marrow|age:5mpf|genotype:WT,GSM6035263,GSM6035263: WT 5mpf scRNA seq; Danio rerio; RNA Seq,GSM6035263 r1,GSM6035263,1,10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP368307,,loader:fastq load.py,WT_S1_L004_I1_001.fastq.gz WT_S1_L004_R1_001.fastq.gz WT_S1_L004_R2_001.fastq.gz,fastq fastq fastq,7741554113.0,60957119.0,GSM6035263 r4,0:8 1:28 2:91,A:1655590157;C:1185244017;G:1323146581;T:1379127206;N:3989868,8,28,91,,1655590157,1185244017,1323146581,1379127206,3989868,SRX14788265,SRS12547159,SRA1400926,"Institute of Cancer and Genomic Sciences, University of Birminhgam","Institute of Cancer and Genomic Sciences, University of Birminhgam",1,0.93299,,0.13493,,0.82852,,0.55166,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-04-08,Adult,Adult,Marrow,Renal System 69446,SRR18687240,SRX14788264,SRS12547155,SRP368307,PRJNA824844,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals,GSE200503,Other,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability,,,,Mutant 12mpf scRNAseq,GSM6035262,,source name:wkm|tissue:marrow|age:12mpf|genotype:gata2a / ,Mutant 12mpf scRNAseq,scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11,wkm,cells were not treated,10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf,tissue:marrow|age:12mpf|genotype:gata2a / ,GSM6035262,GSM6035262: Mutant 12mpf scRNAseq; Danio rerio; RNA Seq,GSM6035262 r1,GSM6035262,1,10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP368307,,loader:fastq load.py,mutant_S2_L001_I1_001.fastq.gz mutant_S2_L001_R1_001.fastq.gz mutant_S2_L001_R2_001.fastq.gz,fastq fastq fastq,2802332148.0,21229789.0,GSM6035262 r1,0:8 1:26 2:98,A:640368763;C:436216313;G:577751307;T:426047488;N:135451,8,26,98,,640368763,436216313,577751307,426047488,135451,SRX14788264,SRS12547155,SRA1400926,"Institute of Cancer and Genomic Sciences, University of Birminhgam","Institute of Cancer and Genomic Sciences, University of Birminhgam",1,0.95554,,0.01147,,0.92565,,0.57239,,98,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-04-08,Adult,Adult,Marrow,Renal System 69447,SRR18687241,SRX14788264,SRS12547155,SRP368307,PRJNA824844,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals,GSE200503,Other,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability,,,,Mutant 12mpf scRNAseq,GSM6035262,,source name:wkm|tissue:marrow|age:12mpf|genotype:gata2a / ,Mutant 12mpf scRNAseq,scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11,wkm,cells were not treated,10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf,tissue:marrow|age:12mpf|genotype:gata2a / ,GSM6035262,GSM6035262: Mutant 12mpf scRNAseq; Danio rerio; RNA Seq,GSM6035262 r1,GSM6035262,1,10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP368307,,loader:fastq load.py,mutant_S2_L002_I1_001.fastq.gz mutant_S2_L002_R1_001.fastq.gz mutant_S2_L002_R2_001.fastq.gz,fastq fastq fastq,2716435392.0,20579056.0,GSM6035262 r2,0:8 1:26 2:98,A:630665836;C:423337212;G:549434401;T:413134647;N:175392,8,26,98,,630665836,423337212,549434401,413134647,175392,SRX14788264,SRS12547155,SRA1400926,"Institute of Cancer and Genomic Sciences, University of Birminhgam","Institute of Cancer and Genomic Sciences, University of Birminhgam",1,0.95616,,0.01121,,0.92638,,0.59372,,98,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-04-08,Adult,Adult,Marrow,Renal System 69448,SRR18687242,SRX14788264,SRS12547155,SRP368307,PRJNA824844,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals,GSE200503,Other,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability,,,,Mutant 12mpf scRNAseq,GSM6035262,,source name:wkm|tissue:marrow|age:12mpf|genotype:gata2a / ,Mutant 12mpf scRNAseq,scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11,wkm,cells were not treated,10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf,tissue:marrow|age:12mpf|genotype:gata2a / ,GSM6035262,GSM6035262: Mutant 12mpf scRNAseq; Danio rerio; RNA Seq,GSM6035262 r1,GSM6035262,1,10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP368307,,loader:fastq load.py,mutant_S2_L003_I1_001.fastq.gz mutant_S2_L003_R1_001.fastq.gz mutant_S2_L003_R2_001.fastq.gz,fastq fastq fastq,2866261860.0,21714105.0,GSM6035262 r3,0:8 1:26 2:98,A:662138328;C:448896468;G:581624031;T:434958720;N:364743,8,26,98,,662138328,448896468,581624031,434958720,364743,SRX14788264,SRS12547155,SRA1400926,"Institute of Cancer and Genomic Sciences, University of Birminhgam","Institute of Cancer and Genomic Sciences, University of Birminhgam",1,0.95475,,0.0112,,0.9264,,0.57664,,98,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-04-08,Adult,Adult,Marrow,Renal System 69449,SRR18687243,SRX14788264,SRS12547155,SRP368307,PRJNA824844,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals,GSE200503,Other,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability,,,,Mutant 12mpf scRNAseq,GSM6035262,,source name:wkm|tissue:marrow|age:12mpf|genotype:gata2a / ,Mutant 12mpf scRNAseq,scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11,wkm,cells were not treated,10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf,tissue:marrow|age:12mpf|genotype:gata2a / ,GSM6035262,GSM6035262: Mutant 12mpf scRNAseq; Danio rerio; RNA Seq,GSM6035262 r1,GSM6035262,1,10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP368307,,loader:fastq load.py,mutant_S2_L004_I1_001.fastq.gz mutant_S2_L004_R1_001.fastq.gz mutant_S2_L004_R2_001.fastq.gz,fastq fastq fastq,2778700584.0,21050762.0,GSM6035262 r4,0:8 1:26 2:98,A:646107299;C:435138523;G:558295882;T:423168974;N:263998,8,26,98,,646107299,435138523,558295882,423168974,263998,SRX14788264,SRS12547155,SRA1400926,"Institute of Cancer and Genomic Sciences, University of Birminhgam","Institute of Cancer and Genomic Sciences, University of Birminhgam",1,0.95523,,0.01148,,0.92612,,0.594,,98,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-04-08,Adult,Adult,Marrow,Renal System 69450,SRR18687249,SRX14788262,SRS12547153,SRP368307,PRJNA824844,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals,GSE200503,Other,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability,,,,WT 12mpf scRNAseq,GSM6035261,,source name:wkm|tissue:marrow|age:12mpf|genotype:WT,WT 12mpf scRNAseq,scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11,wkm,cells were not treated,10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf,tissue:marrow|age:12mpf|genotype:WT,GSM6035261,GSM6035261: WT 12mpf scRNAseq; Danio rerio; RNA Seq,GSM6035261 r1,GSM6035261,1,10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP368307,,loader:fastq load.py,WT-12mpf_S1_L001_I1_001.fastq.gz WT-12mpf_S1_L001_R1_001.fastq.gz WT-12mpf_S1_L001_R2_001.fastq.gz,fastq fastq fastq,2871526284.0,21753987.0,GSM6035261 r1,0:8 1:26 2:98,A:657935861;C:458782361;G:577643976;T:437389248;N:139280,8,26,98,,657935861,458782361,577643976,437389248,139280,SRX14788262,SRS12547153,SRA1400926,"Institute of Cancer and Genomic Sciences, University of Birminhgam","Institute of Cancer and Genomic Sciences, University of Birminhgam",1,0.95618,,0.01409,,0.93137,,0.57474,,98,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-04-08,Adult,Adult,Marrow,Renal System 69451,SRR18687250,SRX14788262,SRS12547153,SRP368307,PRJNA824844,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals,GSE200503,Other,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability,,,,WT 12mpf scRNAseq,GSM6035261,,source name:wkm|tissue:marrow|age:12mpf|genotype:WT,WT 12mpf scRNAseq,scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11,wkm,cells were not treated,10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf,tissue:marrow|age:12mpf|genotype:WT,GSM6035261,GSM6035261: WT 12mpf scRNAseq; Danio rerio; RNA Seq,GSM6035261 r1,GSM6035261,1,10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP368307,,loader:fastq load.py,WT-12mpf_S1_L002_I1_001.fastq.gz WT-12mpf_S1_L002_R1_001.fastq.gz WT-12mpf_S1_L002_R2_001.fastq.gz,fastq fastq fastq,2786830992.0,21112356.0,GSM6035261 r2,0:8 1:26 2:98,A:646477118;C:445716938;G:552088162;T:424546694;N:181976,8,26,98,,646477118,445716938,552088162,424546694,181976,SRX14788262,SRS12547153,SRA1400926,"Institute of Cancer and Genomic Sciences, University of Birminhgam","Institute of Cancer and Genomic Sciences, University of Birminhgam",1,0.95703,,0.01387,,0.93117,,0.57965,,98,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-04-08,Adult,Adult,Marrow,Renal System 69452,SRR18687251,SRX14788262,SRS12547153,SRP368307,PRJNA824844,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals,GSE200503,Other,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability,,,,WT 12mpf scRNAseq,GSM6035261,,source name:wkm|tissue:marrow|age:12mpf|genotype:WT,WT 12mpf scRNAseq,scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11,wkm,cells were not treated,10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf,tissue:marrow|age:12mpf|genotype:WT,GSM6035261,GSM6035261: WT 12mpf scRNAseq; Danio rerio; RNA Seq,GSM6035261 r1,GSM6035261,1,10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP368307,,loader:fastq load.py,WT-12mpf_S1_L003_I1_001.fastq.gz WT-12mpf_S1_L003_R1_001.fastq.gz WT-12mpf_S1_L003_R2_001.fastq.gz,fastq fastq fastq,2940233472.0,22274496.0,GSM6035261 r3,0:8 1:26 2:98,A:678078355;C:472082276;G:585591377;T:446774858;N:373742,8,26,98,,678078355,472082276,585591377,446774858,373742,SRX14788262,SRS12547153,SRA1400926,"Institute of Cancer and Genomic Sciences, University of Birminhgam","Institute of Cancer and Genomic Sciences, University of Birminhgam",1,0.95649,,0.01398,,0.93237,,0.5686,,98,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-04-08,Adult,Adult,Marrow,Renal System 69453,SRR18687252,SRX14788262,SRS12547153,SRP368307,PRJNA824844,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals,GSE200503,Other,Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability,,,,WT 12mpf scRNAseq,GSM6035261,,source name:wkm|tissue:marrow|age:12mpf|genotype:WT,WT 12mpf scRNAseq,scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11,wkm,cells were not treated,10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf,tissue:marrow|age:12mpf|genotype:WT,GSM6035261,GSM6035261: WT 12mpf scRNAseq; Danio rerio; RNA Seq,GSM6035261 r1,GSM6035261,1,10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP368307,,loader:fastq load.py,WT-12mpf_S1_L004_I1_001.fastq.gz WT-12mpf_S1_L004_R1_001.fastq.gz WT-12mpf_S1_L004_R2_001.fastq.gz,fastq fastq fastq,2850270720.0,21592960.0,GSM6035261 r4,0:8 1:26 2:98,A:661215163;C:457617537;G:562445244;T:434561966;N:270170,8,26,98,,661215163,457617537,562445244,434561966,270170,SRX14788262,SRS12547153,SRA1400926,"Institute of Cancer and Genomic Sciences, University of Birminhgam","Institute of Cancer and Genomic Sciences, University of Birminhgam",1,0.952,,0.0139,,0.93188,,0.56069,,98,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-04-08,Adult,Adult,Marrow,Renal System 76638,SRR25247896,SRX20994112,SRS18268519,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow lckmCherry cd79aGFP Population M1 Sample 56,GSM7595977,,source name:Marrow|tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow lckmCherry cd79aGFP Population M1 Sample 56,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79aGFP|treatment:NA,GSM7595977,GSM7595977: Marrow lckmCherry cd79aGFP Population M1 Sample 56; Danio rerio; RNA Seq,GSM7595977 r1,GSM7595977,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,56_S68_R1_001.fastq.gz 56_S68_R2_001.fastq.gz,fastq fastq,9351083002.0,30963851.0,GSM7595977 r1,0:151 1:151,A:2790598714;C:1668663045;G:1882128783;T:3009655305;N:37155,151,151,,,2790598714,1668663045,1882128783,3009655305,37155,SRX20994112,SRS18268519,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.71935,0.53678,0.10054,0.10479,0.88895,0.94442,0.71659,0.73656,151,151,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76639,SRR25247897,SRX20994111,SRS18268517,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow lckmCherry cd79aGFP Population M1 Sample 55,GSM7595976,,source name:Marrow|tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow lckmCherry cd79aGFP Population M1 Sample 55,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79aGFP|treatment:NA,GSM7595976,GSM7595976: Marrow lckmCherry cd79aGFP Population M1 Sample 55; Danio rerio; RNA Seq,GSM7595976 r1,GSM7595976,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,55_S67_R1_001.fastq.gz 55_S67_R2_001.fastq.gz,fastq fastq,9888413482.0,32743091.0,GSM7595976 r1,0:151 1:151,A:2884186543;C:1849928947;G:2064604866;T:3089653973;N:39153,151,151,,,2884186543,1849928947,2064604866,3089653973,39153,SRX20994111,SRS18268517,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.74087,0.57449,0.10781,0.10777,0.88937,0.93768,0.69241,0.41557,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76640,SRR25247898,SRX20994110,SRS18268518,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow lckmCherry cd79aGFP Population M1 Sample 54,GSM7595975,,source name:Marrow|tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow lckmCherry cd79aGFP Population M1 Sample 54,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79aGFP|treatment:NA,GSM7595975,GSM7595975: Marrow lckmCherry cd79aGFP Population M1 Sample 54; Danio rerio; RNA Seq,GSM7595975 r1,GSM7595975,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,54_S66_R1_001.fastq.gz 54_S66_R2_001.fastq.gz,fastq fastq,10451102298.0,34606299.0,GSM7595975 r1,0:151 1:151,A:3121848970;C:1864364809;G:2100878796;T:3363967914;N:41809,151,151,,,3121848970,1864364809,2100878796,3363967914,41809,SRX20994110,SRS18268518,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.72731,0.54788,0.10584,0.10817,0.88629,0.93941,0.70276,0.71442,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76650,SRR25247908,SRX20994100,SRS18268507,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow rag2RFP cd79aGFP Population M3B Sample 44,GSM7595965,,source name:Marrow|tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow rag2RFP cd79aGFP Population M3B Sample 44,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79aGFP|treatment:NA,GSM7595965,GSM7595965: Marrow rag2RFP cd79aGFP Population M3B Sample 44; Danio rerio; RNA Seq,GSM7595965 r1,GSM7595965,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,44_S56_R2_001.fastq.gz 44_S56_R1_001.fastq.gz,fastq fastq,9758039176.0,32311388.0,GSM7595965 r1,0:151 1:151,A:2914004460;C:1731748893;G:2001541675;T:3110706309;N:37839,151,151,,,2914004460,1731748893,2001541675,3110706309,37839,SRX20994100,SRS18268507,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.68224,0.53012,0.15745,0.15669,0.89027,0.93766,0.67516,0.69738,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76651,SRR25247909,SRX20994099,SRS18268506,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow rag2RFP cd79aGFP Population M3B Sample 43,GSM7595964,,source name:Marrow|tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow rag2RFP cd79aGFP Population M3B Sample 43,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79aGFP|treatment:NA,GSM7595964,GSM7595964: Marrow rag2RFP cd79aGFP Population M3B Sample 43; Danio rerio; RNA Seq,GSM7595964 r1,GSM7595964,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,43_S55_R1_001.fastq.gz 43_S55_R2_001.fastq.gz,fastq fastq,10556595730.0,34955615.0,GSM7595964 r1,0:151 1:151,A:3074035126;C:1954032677;G:2284765668;T:3243720662;N:41597,151,151,,,3074035126,1954032677,2284765668,3243720662,41597,SRX20994099,SRS18268506,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.69449,0.54884,0.14567,0.14377,0.88485,0.93748,0.68668,0.7032,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76652,SRR25247910,SRX20994098,SRS18268505,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow rag2RFP cd79aGFP Population M3B Sample 42,GSM7595963,,source name:Marrow|tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow rag2RFP cd79aGFP Population M3B Sample 42,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79aGFP|treatment:NA,GSM7595963,GSM7595963: Marrow rag2RFP cd79aGFP Population M3B Sample 42; Danio rerio; RNA Seq,GSM7595963 r1,GSM7595963,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,42_S54_R2_001.fastq.gz 42_S54_R1_001.fastq.gz,fastq fastq,9056440930.0,29988215.0,GSM7595963 r1,0:151 1:151,A:2664832448;C:1675724049;G:1879251595;T:2836597271;N:35567,151,151,,,2664832448,1675724049,1879251595,2836597271,35567,SRX20994098,SRS18268505,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.74527,0.59162,0.15106,0.16614,0.87527,0.93288,0.67916,0.69017,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76653,SRR25247911,SRX20994097,SRS18268504,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow rag2RFP cd79aGFP Population M3A Sample 41,GSM7595962,,source name:Marrow|tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow rag2RFP cd79aGFP Population M3A Sample 41,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79aGFP|treatment:NA,GSM7595962,GSM7595962: Marrow rag2RFP cd79aGFP Population M3A Sample 41; Danio rerio; RNA Seq,GSM7595962 r1,GSM7595962,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,41_S53_R1_001.fastq.gz 41_S53_R2_001.fastq.gz,fastq fastq,9203316516.0,30474558.0,GSM7595962 r1,0:151 1:151,A:2725901989;C:1645779996;G:1942649566;T:2888948599;N:36366,151,151,,,2725901989,1645779996,1942649566,2888948599,36366,SRX20994097,SRS18268504,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.67888,0.52034,0.12258,0.11213,0.86062,0.92468,0.66237,0.68597,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76654,SRR25247912,SRX20994096,SRS18268503,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow rag2RFP cd79aGFP Population M3A Sample 40,GSM7595961,,source name:Marrow|tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow rag2RFP cd79aGFP Population M3A Sample 40,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79aGFP|treatment:NA,GSM7595961,GSM7595961: Marrow rag2RFP cd79aGFP Population M3A Sample 40; Danio rerio; RNA Seq,GSM7595961 r1,GSM7595961,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,40_S52_R2_001.fastq.gz 40_S52_R1_001.fastq.gz,fastq fastq,9646930054.0,31943477.0,GSM7595961 r1,0:151 1:151,A:2834546007;C:1761986037;G:1973855821;T:3076503975;N:38214,151,151,,,2834546007,1761986037,1973855821,3076503975,38214,SRX20994096,SRS18268503,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.76551,0.60892,0.13414,0.13895,0.86048,0.9207,0.65791,0.67293,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76655,SRR25247913,SRX20994095,SRS18268502,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow rag2RFP cd79aGFP Population M3A Sample 39,GSM7595960,,source name:Marrow|tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow rag2RFP cd79aGFP Population M3A Sample 39,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79aGFP|treatment:NA,GSM7595960,GSM7595960: Marrow rag2RFP cd79aGFP Population M3A Sample 39; Danio rerio; RNA Seq,GSM7595960 r1,GSM7595960,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,39_S51_R1_001.fastq.gz 39_S51_R2_001.fastq.gz,fastq fastq,8440558740.0,27948870.0,GSM7595960 r1,0:151 1:151,A:2490529515;C:1538128719;G:1758588428;T:2653278666;N:33412,151,151,,,2490529515,1538128719,1758588428,2653278666,33412,SRX20994095,SRS18268502,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.74478,0.59902,0.13437,0.14723,0.86663,0.92616,0.65496,0.6824,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76656,SRR25247914,SRX20994094,SRS18268501,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow rag2RFP cd79aGFP Population M1 Sample 36,GSM7595959,,source name:Marrow|tissue:Marrow|cell type:Early B committed|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow rag2RFP cd79aGFP Population M1 Sample 36,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:Early B committed|genotype:rag2RFP cd79aGFP|treatment:NA,GSM7595959,GSM7595959: Marrow rag2RFP cd79aGFP Population M1 Sample 36; Danio rerio; RNA Seq,GSM7595959 r1,GSM7595959,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,36_S48_R1_001.fastq.gz 36_S48_R2_001.fastq.gz,fastq fastq,8449201376.0,27977488.0,GSM7595959 r1,0:151 1:151,A:2435565387;C:1600925575;G:1814354263;T:2598322866;N:33285,151,151,,,2435565387,1600925575,1814354263,2598322866,33285,SRX20994094,SRS18268501,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.68458,0.50808,0.15645,0.14862,0.88067,0.93385,0.67951,0.69099,151,151,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76669,SRR25247926,SRX20994081,SRS18268488,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow lckmCherry cd79bGFP Population M1 Sample 23,GSM7595946,,source name:Marrow|tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow lckmCherry cd79bGFP Population M1 Sample 23,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79bGFP|treatment:NA,GSM7595946,GSM7595946: Marrow lckmCherry cd79bGFP Population M1 Sample 23; Danio rerio; RNA Seq,GSM7595946 r1,GSM7595946,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,23_S35_R1_001.fastq.gz 23_S35_R2_001.fastq.gz,fastq fastq,9087292344.0,30090372.0,GSM7595946 r1,0:151 1:151,A:2696974908;C:1687411669;G:1887706429;T:2815163605;N:35733,151,151,,,2696974908,1687411669,1887706429,2815163605,35733,SRX20994081,SRS18268488,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.6653,0.45253,0.10733,0.09681,0.90806,0.94935,0.72764,0.73406,151,151,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76670,SRR25247927,SRX20994080,SRS18268487,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow lckmCherry cd79bGFP Population M1 Sample 22,GSM7595945,,source name:Marrow|tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow lckmCherry cd79bGFP Population M1 Sample 22,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79bGFP|treatment:NA,GSM7595945,GSM7595945: Marrow lckmCherry cd79bGFP Population M1 Sample 22; Danio rerio; RNA Seq,GSM7595945 r1,GSM7595945,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,22_S34_R1_001.fastq.gz 22_S34_R2_001.fastq.gz,fastq fastq,9623138796.0,31864698.0,GSM7595945 r1,0:151 1:151,A:2754394984;C:1823594508;G:2149500970;T:2895610034;N:38300,151,151,,,2754394984,1823594508,2149500970,2895610034,38300,SRX20994080,SRS18268487,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.47113,0.29499,0.09705,0.06858,0.94095,0.96349,0.70694,0.72308,151,151,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76671,SRR25247929,SRX20994079,SRS18268486,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow lckmCherry cd79bGFP Population M1 Sample 21,GSM7595944,,source name:Marrow|tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow lckmCherry cd79bGFP Population M1 Sample 21,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79bGFP|treatment:NA,GSM7595944,GSM7595944: Marrow lckmCherry cd79bGFP Population M1 Sample 21; Danio rerio; RNA Seq,GSM7595944 r1,GSM7595944,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,21_S33_R2_001.fastq.gz 21_S33_R1_001.fastq.gz,fastq fastq,7877331458.0,26083879.0,GSM7595944 r1,0:151 1:151,A:2282670114;C:1496631823;G:1685330538;T:2412668409;N:30574,151,151,,,2282670114,1496631823,1685330538,2412668409,30574,SRX20994079,SRS18268486,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.59088,0.41604,0.11324,0.09655,0.93685,0.95692,0.67515,0.72761,151,151,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76674,SRR25247932,SRX20994076,SRS18268483,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow rag2RFP cd79bGFP Population M4 Sample 18,GSM7595941,,source name:Marrow|tissue:Marrow|cell type:B Stage III|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow rag2RFP cd79bGFP Population M4 Sample 18,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:B Stage III|genotype:rag2RFP cd79bGFP|treatment:NA,GSM7595941,GSM7595941: Marrow rag2RFP cd79bGFP Population M4 Sample 18; Danio rerio; RNA Seq,GSM7595941 r1,GSM7595941,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,18_S30_R1_001.fastq.gz 18_S30_R2_001.fastq.gz,fastq fastq,9378458396.0,31054498.0,GSM7595941 r1,0:151 1:151,A:2719764060;C:1763237221;G:1999860307;T:2895559786;N:37022,151,151,,,2719764060,1763237221,1999860307,2895559786,37022,SRX20994076,SRS18268483,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.75321,0.57729,0.14283,0.15696,0.89708,0.94296,0.72648,0.40661,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76675,SRR25247936,SRX20994075,SRS18268482,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow rag2RFP cd79bGFP Population M4 Sample 17,GSM7595940,,source name:Marrow|tissue:Marrow|cell type:B Stage III|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow rag2RFP cd79bGFP Population M4 Sample 17,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:B Stage III|genotype:rag2RFP cd79bGFP|treatment:NA,GSM7595940,GSM7595940: Marrow rag2RFP cd79bGFP Population M4 Sample 17; Danio rerio; RNA Seq,GSM7595940 r1,GSM7595940,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,17_S29_R1_001.fastq.gz 17_S29_R2_001.fastq.gz,fastq fastq,8603160674.0,28487287.0,GSM7595940 r1,0:151 1:151,A:2487183090;C:1628390382;G:1810834659;T:2676718560;N:33983,151,151,,,2487183090,1628390382,1810834659,2676718560,33983,SRX20994075,SRS18268482,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.75738,0.57611,0.12217,0.12508,0.8898,0.93943,0.68863,0.39147,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76676,SRR25247933,SRX20994074,SRS18268481,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow rag2RFP cd79bGFP Population M4 Sample 16,GSM7595939,,source name:Marrow|tissue:Marrow|cell type:B Stage III|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow rag2RFP cd79bGFP Population M4 Sample 16,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:B Stage III|genotype:rag2RFP cd79bGFP|treatment:NA,GSM7595939,GSM7595939: Marrow rag2RFP cd79bGFP Population M4 Sample 16; Danio rerio; RNA Seq,GSM7595939 r1,GSM7595939,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,16_S28_R1_001.fastq.gz 16_S28_R2_001.fastq.gz,fastq fastq,12335217784.0,40845092.0,GSM7595939 r1,0:151 1:151,A:3615039679;C:2300903967;G:2575715695;T:3843509545;N:48898,151,151,,,3615039679,2300903967,2575715695,3843509545,48898,SRX20994074,SRS18268481,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.68959,0.50352,0.1172,0.10233,0.90352,0.94537,0.72822,0.74253,151,151,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76677,SRR25247934,SRX20994073,SRS18268480,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow rag2RFP cd79bGFP Population M3B Sample 15,GSM7595938,,source name:Marrow|tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow rag2RFP cd79bGFP Population M3B Sample 15,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79bGFP|treatment:NA,GSM7595938,GSM7595938: Marrow rag2RFP cd79bGFP Population M3B Sample 15; Danio rerio; RNA Seq,GSM7595938 r1,GSM7595938,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,15_S27_R1_001.fastq.gz 15_S27_R2_001.fastq.gz,fastq fastq,8202696594.0,27161247.0,GSM7595938 r1,0:151 1:151,A:2344172206;C:1580848264;G:1802238700;T:2475405027;N:32397,151,151,,,2344172206,1580848264,1802238700,2475405027,32397,SRX20994073,SRS18268480,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.63815,0.43487,0.08008,0.06825,0.90218,0.94483,0.65063,0.66839,151,151,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76678,SRR25247935,SRX20994072,SRS18268478,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow rag2RFP cd79bGFP Population M3B Sample 14,GSM7595937,,source name:Marrow|tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow rag2RFP cd79bGFP Population M3B Sample 14,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79bGFP|treatment:NA,GSM7595937,GSM7595937: Marrow rag2RFP cd79bGFP Population M3B Sample 14; Danio rerio; RNA Seq,GSM7595937 r1,GSM7595937,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,14_S26_R2_001.fastq.gz 14_S26_R1_001.fastq.gz,fastq fastq,7915147294.0,26209097.0,GSM7595937 r1,0:151 1:151,A:2265670905;C:1520031310;G:1849059138;T:2280354641;N:31300,151,151,,,2265670905,1520031310,1849059138,2280354641,31300,SRX20994072,SRS18268478,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.53533,0.39855,0.13942,0.1317,0.9151,0.94714,0.6754,0.68314,151,151,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76679,SRR25247937,SRX20994071,SRS18268479,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow rag2RFP cd79bGFP Population M3B Sample 13,GSM7595936,,source name:Marrow|tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow rag2RFP cd79bGFP Population M3B Sample 13,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79bGFP|treatment:NA,GSM7595936,GSM7595936: Marrow rag2RFP cd79bGFP Population M3B Sample 13; Danio rerio; RNA Seq,GSM7595936 r1,GSM7595936,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,13_S25_R1_001.fastq.gz 13_S25_R2_001.fastq.gz,fastq fastq,9721695892.0,32191046.0,GSM7595936 r1,0:151 1:151,A:2858891195;C:1802515744;G:2029257538;T:3030992999;N:38416,151,151,,,2858891195,1802515744,2029257538,3030992999,38416,SRX20994071,SRS18268479,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.76749,0.60878,0.1349,0.15464,0.87604,0.93365,0.67533,0.65373,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76680,SRR25247938,SRX20994070,SRS18268477,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow rag2RFP cd79bGFP Population M3A Sample 12,GSM7595935,,source name:Marrow|tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow rag2RFP cd79bGFP Population M3A Sample 12,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79bGFP|treatment:NA,GSM7595935,GSM7595935: Marrow rag2RFP cd79bGFP Population M3A Sample 12; Danio rerio; RNA Seq,GSM7595935 r1,GSM7595935,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,12_S24_R1_001.fastq.gz 12_S24_R2_001.fastq.gz,fastq fastq,8731763750.0,28913125.0,GSM7595935 r1,0:151 1:151,A:2551441984;C:1639877964;G:1850759915;T:2689649693;N:34194,151,151,,,2551441984,1639877964,1850759915,2689649693,34194,SRX20994070,SRS18268477,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.74961,0.60373,0.12646,0.15649,0.87487,0.93332,0.6854,0.70294,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76681,SRR25247939,SRX20994069,SRS18268476,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow rag2RFP cd79bGFP Population M3A Sample 11,GSM7595934,,source name:Marrow|tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow rag2RFP cd79bGFP Population M3A Sample 11,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79bGFP|treatment:NA,GSM7595934,GSM7595934: Marrow rag2RFP cd79bGFP Population M3A Sample 11; Danio rerio; RNA Seq,GSM7595934 r1,GSM7595934,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,11_S23_R1_001.fastq.gz 11_S23_R2_001.fastq.gz,fastq fastq,8131157626.0,26924363.0,GSM7595934 r1,0:151 1:151,A:2378241179;C:1520823030;G:1694205993;T:2537855107;N:32317,151,151,,,2378241179,1520823030,1694205993,2537855107,32317,SRX20994069,SRS18268476,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.7694,0.58873,0.12189,0.13976,0.87432,0.93332,0.6609,0.68659,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76682,SRR25247940,SRX20994068,SRS18268475,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow rag2RFP cd79bGFP Population M3A Sample 10,GSM7595933,,source name:Marrow|tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow rag2RFP cd79bGFP Population M3A Sample 10,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79bGFP|treatment:NA,GSM7595933,GSM7595933: Marrow rag2RFP cd79bGFP Population M3A Sample 10; Danio rerio; RNA Seq,GSM7595933 r1,GSM7595933,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,10_S22_R1_001.fastq.gz 10_S22_R2_001.fastq.gz,fastq fastq,8963294466.0,29679783.0,GSM7595933 r1,0:151 1:151,A:2619732708;C:1669568274;G:1858403783;T:2815553963;N:35738,151,151,,,2619732708,1669568274,1858403783,2815553963,35738,SRX20994068,SRS18268475,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.77821,0.60379,0.10495,0.12779,0.86825,0.92492,0.62624,0.60864,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76683,SRR25247944,SRX20994067,SRS18268474,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow rag2RFP cd79bGFP Population M1 Sample 8,GSM7595932,,source name:Marrow|tissue:Marrow|cell type:Early B committed|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow rag2RFP cd79bGFP Population M1 Sample 8,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:Early B committed|genotype:rag2RFP cd79bGFP|treatment:NA,GSM7595932,GSM7595932: Marrow rag2RFP cd79bGFP Population M1 Sample 8; Danio rerio; RNA Seq,GSM7595932 r1,GSM7595932,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,8_S20_R1_001.fastq.gz 8_S20_R2_001.fastq.gz,fastq fastq,9142544452.0,30273326.0,GSM7595932 r1,0:151 1:151,A:2630198533;C:1744556837;G:1930871463;T:2836881708;N:35911,151,151,,,2630198533,1744556837,1930871463,2836881708,35911,SRX20994067,SRS18268474,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.7212,0.52336,0.12114,0.1298,0.89929,0.94259,0.67128,0.68712,151,151,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System 76684,SRR25247941,SRX20994066,SRS18268473,SRP448831,PRJNA994052,Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model,GSE237139,Transcriptome Analysis,The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.,,pubmed:38656392,,Marrow rag2RFP cd79bGFP Population M1 Sample 7,GSM7595931,,source name:Marrow|tissue:Marrow|cell type:Early B committed|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing,Marrow rag2RFP cd79bGFP Population M1 Sample 7,Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample,Marrow,,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare.,tissue:Marrow|cell type:Early B committed|genotype:rag2RFP cd79bGFP|treatment:NA,GSM7595931,GSM7595931: Marrow rag2RFP cd79bGFP Population M1 Sample 7; Danio rerio; RNA Seq,GSM7595931 r1,GSM7595931,1,Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP448831,,loader:fastq load.py,7_S19_R1_001.fastq.gz 7_S19_R2_001.fastq.gz,fastq fastq,7906272118.0,26179709.0,GSM7595931 r1,0:151 1:151,A:2254838087;C:1527167803;G:1677900707;T:2446333840;N:31681,151,151,,,2254838087,1527167803,1677900707,2446333840,31681,SRX20994066,SRS18268473,SRA1671790,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",2,0.72774,0.52811,0.10506,0.09722,0.90443,0.94339,0.65125,0.68364,151,151,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,lexogen,bulk,bulk,bulk,,United States,2023-07-12,Undetermined,Undetermined,Marrow,Renal System