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Overexpression of epoa through the lyve1b promoter which is specifically expressed in vein lymphatic vessels and CHT vein endothelial cells rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.", null, null, null, "vein endothelium cells Day5 rep2", "GSM7899809", null, "source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing", "vein endothelium cells Day5 rep2", "Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value\u226420 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. 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However the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study we showed that erythrocytes predominantly reside inside the blood vessels of the CHT while neutrophils stay outside. Ectopic vascular endothelium induced by Bone Morphogenetic Protein 2bBmp2b overexpression attracts both cell types with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter which is specifically expressed in vein lymphatic vessels and CHT vein endothelial cells rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.", null, null, null, "vein endothelium cells Day5 rep1", "GSM7899808", null, "source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing", "vein endothelium cells Day5 rep1", "Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value\u226420 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with \u201c rna strandness RF\u201d and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Caudal hematopoietic tissue", null, "Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer\u2019s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.", null, "tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment", "GSM7899808", "GSM7899808: vein endothelium cells Day5 rep1; Danio rerio; RNA Seq", "GSM7899808 r1", "GSM7899808", "1", "Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. 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However the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study we showed that erythrocytes predominantly reside inside the blood vessels of the CHT while neutrophils stay outside. Ectopic vascular endothelium induced by Bone Morphogenetic Protein 2bBmp2b overexpression attracts both cell types with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter which is specifically expressed in vein lymphatic vessels and CHT vein endothelial cells rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.", null, null, null, "non vein endothelium cells Control Day5 rep2", "GSM7899807", null, "source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing", "non vein endothelium cells Control Day5 rep2", "Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value\u226420 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with \u201c rna strandness RF\u201d and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Caudal hematopoietic tissue", null, "Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer\u2019s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.", null, "tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment", "GSM7899807", "GSM7899807: non vein endothelium cells Control Day5 rep2; Danio rerio; RNA Seq", "GSM7899807 r1", "GSM7899807", "1", "Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP471831", null, "loader:fastq load.py", "non-vein_endothelium_cells-2_1.fq.gz non-vein_endothelium_cells-2_2.fq.gz", "fastq fastq", 9363942600.0, 31213142.0, "GSM7899807 r1", "0:150 1:150", "A:2523111369;C:2155598161;G:2171776473;T:2513164552;N:292045", 150, 150, null, null, 2523111369, 2155598161, 2171776473, 2513164552, 292045, "SRX22524050", "SRS19535495", "SRA1750986", "South China University of Technology", "South China University of Technology", 2, 0.93879, 0.93706, 0.10971, 0.10945, 0.76721, 0.76737, 0.51346, 0.51513, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2023-11-14", "Larval", "Larval", "Blood", "Hematopoietic System"], [28905, "SRR26827535", "SRX22524049", "SRS19535494", "SRP471831", "PRJNA1040223", "The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish", "GSE247730", "Transcriptome Analysis", "Neutrophils and erythrocytes are vital to the immune system and oxygen transport respectively. However the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study we showed that erythrocytes predominantly reside inside the blood vessels of the CHT while neutrophils stay outside. Ectopic vascular endothelium induced by Bone Morphogenetic Protein 2bBmp2b overexpression attracts both cell types with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter which is specifically expressed in vein lymphatic vessels and CHT vein endothelial cells rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.", null, null, null, "non vein endothelium cells Control Day5 rep1", "GSM7899806", null, "source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing", "non vein endothelium cells Control Day5 rep1", "Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value\u226420 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with \u201c rna strandness RF\u201d and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Caudal hematopoietic tissue", null, "Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer\u2019s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.", null, "tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment", "GSM7899806", "GSM7899806: non vein endothelium cells Control Day5 rep1; Danio rerio; RNA Seq", "GSM7899806 r1", "GSM7899806", "1", "Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP471831", null, "loader:fastq load.py", "non-vein_endothelium_cells-1_1.fq.gz non-vein_endothelium_cells-1_2.fq.gz", "fastq fastq", 8396176800.0, 27987256.0, "GSM7899806 r1", "0:150 1:150", "A:2190594419;C:1990596503;G:2019391921;T:2194713332;N:880625", 150, 150, null, null, 2190594419, 1990596503, 2019391921, 2194713332, 880625, "SRX22524049", "SRS19535494", "SRA1750986", "South China University of Technology", "South China University of Technology", 2, 0.94508, 0.94385, 0.0967, 0.09697, 0.77642, 0.77632, 0.49896, 0.49962, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2023-11-14", "Larval", "Larval", "Blood", "Hematopoietic System"], [30018, "SRR27988043", "SRX23641260", "SRS20476222", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.", null, null, null, "hamp / 36 hpf blood", "zebrafish hamp / 36 hpf blood replicate 3", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:hamp knockdown|sample type:tissue sample|treatment:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq hamp / 36 hpf blood replicate 3", "B 6", "B 6", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "KO-3_R2_001.fastq.gz KO-3_R1_001.fastq.gz", "fastq fastq", 8752665900.0, 29175553.0, "KO 3 R1 001.fastq.gz", "0:150 1:150", "A:2204170575;C:2174083961;G:2224694970;T:2149603712;N:112682", 150, 150, null, null, 2204170575, 2174083961, 2224694970, 2149603712, 112682, "SRX23641260", "SRS20476222", "SRA1803422", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.91553, 0.91645, 0.01276, 0.01288, 0.85884, 0.85839, 0.35101, 0.40996, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-02-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [30019, "SRR27988044", "SRX23641259", "SRS20476221", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.", null, null, null, "hamp / 36 hpf blood", "zebrafish hamp / 36 hpf blood replicate 2", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:hamp knockdown|sample type:tissue sample|treatment:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq hamp / 36 hpf blood replicate 2", "B 5", "B 5", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "KO-2_R1_001.fastq.gz KO-2_R2_001.fastq.gz", "fastq fastq", 8060498700.0, 26868329.0, "KO 2 R1 001.fastq.gz", "0:150 1:150", "A:2045797336;C:1985847523;G:2035528018;T:1993222840;N:102983", 150, 150, null, null, 2045797336, 1985847523, 2035528018, 1993222840, 102983, "SRX23641259", "SRS20476221", "SRA1803422", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.9213, 0.92027, 0.0167, 0.01676, 0.8242, 0.82475, 0.41081, 0.41111, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-02-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [30020, "SRR27988045", "SRX23641258", "SRS20476220", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.", null, null, null, "hamp / 36 hpf blood", "zebrafish hamp / 36 hpf blood replicate 1", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:hamp knockdown|sample type:tissue sample|treatment:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq hamp / 36 hpf blood replicate 1", "B 4", "B 4", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "KO-1_R1_001.fastq.gz KO-1_R2_001.fastq.gz", "fastq fastq", 8707637700.0, 29025459.0, "KO 1 R1 001.fastq.gz", "0:150 1:150", "A:2222026435;C:2133480283;G:2182087972;T:2169932447;N:110563", 150, 150, null, null, 2222026435, 2133480283, 2182087972, 2169932447, 110563, "SRX23641258", "SRS20476220", "SRA1803422", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.91531, 0.91359, 0.02185, 0.0221, 0.81213, 0.8128, 0.37868, 0.42351, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-02-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [30021, "SRR27988046", "SRX23641257", "SRS20476219", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.", null, null, null, "wild type 36 hpf blood", "zebrafish wild type 36 hpf blood replicate 3", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:wild type|sample type:tissue sample|treatment:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq wild type 36 hpf blood replicate 3", "B 3", "B 3", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT-3_R1_001.fastq.gz WT-3_R2_001.fastq.gz", "fastq fastq", 8829371400.0, 29431238.0, "WT 3 R1 001.fastq.gz", "0:150 1:150", "A:2278837675;C:2141723937;G:2193442375;T:2215253519;N:113894", 150, 150, null, null, 2278837675, 2141723937, 2193442375, 2215253519, 113894, "SRX23641257", "SRS20476219", "SRA1803422", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.90531, 0.9043, 0.03015, 0.03017, 0.8101, 0.8112, 0.43085, 0.43002, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-02-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [30022, "SRR27988047", "SRX23641256", "SRS20476218", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.", null, null, null, "wild type 36 hpf blood", "zebrafish wild type 36 hpf blood replicate 2", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:wild type|sample type:tissue sample|treatment:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq wild type 36 hpf blood replicate 2", "B 2", "B 2", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT-2_R1_001.fastq.gz WT-2_R2_001.fastq.gz", "fastq fastq", 7365643800.0, 24552146.0, "WT 2 R1 001.fastq.gz", "0:150 1:150", "A:1867985067;C:1819016430;G:1870006707;T:1808540769;N:94827", 150, 150, null, null, 1867985067, 1819016430, 1870006707, 1808540769, 94827, "SRX23641256", "SRS20476218", "SRA1803422", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.90612, 0.90536, 0.01714, 0.01746, 0.88109, 0.88156, 0.32469, 0.39232, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-02-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [30023, "SRR27988048", "SRX23641255", "SRS20476217", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.", null, null, null, "wild type 36 hpf blood", "zebrafish wild type 36 hpf blood replicate 1", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:wild type|sample type:tissue sample|treatment:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq wild type 36 hpf blood replicate 1", "B 1", "B 1", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT-1_R1_001.fastq.gz WT-1_R2_001.fastq.gz", "fastq fastq", 8631863400.0, 28772878.0, "WT 1 R1 001.fastq.gz", "0:150 1:150", "A:2186212554;C:2135990723;G:2179142081;T:2130408485;N:109557", 150, 150, null, null, 2186212554, 2135990723, 2179142081, 2130408485, 109557, "SRX23641255", "SRS20476217", "SRA1803422", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.90461, 0.90281, 0.01388, 0.01365, 0.83871, 0.83895, 0.36511, 0.41074, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-02-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [33158, "SRR29791088", "SRX25290435", "SRS21969151", "SRP519440", "PRJNA1134759", "Developmental trajectory and evolutionary origin of thymic mimetic cells [dataset 2]", "GSE272064", "Transcriptome Analysis", "The generation of self tolerant repertoires of T cells depends on the expression of peripheral self antigens in the thymic epithelium and the presence of small populations of cells mimicking the diverse phenotypes of peripheral tissues. Whereas the molecular underpinnings of self antigen expression have been extensively studied the developmental origins and differentiation pathways of thymic mimetic cells remain to be identified. Moreover the histological identification of myoid and other peripheral cell types as components of the thymic microenvironment of many vertebrate species raises questions as to the evolutionary origin of this unique tolerance mechanism. Here we show that during mouse development mimetic cells appear in the microenvironment in two successive waves. Cells exhibiting transcriptional signatures characteristic of muscle ionocyte goblet and ciliated cells emerge before birth whereas others for instance those mimicking enterohepatic cells and skin keratinocytes appear postnatally. These two groups also respond differently to modulations of TEC progenitor pools caused by deletions of Foxn1 and Ascl1 expression of a hypomorphic Foxn1 transcription factor and overexpression of Bmp4 and Fgf7 signalling molecules. Differences in mimetic cell populations were also observed in thymic microenvironments reconstructed by replacement of mouse Foxn1 with evolutionarily ancient Foxn1/4 gene family members including the Foxn4 gene of the cephalochordate amphioxus and the Foxn4 and Foxn1 genes of a cartilaginous fish. Whereas some cell types such as ciliated cells develop in the thymus in the absence of Foxn1 mimetic cells appearing postnatally such as enterohepatic cells require the activity of the vertebrate specific transcription factor Foxn1. The thymus of cartilaginous fishes and the thymoid of lampreys a representative of jawless vertebrates that exhibit an alternative adaptive immune system also harbour cells expressing genes encoding peripheral tissue components such as the liver specific protein transthyretin. Our findings suggest an evolutionary model of successive changes of thymic epithelial genetic networks enabling the coordinated contribution of peripheral antigen expression and mimetic cell formation to achieve central tolerance for vertebrate specific innovations of certain tissues such as the liver. Overall design: Cells from whole thymic tissue from zebrafish were prepared and subjected to bulk RNAseq. Foxn1+/+ samples and foxn1 / samples were sequenced.", null, null, null, "Dr thymus foxn1 / rep3", "GSM8392364", null, "source name:thymus|tissue:thymus|cell type:thymus cells|genotype:foxn1 / |geo loc name:missing|collection date:missing", "Dr thymus foxn1 / rep3", "Transcriptomes were analyzed on the Galaxy platform. Adapters were trimmed with TrimGalore! version 0.4.3.1. Reads were aligned to the reference genome with Hisat2 version 2.1.0. Counts were generated with featureCounts version 1.6.1.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files containing raw counts for each sample", "thymus", null, "Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.", null, "tissue:thymus|cell type:thymus cells|genotype:foxn1 / ", "GSM8392364", "GSM8392364: Dr thymus foxn1 / rep3; Danio rerio; RNA Seq", "GSM8392364 r1", "GSM8392364", "1", "Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP519440", null, null, "BK6_R1.fastq.gz BK6_R2.fastq.gz", "fastq fastq", 40416715568.0, 133830184.0, "GSM8392364 r1", "0:151 1:151", "A:11536946706;C:8490306261;G:9295609599;T:11092005423;N:1847579", 151, 151, null, null, 11536946706, 8490306261, 9295609599, 11092005423, 1847579, "SRX25290435", "SRS21969151", "SRA1922343", "Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics", "Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics", 2, 0.89276, 0.89283, 0.11419, 0.11482, 0.73306, 0.73409, 0.46305, 0.46571, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Germany", "2024-07-11", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [33159, "SRR29791089", "SRX25290434", "SRS21969152", "SRP519440", "PRJNA1134759", "Developmental trajectory and evolutionary origin of thymic mimetic cells [dataset 2]", "GSE272064", "Transcriptome Analysis", "The generation of self tolerant repertoires of T cells depends on the expression of peripheral self antigens in the thymic epithelium and the presence of small populations of cells mimicking the diverse phenotypes of peripheral tissues. Whereas the molecular underpinnings of self antigen expression have been extensively studied the developmental origins and differentiation pathways of thymic mimetic cells remain to be identified. Moreover the histological identification of myoid and other peripheral cell types as components of the thymic microenvironment of many vertebrate species raises questions as to the evolutionary origin of this unique tolerance mechanism. Here we show that during mouse development mimetic cells appear in the microenvironment in two successive waves. Cells exhibiting transcriptional signatures characteristic of muscle ionocyte goblet and ciliated cells emerge before birth whereas others for instance those mimicking enterohepatic cells and skin keratinocytes appear postnatally. These two groups also respond differently to modulations of TEC progenitor pools caused by deletions of Foxn1 and Ascl1 expression of a hypomorphic Foxn1 transcription factor and overexpression of Bmp4 and Fgf7 signalling molecules. Differences in mimetic cell populations were also observed in thymic microenvironments reconstructed by replacement of mouse Foxn1 with evolutionarily ancient Foxn1/4 gene family members including the Foxn4 gene of the cephalochordate amphioxus and the Foxn4 and Foxn1 genes of a cartilaginous fish. Whereas some cell types such as ciliated cells develop in the thymus in the absence of Foxn1 mimetic cells appearing postnatally such as enterohepatic cells require the activity of the vertebrate specific transcription factor Foxn1. The thymus of cartilaginous fishes and the thymoid of lampreys a representative of jawless vertebrates that exhibit an alternative adaptive immune system also harbour cells expressing genes encoding peripheral tissue components such as the liver specific protein transthyretin. Our findings suggest an evolutionary model of successive changes of thymic epithelial genetic networks enabling the coordinated contribution of peripheral antigen expression and mimetic cell formation to achieve central tolerance for vertebrate specific innovations of certain tissues such as the liver. Overall design: Cells from whole thymic tissue from zebrafish were prepared and subjected to bulk RNAseq. Foxn1+/+ samples and foxn1 / samples were sequenced.", null, null, null, "Dr thymus foxn1 / rep2", "GSM8392363", null, "source name:thymus|tissue:thymus|cell type:thymus cells|genotype:foxn1 / |geo loc name:missing|collection date:missing", "Dr thymus foxn1 / rep2", "Transcriptomes were analyzed on the Galaxy platform. Adapters were trimmed with TrimGalore! version 0.4.3.1. Reads were aligned to the reference genome with Hisat2 version 2.1.0. Counts were generated with featureCounts version 1.6.1.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files containing raw counts for each sample", "thymus", null, "Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.", null, "tissue:thymus|cell type:thymus cells|genotype:foxn1 / ", "GSM8392363", "GSM8392363: Dr thymus foxn1 / rep2; Danio rerio; RNA Seq", "GSM8392363 r1", "GSM8392363", "1", "Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP519440", null, null, "BK5_R1.fastq.gz BK5_R2.fastq.gz", "fastq fastq", 41734368446.0, 138193273.0, "GSM8392363 r1", "0:151 1:151", "A:12015023285;C:8850050726;G:9485443497;T:11381944831;N:1906107", 151, 151, null, null, 12015023285, 8850050726, 9485443497, 11381944831, 1906107, "SRX25290434", "SRS21969152", "SRA1922343", "Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics", "Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics", 2, 0.88856, 0.88918, 0.11978, 0.11946, 0.73003, 0.732, 0.44244, 0.43125, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Germany", "2024-07-11", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [33160, "SRR29791090", "SRX25290433", "SRS21969150", "SRP519440", "PRJNA1134759", "Developmental trajectory and evolutionary origin of thymic mimetic cells [dataset 2]", "GSE272064", "Transcriptome Analysis", "The generation of self tolerant repertoires of T cells depends on the expression of peripheral self antigens in the thymic epithelium and the presence of small populations of cells mimicking the diverse phenotypes of peripheral tissues. Whereas the molecular underpinnings of self antigen expression have been extensively studied the developmental origins and differentiation pathways of thymic mimetic cells remain to be identified. Moreover the histological identification of myoid and other peripheral cell types as components of the thymic microenvironment of many vertebrate species raises questions as to the evolutionary origin of this unique tolerance mechanism. Here we show that during mouse development mimetic cells appear in the microenvironment in two successive waves. Cells exhibiting transcriptional signatures characteristic of muscle ionocyte goblet and ciliated cells emerge before birth whereas others for instance those mimicking enterohepatic cells and skin keratinocytes appear postnatally. These two groups also respond differently to modulations of TEC progenitor pools caused by deletions of Foxn1 and Ascl1 expression of a hypomorphic Foxn1 transcription factor and overexpression of Bmp4 and Fgf7 signalling molecules. Differences in mimetic cell populations were also observed in thymic microenvironments reconstructed by replacement of mouse Foxn1 with evolutionarily ancient Foxn1/4 gene family members including the Foxn4 gene of the cephalochordate amphioxus and the Foxn4 and Foxn1 genes of a cartilaginous fish. Whereas some cell types such as ciliated cells develop in the thymus in the absence of Foxn1 mimetic cells appearing postnatally such as enterohepatic cells require the activity of the vertebrate specific transcription factor Foxn1. The thymus of cartilaginous fishes and the thymoid of lampreys a representative of jawless vertebrates that exhibit an alternative adaptive immune system also harbour cells expressing genes encoding peripheral tissue components such as the liver specific protein transthyretin. Our findings suggest an evolutionary model of successive changes of thymic epithelial genetic networks enabling the coordinated contribution of peripheral antigen expression and mimetic cell formation to achieve central tolerance for vertebrate specific innovations of certain tissues such as the liver. Overall design: Cells from whole thymic tissue from zebrafish were prepared and subjected to bulk RNAseq. Foxn1+/+ samples and foxn1 / samples were sequenced.", null, null, null, "Dr thymus foxn1 / rep1", "GSM8392362", null, "source name:thymus|tissue:thymus|cell type:thymus cells|genotype:foxn1 / |geo loc name:missing|collection date:missing", "Dr thymus foxn1 / rep1", "Transcriptomes were analyzed on the Galaxy platform. Adapters were trimmed with TrimGalore! version 0.4.3.1. Reads were aligned to the reference genome with Hisat2 version 2.1.0. Counts were generated with featureCounts version 1.6.1.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files containing raw counts for each sample", "thymus", null, "Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.", null, "tissue:thymus|cell type:thymus cells|genotype:foxn1 / ", "GSM8392362", "GSM8392362: Dr thymus foxn1 / rep1; Danio rerio; RNA Seq", "GSM8392362 r1", "GSM8392362", "1", "Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP519440", null, null, "BK4_R2.fastq.gz BK4_R1.fastq.gz", "fastq fastq", 39302001858.0, 130139079.0, "GSM8392362 r1", "0:151 1:151", "A:11220466966;C:8305776940;G:9105878447;T:10668104948;N:1774557", 151, 151, null, null, 11220466966, 8305776940, 9105878447, 10668104948, 1774557, "SRX25290433", "SRS21969150", "SRA1922343", "Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics", "Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics", 2, 0.89299, 0.89318, 0.11306, 0.1139, 0.74123, 0.74345, 0.45102, 0.46093, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Germany", "2024-07-11", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [33161, "SRR29791091", "SRX25290432", "SRS21969149", "SRP519440", "PRJNA1134759", "Developmental trajectory and evolutionary origin of thymic mimetic cells [dataset 2]", "GSE272064", "Transcriptome Analysis", "The generation of self tolerant repertoires of T cells depends on the expression of peripheral self antigens in the thymic epithelium and the presence of small populations of cells mimicking the diverse phenotypes of peripheral tissues. Whereas the molecular underpinnings of self antigen expression have been extensively studied the developmental origins and differentiation pathways of thymic mimetic cells remain to be identified. Moreover the histological identification of myoid and other peripheral cell types as components of the thymic microenvironment of many vertebrate species raises questions as to the evolutionary origin of this unique tolerance mechanism. Here we show that during mouse development mimetic cells appear in the microenvironment in two successive waves. Cells exhibiting transcriptional signatures characteristic of muscle ionocyte goblet and ciliated cells emerge before birth whereas others for instance those mimicking enterohepatic cells and skin keratinocytes appear postnatally. These two groups also respond differently to modulations of TEC progenitor pools caused by deletions of Foxn1 and Ascl1 expression of a hypomorphic Foxn1 transcription factor and overexpression of Bmp4 and Fgf7 signalling molecules. Differences in mimetic cell populations were also observed in thymic microenvironments reconstructed by replacement of mouse Foxn1 with evolutionarily ancient Foxn1/4 gene family members including the Foxn4 gene of the cephalochordate amphioxus and the Foxn4 and Foxn1 genes of a cartilaginous fish. Whereas some cell types such as ciliated cells develop in the thymus in the absence of Foxn1 mimetic cells appearing postnatally such as enterohepatic cells require the activity of the vertebrate specific transcription factor Foxn1. The thymus of cartilaginous fishes and the thymoid of lampreys a representative of jawless vertebrates that exhibit an alternative adaptive immune system also harbour cells expressing genes encoding peripheral tissue components such as the liver specific protein transthyretin. Our findings suggest an evolutionary model of successive changes of thymic epithelial genetic networks enabling the coordinated contribution of peripheral antigen expression and mimetic cell formation to achieve central tolerance for vertebrate specific innovations of certain tissues such as the liver. Overall design: Cells from whole thymic tissue from zebrafish were prepared and subjected to bulk RNAseq. Foxn1+/+ samples and foxn1 / samples were sequenced.", null, null, null, "Dr thymus foxn1+/+ rep3", "GSM8392361", null, "source name:thymus|tissue:thymus|cell type:thymus cells|genotype:foxn1+/+|geo loc name:missing|collection date:missing", "Dr thymus foxn1+/+ rep3", "Transcriptomes were analyzed on the Galaxy platform. Adapters were trimmed with TrimGalore! version 0.4.3.1. Reads were aligned to the reference genome with Hisat2 version 2.1.0. Counts were generated with featureCounts version 1.6.1.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files containing raw counts for each sample", "thymus", null, "Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.", null, "tissue:thymus|cell type:thymus cells|genotype:foxn1+/+", "GSM8392361", "GSM8392361: Dr thymus foxn1+/+ rep3; Danio rerio; RNA Seq", "GSM8392361 r1", "GSM8392361", "1", "Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP519440", null, null, "BK3_R1.fastq.gz BK3_R2.fastq.gz", "fastq fastq", 37243022634.0, 123321267.0, "GSM8392361 r1", "0:151 1:151", "A:10858514997;C:7805630226;G:8359994769;T:10217208022;N:1674620", 151, 151, null, null, 10858514997, 7805630226, 8359994769, 10217208022, 1674620, "SRX25290432", "SRS21969149", "SRA1922343", "Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics", "Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics", 2, 0.87732, 0.87686, 0.20353, 0.20336, 0.73261, 0.7343, 0.49192, 0.4924, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Germany", "2024-07-11", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [33162, "SRR29791092", "SRX25290431", "SRS21969148", "SRP519440", "PRJNA1134759", "Developmental trajectory and evolutionary origin of thymic mimetic cells [dataset 2]", "GSE272064", "Transcriptome Analysis", "The generation of self tolerant repertoires of T cells depends on the expression of peripheral self antigens in the thymic epithelium and the presence of small populations of cells mimicking the diverse phenotypes of peripheral tissues. Whereas the molecular underpinnings of self antigen expression have been extensively studied the developmental origins and differentiation pathways of thymic mimetic cells remain to be identified. Moreover the histological identification of myoid and other peripheral cell types as components of the thymic microenvironment of many vertebrate species raises questions as to the evolutionary origin of this unique tolerance mechanism. Here we show that during mouse development mimetic cells appear in the microenvironment in two successive waves. Cells exhibiting transcriptional signatures characteristic of muscle ionocyte goblet and ciliated cells emerge before birth whereas others for instance those mimicking enterohepatic cells and skin keratinocytes appear postnatally. These two groups also respond differently to modulations of TEC progenitor pools caused by deletions of Foxn1 and Ascl1 expression of a hypomorphic Foxn1 transcription factor and overexpression of Bmp4 and Fgf7 signalling molecules. Differences in mimetic cell populations were also observed in thymic microenvironments reconstructed by replacement of mouse Foxn1 with evolutionarily ancient Foxn1/4 gene family members including the Foxn4 gene of the cephalochordate amphioxus and the Foxn4 and Foxn1 genes of a cartilaginous fish. Whereas some cell types such as ciliated cells develop in the thymus in the absence of Foxn1 mimetic cells appearing postnatally such as enterohepatic cells require the activity of the vertebrate specific transcription factor Foxn1. The thymus of cartilaginous fishes and the thymoid of lampreys a representative of jawless vertebrates that exhibit an alternative adaptive immune system also harbour cells expressing genes encoding peripheral tissue components such as the liver specific protein transthyretin. Our findings suggest an evolutionary model of successive changes of thymic epithelial genetic networks enabling the coordinated contribution of peripheral antigen expression and mimetic cell formation to achieve central tolerance for vertebrate specific innovations of certain tissues such as the liver. Overall design: Cells from whole thymic tissue from zebrafish were prepared and subjected to bulk RNAseq. Foxn1+/+ samples and foxn1 / samples were sequenced.", null, null, null, "Dr thymus foxn1+/+ rep2", "GSM8392360", null, "source name:thymus|tissue:thymus|cell type:thymus cells|genotype:foxn1+/+|geo loc name:missing|collection date:missing", "Dr thymus foxn1+/+ rep2", "Transcriptomes were analyzed on the Galaxy platform. Adapters were trimmed with TrimGalore! version 0.4.3.1. Reads were aligned to the reference genome with Hisat2 version 2.1.0. Counts were generated with featureCounts version 1.6.1.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files containing raw counts for each sample", "thymus", null, "Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.", null, "tissue:thymus|cell type:thymus cells|genotype:foxn1+/+", "GSM8392360", "GSM8392360: Dr thymus foxn1+/+ rep2; Danio rerio; RNA Seq", "GSM8392360 r1", "GSM8392360", "1", "Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP519440", null, null, "BK2_R1.fastq.gz BK2_R2.fastq.gz", "fastq fastq", 34154139756.0, 113093178.0, "GSM8392360 r1", "0:151 1:151", "A:9754575779;C:7198913431;G:7834944597;T:9364172876;N:1533073", 151, 151, null, null, 9754575779, 7198913431, 7834944597, 9364172876, 1533073, "SRX25290431", "SRS21969148", "SRA1922343", "Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics", "Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics", 2, 0.87955, 0.88145, 0.18817, 0.18856, 0.72707, 0.72839, 0.49921, 0.49737, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Germany", "2024-07-11", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [33163, "SRR29791093", "SRX25290430", "SRS21969147", "SRP519440", "PRJNA1134759", "Developmental trajectory and evolutionary origin of thymic mimetic cells [dataset 2]", "GSE272064", "Transcriptome Analysis", "The generation of self tolerant repertoires of T cells depends on the expression of peripheral self antigens in the thymic epithelium and the presence of small populations of cells mimicking the diverse phenotypes of peripheral tissues. Whereas the molecular underpinnings of self antigen expression have been extensively studied the developmental origins and differentiation pathways of thymic mimetic cells remain to be identified. Moreover the histological identification of myoid and other peripheral cell types as components of the thymic microenvironment of many vertebrate species raises questions as to the evolutionary origin of this unique tolerance mechanism. Here we show that during mouse development mimetic cells appear in the microenvironment in two successive waves. Cells exhibiting transcriptional signatures characteristic of muscle ionocyte goblet and ciliated cells emerge before birth whereas others for instance those mimicking enterohepatic cells and skin keratinocytes appear postnatally. These two groups also respond differently to modulations of TEC progenitor pools caused by deletions of Foxn1 and Ascl1 expression of a hypomorphic Foxn1 transcription factor and overexpression of Bmp4 and Fgf7 signalling molecules. Differences in mimetic cell populations were also observed in thymic microenvironments reconstructed by replacement of mouse Foxn1 with evolutionarily ancient Foxn1/4 gene family members including the Foxn4 gene of the cephalochordate amphioxus and the Foxn4 and Foxn1 genes of a cartilaginous fish. Whereas some cell types such as ciliated cells develop in the thymus in the absence of Foxn1 mimetic cells appearing postnatally such as enterohepatic cells require the activity of the vertebrate specific transcription factor Foxn1. The thymus of cartilaginous fishes and the thymoid of lampreys a representative of jawless vertebrates that exhibit an alternative adaptive immune system also harbour cells expressing genes encoding peripheral tissue components such as the liver specific protein transthyretin. Our findings suggest an evolutionary model of successive changes of thymic epithelial genetic networks enabling the coordinated contribution of peripheral antigen expression and mimetic cell formation to achieve central tolerance for vertebrate specific innovations of certain tissues such as the liver. Overall design: Cells from whole thymic tissue from zebrafish were prepared and subjected to bulk RNAseq. Foxn1+/+ samples and foxn1 / samples were sequenced.", null, null, null, "Dr thymus foxn1+/+ rep1", "GSM8392359", null, "source name:thymus|tissue:thymus|cell type:thymus cells|genotype:foxn1+/+|geo loc name:missing|collection date:missing", "Dr thymus foxn1+/+ rep1", "Transcriptomes were analyzed on the Galaxy platform. Adapters were trimmed with TrimGalore! version 0.4.3.1. Reads were aligned to the reference genome with Hisat2 version 2.1.0. Counts were generated with featureCounts version 1.6.1.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files containing raw counts for each sample", "thymus", null, "Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.", null, "tissue:thymus|cell type:thymus cells|genotype:foxn1+/+", "GSM8392359", "GSM8392359: Dr thymus foxn1+/+ rep1; Danio rerio; RNA Seq", "GSM8392359 r1", "GSM8392359", "1", "Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP519440", null, null, "BK1_R2.fastq.gz BK1_R1.fastq.gz", "fastq fastq", 48045652026.0, 159091563.0, "GSM8392359 r1", "0:151 1:151", "A:13986882382;C:9969611893;G:10712447624;T:13374538759;N:2171368", 151, 151, null, null, 13986882382, 9969611893, 10712447624, 13374538759, 2171368, "SRX25290430", "SRS21969147", "SRA1922343", "Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics", "Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics", 2, 0.87379, 0.87656, 0.21786, 0.2191, 0.73815, 0.73975, 0.49869, 0.49808, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Germany", "2024-07-11", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [62955, "SRR13519935", "SRX9930983", "SRS8106457", "SRP303120", "PRJNA694557", "Slc20a1b is essential for hematopoietic stem/progenitor cell expansion in zebrafish", "GSE165415", "Transcriptome Analysis", "Hematopoietic stem and progenitor cells HSPCs are able to self renew and can give rise to all blood lineages throughout their lifetime yet the mechanisms regulating HSPC development have yet to be discovered. In this study we characterized a hematopoiesis defective zebrafish mutant line named smu07 which was obtained from our previous forward genetic screening and found the HSPC expansion deficiency in the mutant. Positional cloning identified that slc20a1b which encodes a sodium phosphate cotransporter contributed to the smu07 blood phenotype. Further analysis demonstrated that mutation of slc20a1b affects HSPC expansion through cell cycle arrest at G2/M phases in a cell autonomous manner. Our study shows that slc20a1b is a vital regulator for HSPC proliferation in zebrafish early hematopoiesis and provides valuable insights into HSPC development. Overall design: A mini bulk RNA Seq analysis to compare the expression profiles of wild type HSPCs and smu07 mutant HSPCs", null, "pubmed:33751369", null, "Mutant HSPCs sample2", "GSM5033015", null, "tissue:Hematopoietic Stem/Progenitor Cell|strain:AB|genotype:Smu07 mutant|age:4 dpf|facs gate:cd41:eGFP low", "Mutant HSPCs sample2", "Clean fastq files were applied to FASTQC for quality control. post quality control the clean reads were mapped to the zebrafish GRCz11 reference genome using STAR. The mapped reads were then counted using FeatureCounts from Rsubread. The counts matrix was applied to DESeq2 for normalization differentially expressed genes identification and sample to sample distance analysis. GO terms enrichment was performed using the online resource Metascape. Genome build: GRCz11 Supplementary files format and content: Normalized counts TPM matrix", "Hematopoietic Stem/Progenitor Cell", "The embryos underwent no further treatment.", "The 4 dpf larvae were grind and enzyme digested into single cells. The cells were then applied to FACS to sort the HSPCs. Approximately 500 cells from each group were collected and applied to the Discover sc WTA v2 kit Vazyme N711 03 for cell lysis reverse transcription amplification and library construction.", "Zebrafish embroys were maintained in egg water in 28 \u00b0C till 4 dpf for sacrification.", "strain:AB|genotype:Smu07 mutant|age:4 dpf|facs gate:cd41:eGFP low", "GSM5033015", "GSM5033015: Mutant HSPCs sample2; Danio rerio; RNA Seq", "GSM5033015", null, "1", "The 4 dpf larvae were grind and enzyme digested into single cells. The cells were then applied to FACS to sort the HSPCs. Approximately 500 cells from each group were collected and applied to the Discover sc WTA v2 kit Vazyme N711 03 for cell lysis reverse transcription amplification and library construction.", "GEO Accession:GSM5033015", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303120", null, null, "mut_s2_1.fq.gz mut_s2_2.fq.gz", "fastq fastq", 26776953600.0, 89256512.0, "GSM5033015 r1", "0:150 1:150", "A:6950803865;C:6328522725;G:6423534554;T:7073865657;N:226799", 150, 150, null, null, 6950803865, 6328522725, 6423534554, 7073865657, 226799, "SRX9930983", "SRS8106457", "SRA1187446", "GEO", "South China University of Technology", 2, 0.94573, 0.94677, 0.11184, 0.11217, 0.77546, 0.77644, 0.55902, 0.56264, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-25", "Larval", "Larval", "Blood", "Hematopoietic System"], [62956, "SRR13519934", "SRX9930982", "SRS8106456", "SRP303120", "PRJNA694557", "Slc20a1b is essential for hematopoietic stem/progenitor cell expansion in zebrafish", "GSE165415", "Transcriptome Analysis", "Hematopoietic stem and progenitor cells HSPCs are able to self renew and can give rise to all blood lineages throughout their lifetime yet the mechanisms regulating HSPC development have yet to be discovered. In this study we characterized a hematopoiesis defective zebrafish mutant line named smu07 which was obtained from our previous forward genetic screening and found the HSPC expansion deficiency in the mutant. Positional cloning identified that slc20a1b which encodes a sodium phosphate cotransporter contributed to the smu07 blood phenotype. Further analysis demonstrated that mutation of slc20a1b affects HSPC expansion through cell cycle arrest at G2/M phases in a cell autonomous manner. Our study shows that slc20a1b is a vital regulator for HSPC proliferation in zebrafish early hematopoiesis and provides valuable insights into HSPC development. Overall design: A mini bulk RNA Seq analysis to compare the expression profiles of wild type HSPCs and smu07 mutant HSPCs", null, "pubmed:33751369", null, "Mutant HSPCs sample1", "GSM5033014", null, "tissue:Hematopoietic Stem/Progenitor Cell|strain:AB|genotype:Smu07 mutant|age:4 dpf|facs gate:cd41:eGFP low", "Mutant HSPCs sample1", "Clean fastq files were applied to FASTQC for quality control. post quality control the clean reads were mapped to the zebrafish GRCz11 reference genome using STAR. The mapped reads were then counted using FeatureCounts from Rsubread. The counts matrix was applied to DESeq2 for normalization differentially expressed genes identification and sample to sample distance analysis. GO terms enrichment was performed using the online resource Metascape. Genome build: GRCz11 Supplementary files format and content: Normalized counts TPM matrix", "Hematopoietic Stem/Progenitor Cell", "The embryos underwent no further treatment.", "The 4 dpf larvae were grind and enzyme digested into single cells. The cells were then applied to FACS to sort the HSPCs. Approximately 500 cells from each group were collected and applied to the Discover sc WTA v2 kit Vazyme N711 03 for cell lysis reverse transcription amplification and library construction.", "Zebrafish embroys were maintained in egg water in 28 \u00b0C till 4 dpf for sacrification.", "strain:AB|genotype:Smu07 mutant|age:4 dpf|facs gate:cd41:eGFP low", "GSM5033014", "GSM5033014: Mutant HSPCs sample1; Danio rerio; RNA Seq", "GSM5033014", null, "1", "The 4 dpf larvae were grind and enzyme digested into single cells. The cells were then applied to FACS to sort the HSPCs. Approximately 500 cells from each group were collected and applied to the Discover sc WTA v2 kit Vazyme N711 03 for cell lysis reverse transcription amplification and library construction.", "GEO Accession:GSM5033014", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303120", null, null, "mut_s1_1.fq.gz mut_s1_2.fq.gz", "fastq fastq", 22228055400.0, 74093518.0, "GSM5033014 r1", "0:150 1:150", "A:5829080820;C:5209630175;G:5237139228;T:5951411290;N:793887", 150, 150, null, null, 5829080820, 5209630175, 5237139228, 5951411290, 793887, "SRX9930982", "SRS8106456", "SRA1187446", "GEO", "South China University of Technology", 2, 0.94324, 0.94335, 0.10823, 0.1086, 0.7713, 0.77118, 0.57437, 0.5727, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-25", "Larval", "Larval", "Blood", "Hematopoietic System"], [62957, "SRR13519933", "SRX9930981", "SRS8106455", "SRP303120", "PRJNA694557", "Slc20a1b is essential for hematopoietic stem/progenitor cell expansion in zebrafish", "GSE165415", "Transcriptome Analysis", "Hematopoietic stem and progenitor cells HSPCs are able to self renew and can give rise to all blood lineages throughout their lifetime yet the mechanisms regulating HSPC development have yet to be discovered. In this study we characterized a hematopoiesis defective zebrafish mutant line named smu07 which was obtained from our previous forward genetic screening and found the HSPC expansion deficiency in the mutant. Positional cloning identified that slc20a1b which encodes a sodium phosphate cotransporter contributed to the smu07 blood phenotype. Further analysis demonstrated that mutation of slc20a1b affects HSPC expansion through cell cycle arrest at G2/M phases in a cell autonomous manner. Our study shows that slc20a1b is a vital regulator for HSPC proliferation in zebrafish early hematopoiesis and provides valuable insights into HSPC development. Overall design: A mini bulk RNA Seq analysis to compare the expression profiles of wild type HSPCs and smu07 mutant HSPCs", null, "pubmed:33751369", null, "Sibling HSPCs sample2", "GSM5033013", null, "tissue:Hematopoietic Stem/Progenitor Cell|strain:AB|genotype:Sibling|age:4 dpf|facs gate:cd41:eGFP low", "Sibling HSPCs sample2", "Clean fastq files were applied to FASTQC for quality control. post quality control the clean reads were mapped to the zebrafish GRCz11 reference genome using STAR. The mapped reads were then counted using FeatureCounts from Rsubread. The counts matrix was applied to DESeq2 for normalization differentially expressed genes identification and sample to sample distance analysis. GO terms enrichment was performed using the online resource Metascape. Genome build: GRCz11 Supplementary files format and content: Normalized counts TPM matrix", "Hematopoietic Stem/Progenitor Cell", "The embryos underwent no further treatment.", "The 4 dpf larvae were grind and enzyme digested into single cells. The cells were then applied to FACS to sort the HSPCs. Approximately 500 cells from each group were collected and applied to the Discover sc WTA v2 kit Vazyme N711 03 for cell lysis reverse transcription amplification and library construction.", "Zebrafish embroys were maintained in egg water in 28 \u00b0C till 4 dpf for sacrification.", "strain:AB|genotype:Sibling|age:4 dpf|facs gate:cd41:eGFP low", "GSM5033013", "GSM5033013: Sibling HSPCs sample2; Danio rerio; RNA Seq", "GSM5033013", null, "1", "The 4 dpf larvae were grind and enzyme digested into single cells. The cells were then applied to FACS to sort the HSPCs. Approximately 500 cells from each group were collected and applied to the Discover sc WTA v2 kit Vazyme N711 03 for cell lysis reverse transcription amplification and library construction.", "GEO Accession:GSM5033013", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303120", null, null, "sib_s2_1.fq.gz sib_s2_2.fq.gz", "fastq fastq", 18434286000.0, 61447620.0, "GSM5033013 r1", "0:150 1:150", "A:4750576966;C:4455099026;G:4347017589;T:4881140912;N:451507", 150, 150, null, null, 4750576966, 4455099026, 4347017589, 4881140912, 451507, "SRX9930981", "SRS8106455", "SRA1187446", "GEO", "South China University of Technology", 2, 0.95734, 0.95687, 0.07293, 0.07264, 0.77863, 0.77808, 0.53586, 0.5353, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-25", "Larval", "Larval", "Blood", "Hematopoietic System"], [62958, "SRR13519932", "SRX9930980", "SRS8106454", "SRP303120", "PRJNA694557", "Slc20a1b is essential for hematopoietic stem/progenitor cell expansion in zebrafish", "GSE165415", "Transcriptome Analysis", "Hematopoietic stem and progenitor cells HSPCs are able to self renew and can give rise to all blood lineages throughout their lifetime yet the mechanisms regulating HSPC development have yet to be discovered. In this study we characterized a hematopoiesis defective zebrafish mutant line named smu07 which was obtained from our previous forward genetic screening and found the HSPC expansion deficiency in the mutant. Positional cloning identified that slc20a1b which encodes a sodium phosphate cotransporter contributed to the smu07 blood phenotype. Further analysis demonstrated that mutation of slc20a1b affects HSPC expansion through cell cycle arrest at G2/M phases in a cell autonomous manner. Our study shows that slc20a1b is a vital regulator for HSPC proliferation in zebrafish early hematopoiesis and provides valuable insights into HSPC development. Overall design: A mini bulk RNA Seq analysis to compare the expression profiles of wild type HSPCs and smu07 mutant HSPCs", null, "pubmed:33751369", null, "Sibling HSPCs sample1", "GSM5033012", null, "tissue:Hematopoietic Stem/Progenitor Cell|strain:AB|genotype:Sibling|age:4 dpf|facs gate:cd41:eGFP low", "Sibling HSPCs sample1", "Clean fastq files were applied to FASTQC for quality control. post quality control the clean reads were mapped to the zebrafish GRCz11 reference genome using STAR. The mapped reads were then counted using FeatureCounts from Rsubread. The counts matrix was applied to DESeq2 for normalization differentially expressed genes identification and sample to sample distance analysis. GO terms enrichment was performed using the online resource Metascape. Genome build: GRCz11 Supplementary files format and content: Normalized counts TPM matrix", "Hematopoietic Stem/Progenitor Cell", "The embryos underwent no further treatment.", "The 4 dpf larvae were grind and enzyme digested into single cells. The cells were then applied to FACS to sort the HSPCs. Approximately 500 cells from each group were collected and applied to the Discover sc WTA v2 kit Vazyme N711 03 for cell lysis reverse transcription amplification and library construction.", "Zebrafish embroys were maintained in egg water in 28 \u00b0C till 4 dpf for sacrification.", "strain:AB|genotype:Sibling|age:4 dpf|facs gate:cd41:eGFP low", "GSM5033012", "GSM5033012: Sibling HSPCs sample1; Danio rerio; RNA Seq", "GSM5033012", null, "1", "The 4 dpf larvae were grind and enzyme digested into single cells. The cells were then applied to FACS to sort the HSPCs. Approximately 500 cells from each group were collected and applied to the Discover sc WTA v2 kit Vazyme N711 03 for cell lysis reverse transcription amplification and library construction.", "GEO Accession:GSM5033012", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303120", null, null, "sib_s1_1.fq.gz sib_s1_2.fq.gz", "fastq fastq", 16659472500.0, 55531575.0, "GSM5033012 r1", "0:150 1:150", "A:4292010846;C:4032689463;G:3921477069;T:4412886880;N:408242", 150, 150, null, null, 4292010846, 4032689463, 3921477069, 4412886880, 408242, "SRX9930980", "SRS8106454", "SRA1187446", "GEO", "South China University of Technology", 2, 0.95812, 0.9589, 0.0691, 0.0693, 0.77944, 0.77875, 0.52349, 0.53349, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-25", "Larval", "Larval", "Blood", "Hematopoietic System"], [76522, "SRR24999166", "SRX20755041", "SRS18043618", "SRP445421", "PRJNA986547", "Znf687 recruits Brd4 Smrt complex to regulate gfi1aa expression during neutrophil development", "GSE235609", "Transcriptome Analysis", "Neutrophils are key component of the innate immune system in vertebrates. Diverse transcription factors and cofactors act in a well coordinated manner to ensure proper neutrophil development. Dysregulation of the transcriptional program triggering neutrophil differentiation is associated with various human hematologic disorders such as neutropenia neutrophilia and leukemia. In the current study we show the zinc finger protein Znf687 is a lineage specific transcription factor whose deficiency leads to an impaired neutrophil development in zebrafish. Mechanistically Znf687 functions as a negative regulator of gfi1aa a pivotal modulator in terminal granulopoiesis to regulate neutrophil maturation. Moreover we found BRD4 an important epigenetic regulator interacts with ZNF687 in neutrophils. Deficiency of brd4 results in similar defective neutrophil development as observed in znf687 mutant zebrafish. Biochemical and genetic analyses further reveal that instead of serving as a canonical transcriptional coactivator Brd4 directly interacts and bridges Znf687 and Smrt nuclear corepressor on gfi1aa gene's promoter to exert transcription repression. Overall our work not only indicates Znf687 and Brd4 are reciprocally required in promoting granulopoiesis but also provides new insights into the role of the two crucial regulators in transcriptional repression. Overall design: We found that Znf687 served as a transcription repressor.we speculated that the aberrant upregulation of certain downstream target of Znf687 would be responsible for the defective neutrophil differentiation. Then RNA sequencing RNA seq analyses were conducted in the remaining mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", null, "pubmed:38326409", null, "Tgmpx:eGFP 2", "GSM7506191", null, "source name:hematopoietic|tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:WT|treatment:control|geo loc name:missing|collection date:missing", "Tgmpx:eGFP 2", "We filter the low quality reads More than 20% of the bases qualities are lower than 10 reads with adaptors and reads with unknown bases N bases more than 5% to get the clean reads. We use fastp to filter. We use HISATv2.0.4 to do the mapping step. We mapped clean reads to reference using Bowtie2v2.2.6 and then calculate gene expression level with RSEMv1.2.12. Then we calculate pearson correlation between all samples using cor perform hierarchical clustering between all samples using hclust perform PCA analysis with all samples using princomp and draw the diagrams with ggplot2 with fuctions of R. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "hematopoietic", "mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", "RNA was extracted from sorted cells using RNeasy Micro Qiagen Manchester UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co. Ltd. Nanjing China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer\u2019s instructions.", "Wild type zebrafish without xxx were used as blank to determine the background values in GFP controls.", "tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:WT|treatment:control", "GSM7506191", "GSM7506191: Tgmpx:eGFP 2; Danio rerio; RNA Seq", "GSM7506191 r1", "GSM7506191", "1", "RNA was extracted from sorted cells using RNeasy Micro Qiagen Manchester UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co. Ltd. Nanjing China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP445421", null, null, "R21136162-qtsw-z003-mpx-11-11_combined_R1.fastq.gz R21136162-qtsw-z003-mpx-11-11_combined_R2.fastq.gz", "fastq fastq", 6391196700.0, 21303989.0, "GSM7506191 r1", "0:150 1:150", "A:1663138882;C:1355987073;G:1750924104;T:1621100160;N:46481", 150, 150, null, null, 1663138882, 1355987073, 1750924104, 1621100160, 46481, "SRX20755041", "SRS18043618", "SRA1660768", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", 2, 0.94347, 0.94088, 0.10896, 0.10794, 0.69522, 0.69824, 0.48646, 0.48484, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2023-06-22", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [76523, "SRR24999167", "SRX20755040", "SRS18043617", "SRP445421", "PRJNA986547", "Znf687 recruits Brd4 Smrt complex to regulate gfi1aa expression during neutrophil development", "GSE235609", "Transcriptome Analysis", "Neutrophils are key component of the innate immune system in vertebrates. Diverse transcription factors and cofactors act in a well coordinated manner to ensure proper neutrophil development. Dysregulation of the transcriptional program triggering neutrophil differentiation is associated with various human hematologic disorders such as neutropenia neutrophilia and leukemia. In the current study we show the zinc finger protein Znf687 is a lineage specific transcription factor whose deficiency leads to an impaired neutrophil development in zebrafish. Mechanistically Znf687 functions as a negative regulator of gfi1aa a pivotal modulator in terminal granulopoiesis to regulate neutrophil maturation. Moreover we found BRD4 an important epigenetic regulator interacts with ZNF687 in neutrophils. Deficiency of brd4 results in similar defective neutrophil development as observed in znf687 mutant zebrafish. Biochemical and genetic analyses further reveal that instead of serving as a canonical transcriptional coactivator Brd4 directly interacts and bridges Znf687 and Smrt nuclear corepressor on gfi1aa gene's promoter to exert transcription repression. Overall our work not only indicates Znf687 and Brd4 are reciprocally required in promoting granulopoiesis but also provides new insights into the role of the two crucial regulators in transcriptional repression. Overall design: We found that Znf687 served as a transcription repressor.we speculated that the aberrant upregulation of certain downstream target of Znf687 would be responsible for the defective neutrophil differentiation. Then RNA sequencing RNA seq analyses were conducted in the remaining mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", null, "pubmed:38326409", null, "Tgmpx:eGFP larvae injected with znf687a MO 1", "GSM7506192", null, "source name:hematopoietic|tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:znf687a knowdown|treatment:znf687a MO|geo loc name:missing|collection date:missing", "Tgmpx:eGFP larvae injected with znf687a MO 1", "We filter the low quality reads More than 20% of the bases qualities are lower than 10 reads with adaptors and reads with unknown bases N bases more than 5% to get the clean reads. We use fastp to filter. We use HISATv2.0.4 to do the mapping step. We mapped clean reads to reference using Bowtie2v2.2.6 and then calculate gene expression level with RSEMv1.2.12. Then we calculate pearson correlation between all samples using cor perform hierarchical clustering between all samples using hclust perform PCA analysis with all samples using princomp and draw the diagrams with ggplot2 with fuctions of R. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "hematopoietic", "mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", "RNA was extracted from sorted cells using RNeasy Micro Qiagen Manchester UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co. Ltd. Nanjing China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer\u2019s instructions.", "Wild type zebrafish without xxx were used as blank to determine the background values in GFP controls.", "tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:znf687a knowdown|treatment:znf687a MO", "GSM7506192", "GSM7506192: Tgmpx:eGFP larvae injected with znf687a MO 1; Danio rerio; RNA Seq", "GSM7506192 r1", "GSM7506192", "1", "RNA was extracted from sorted cells using RNeasy Micro Qiagen Manchester UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co. Ltd. Nanjing China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP445421", null, null, "R21136162-qtsw-z003-mo-11-10_combined_R2.fastq.gz R21136162-qtsw-z003-mo-11-10_combined_R1.fastq.gz", "fastq fastq", 5474240400.0, 18247468.0, "GSM7506192 r1", "0:150 1:150", "A:1344187663;C:1136523926;G:1697034586;T:1296453731;N:40494", 150, 150, null, null, 1344187663, 1136523926, 1697034586, 1296453731, 40494, "SRX20755040", "SRS18043617", "SRA1660768", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", 2, 0.85041, 0.8461, 0.08081, 0.07986, 0.74328, 0.746, 0.48356, 0.47751, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2023-06-22", "Multi-stage", "Multi-stage", "Blood", "Hematopoietic System"], [76524, "SRR24999168", "SRX20755039", "SRS18043616", "SRP445421", "PRJNA986547", "Znf687 recruits Brd4 Smrt complex to regulate gfi1aa expression during neutrophil development", "GSE235609", "Transcriptome Analysis", "Neutrophils are key component of the innate immune system in vertebrates. Diverse transcription factors and cofactors act in a well coordinated manner to ensure proper neutrophil development. Dysregulation of the transcriptional program triggering neutrophil differentiation is associated with various human hematologic disorders such as neutropenia neutrophilia and leukemia. In the current study we show the zinc finger protein Znf687 is a lineage specific transcription factor whose deficiency leads to an impaired neutrophil development in zebrafish. Mechanistically Znf687 functions as a negative regulator of gfi1aa a pivotal modulator in terminal granulopoiesis to regulate neutrophil maturation. Moreover we found BRD4 an important epigenetic regulator interacts with ZNF687 in neutrophils. Deficiency of brd4 results in similar defective neutrophil development as observed in znf687 mutant zebrafish. Biochemical and genetic analyses further reveal that instead of serving as a canonical transcriptional coactivator Brd4 directly interacts and bridges Znf687 and Smrt nuclear corepressor on gfi1aa gene's promoter to exert transcription repression. Overall our work not only indicates Znf687 and Brd4 are reciprocally required in promoting granulopoiesis but also provides new insights into the role of the two crucial regulators in transcriptional repression. Overall design: We found that Znf687 served as a transcription repressor.we speculated that the aberrant upregulation of certain downstream target of Znf687 would be responsible for the defective neutrophil differentiation. Then RNA sequencing RNA seq analyses were conducted in the remaining mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", null, "pubmed:38326409", null, "Tgmpx:eGFP larvae injected with znf687a MO 2", "GSM7506193", null, "source name:hematopoietic|tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:znf687a knowdown|treatment:znf7687a MO|geo loc name:missing|collection date:missing", "Tgmpx:eGFP larvae injected with znf687a MO 2", "We filter the low quality reads More than 20% of the bases qualities are lower than 10 reads with adaptors and reads with unknown bases N bases more than 5% to get the clean reads. We use fastp to filter. We use HISATv2.0.4 to do the mapping step. We mapped clean reads to reference using Bowtie2v2.2.6 and then calculate gene expression level with RSEMv1.2.12. Then we calculate pearson correlation between all samples using cor perform hierarchical clustering between all samples using hclust perform PCA analysis with all samples using princomp and draw the diagrams with ggplot2 with fuctions of R. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "hematopoietic", "mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", "RNA was extracted from sorted cells using RNeasy Micro Qiagen Manchester UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co. Ltd. Nanjing China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer\u2019s instructions.", "Wild type zebrafish without xxx were used as blank to determine the background values in GFP controls.", "tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:znf687a knowdown|treatment:znf7687a MO", "GSM7506193", "GSM7506193: Tgmpx:eGFP larvae injected with znf687a MO 2; Danio rerio; RNA Seq", "GSM7506193 r1", "GSM7506193", "1", "RNA was extracted from sorted cells using RNeasy Micro Qiagen Manchester UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co. Ltd. Nanjing China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP445421", null, null, "R21136162-qtsw-z003-mo-11-11_combined_R2.fastq.gz R21136162-qtsw-z003-mo-11-11_combined_R1.fastq.gz", "fastq fastq", 7189581900.0, 23965273.0, "GSM7506193 r1", "0:150 1:150", "A:1383671914;C:1160994305;G:3299098586;T:1345763504;N:53591", 150, 150, null, null, 1383671914, 1160994305, 3299098586, 1345763504, 53591, "SRX20755039", "SRS18043616", "SRA1660768", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", 2, 0.89402, 0.8908, 0.09186, 0.09076, 0.76307, 0.76473, 0.51884, 0.5204, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2023-06-22", "Multi-stage", "Multi-stage", "Blood", "Hematopoietic System"], [76525, "SRR24999169", "SRX20755038", "SRS18043615", "SRP445421", "PRJNA986547", "Znf687 recruits Brd4 Smrt complex to regulate gfi1aa expression during neutrophil development", "GSE235609", "Transcriptome Analysis", "Neutrophils are key component of the innate immune system in vertebrates. Diverse transcription factors and cofactors act in a well coordinated manner to ensure proper neutrophil development. Dysregulation of the transcriptional program triggering neutrophil differentiation is associated with various human hematologic disorders such as neutropenia neutrophilia and leukemia. In the current study we show the zinc finger protein Znf687 is a lineage specific transcription factor whose deficiency leads to an impaired neutrophil development in zebrafish. Mechanistically Znf687 functions as a negative regulator of gfi1aa a pivotal modulator in terminal granulopoiesis to regulate neutrophil maturation. Moreover we found BRD4 an important epigenetic regulator interacts with ZNF687 in neutrophils. Deficiency of brd4 results in similar defective neutrophil development as observed in znf687 mutant zebrafish. Biochemical and genetic analyses further reveal that instead of serving as a canonical transcriptional coactivator Brd4 directly interacts and bridges Znf687 and Smrt nuclear corepressor on gfi1aa gene's promoter to exert transcription repression. Overall our work not only indicates Znf687 and Brd4 are reciprocally required in promoting granulopoiesis but also provides new insights into the role of the two crucial regulators in transcriptional repression. Overall design: We found that Znf687 served as a transcription repressor.we speculated that the aberrant upregulation of certain downstream target of Znf687 would be responsible for the defective neutrophil differentiation. Then RNA sequencing RNA seq analyses were conducted in the remaining mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", null, "pubmed:38326409", null, "Tgmpx:eGFP 1", "GSM7506190", null, "source name:hematopoietic|tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:WT|treatment:control|geo loc name:missing|collection date:missing", "Tgmpx:eGFP 1", "We filter the low quality reads More than 20% of the bases qualities are lower than 10 reads with adaptors and reads with unknown bases N bases more than 5% to get the clean reads. We use fastp to filter. We use HISATv2.0.4 to do the mapping step. We mapped clean reads to reference using Bowtie2v2.2.6 and then calculate gene expression level with RSEMv1.2.12. Then we calculate pearson correlation between all samples using cor perform hierarchical clustering between all samples using hclust perform PCA analysis with all samples using princomp and draw the diagrams with ggplot2 with fuctions of R. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "hematopoietic", "mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", "RNA was extracted from sorted cells using RNeasy Micro Qiagen Manchester UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co. Ltd. Nanjing China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer\u2019s instructions.", "Wild type zebrafish without xxx were used as blank to determine the background values in GFP controls.", "tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:WT|treatment:control", "GSM7506190", "GSM7506190: Tgmpx:eGFP 1; Danio rerio; RNA Seq", "GSM7506190 r1", "GSM7506190", "1", "RNA was extracted from sorted cells using RNeasy Micro Qiagen Manchester UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co. Ltd. Nanjing China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP445421", null, null, "R21136162-qtsw-z003-mpx-11-10_combined_R2.fastq.gz R21136162-qtsw-z003-mpx-11-10_combined_R1.fastq.gz", "fastq fastq", 7364874300.0, 24549581.0, "GSM7506190 r1", "0:150 1:150", "A:1988715009;C:1657810285;G:1778472191;T:1939822538;N:54277", 150, 150, null, null, 1988715009, 1657810285, 1778472191, 1939822538, 54277, "SRX20755038", "SRS18043615", "SRA1660768", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", 2, 0.94842, 0.94741, 0.10807, 0.10703, 0.69451, 0.69552, 0.4957, 0.49509, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2023-06-22", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [76641, "SRR25247899", "SRX20994109", "SRS18268516", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus lckmCherry cd79aGFP Population T4 Sample 53", "GSM7595974", null, "source name:Thymus|tissue:Thymus|cell type:Thymic B|genotype:lckmCherry cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus lckmCherry cd79aGFP Population T4 Sample 53", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:Thymic B|genotype:lckmCherry cd79aGFP|treatment:NA", "GSM7595974", "GSM7595974: Thymus lckmCherry cd79aGFP Population T4 Sample 53; Danio rerio; RNA Seq", "GSM7595974 r1", "GSM7595974", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "53_S65_R2_001.fastq.gz 53_S65_R1_001.fastq.gz", "fastq fastq", 10257924978.0, 33966639.0, "GSM7595974 r1", "0:151 1:151", "A:3041876002;C:1856778277;G:2077467609;T:3281762421;N:40669", 151, 151, null, null, 3041876002, 1856778277, 2077467609, 3281762421, 40669, "SRX20994109", "SRS18268516", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.74686, 0.55687, 0.09361, 0.09952, 0.88538, 0.94302, 0.6544, 0.6924, 151, 151, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76642, "SRR25247900", "SRX20994108", "SRS18268515", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus lckmCherry cd79aGFP Population T4 Sample 52", "GSM7595973", null, "source name:Thymus|tissue:Thymus|cell type:Thymic B|genotype:lckmCherry cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus lckmCherry cd79aGFP Population T4 Sample 52", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:Thymic B|genotype:lckmCherry cd79aGFP|treatment:NA", "GSM7595973", "GSM7595973: Thymus lckmCherry cd79aGFP Population T4 Sample 52; Danio rerio; RNA Seq", "GSM7595973 r1", "GSM7595973", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "52_S64_R1_001.fastq.gz 52_S64_R2_001.fastq.gz", "fastq fastq", 10369663770.0, 34336635.0, "GSM7595973 r1", "0:151 1:151", "A:3082270824;C:1842032766;G:2098848870;T:3346470075;N:41235", 151, 151, null, null, 3082270824, 1842032766, 2098848870, 3346470075, 41235, "SRX20994108", "SRS18268515", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.7463, 0.55849, 0.12388, 0.14088, 0.88028, 0.94369, 0.6854, 0.70968, 151, 151, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76643, "SRR25247901", "SRX20994107", "SRS18268513", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus lckmCherry cd79aGFP Population T4 Sample 51", "GSM7595972", null, "source name:Thymus|tissue:Thymus|cell type:Thymic B|genotype:lckmCherry cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus lckmCherry cd79aGFP Population T4 Sample 51", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:Thymic B|genotype:lckmCherry cd79aGFP|treatment:NA", "GSM7595972", "GSM7595972: Thymus lckmCherry cd79aGFP Population T4 Sample 51; Danio rerio; RNA Seq", "GSM7595972 r1", "GSM7595972", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "51_S63_R2_001.fastq.gz 51_S63_R1_001.fastq.gz", "fastq fastq", 10986483972.0, 36379086.0, "GSM7595972 r1", "0:151 1:151", "A:3203989538;C:2032991258;G:2291606935;T:3457852653;N:43588", 151, 151, null, null, 3203989538, 2032991258, 2291606935, 3457852653, 43588, "SRX20994107", "SRS18268513", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.75607, 0.57028, 0.09825, 0.09786, 0.87992, 0.93795, 0.66505, 0.68991, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76644, "SRR25247905", "SRX20994106", "SRS18268514", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus lckmCherry cd79aGFP Population T2 Sample 50", "GSM7595971", null, "source name:Thymus|tissue:Thymus|cell type:T Stage IV|genotype:lckmCherry cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus lckmCherry cd79aGFP Population T2 Sample 50", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:T Stage IV|genotype:lckmCherry cd79aGFP|treatment:NA", "GSM7595971", "GSM7595971: Thymus lckmCherry cd79aGFP Population T2 Sample 50; Danio rerio; RNA Seq", "GSM7595971 r1", "GSM7595971", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "50_S62_R1_001.fastq.gz 50_S62_R2_001.fastq.gz", "fastq fastq", 11149582998.0, 36919149.0, "GSM7595971 r1", "0:151 1:151", "A:3234571276;C:2073976116;G:2356352649;T:3484638408;N:44549", 151, 151, null, null, 3234571276, 2073976116, 2356352649, 3484638408, 44549, "SRX20994106", "SRS18268514", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.7664, 0.58289, 0.1324, 0.11697, 0.89181, 0.94119, 0.60945, 0.65676, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76645, "SRR25247902", "SRX20994105", "SRS18268512", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus lckmCherry cd79aGFP Population T2 Sample 49", "GSM7595970", null, "source name:Thymus|tissue:Thymus|cell type:T Stage IV|genotype:lckmCherry cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus lckmCherry cd79aGFP Population T2 Sample 49", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:T Stage IV|genotype:lckmCherry cd79aGFP|treatment:NA", "GSM7595970", "GSM7595970: Thymus lckmCherry cd79aGFP Population T2 Sample 49; Danio rerio; RNA Seq", "GSM7595970 r1", "GSM7595970", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "49_S61_R1_001.fastq.gz 49_S61_R2_001.fastq.gz", "fastq fastq", 9322695908.0, 30869854.0, "GSM7595970 r1", "0:151 1:151", "A:2726922200;C:1719173931;G:1967587692;T:2908975055;N:37030", 151, 151, null, null, 2726922200, 1719173931, 1967587692, 2908975055, 37030, "SRX20994105", "SRS18268512", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.7069, 0.50745, 0.13643, 0.11444, 0.88562, 0.93415, 0.61812, 0.62999, 151, 151, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76646, "SRR25247903", "SRX20994104", "SRS18268510", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus lckmCherry cd79aGFP Population T2 Sample 48", "GSM7595969", null, "source name:Thymus|tissue:Thymus|cell type:T Stage IV|genotype:lckmCherry cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus lckmCherry cd79aGFP Population T2 Sample 48", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:T Stage IV|genotype:lckmCherry cd79aGFP|treatment:NA", "GSM7595969", "GSM7595969: Thymus lckmCherry cd79aGFP Population T2 Sample 48; Danio rerio; RNA Seq", "GSM7595969 r1", "GSM7595969", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "48_S60_R1_001.fastq.gz 48_S60_R2_001.fastq.gz", "fastq fastq", 7830804432.0, 25929816.0, "GSM7595969 r1", "0:151 1:151", "A:2320164600;C:1418924520;G:1593915842;T:2497768242;N:31228", 151, 151, null, null, 2320164600, 1418924520, 1593915842, 2497768242, 31228, "SRX20994104", "SRS18268510", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.74989, 0.56664, 0.13383, 0.11897, 0.86947, 0.92626, 0.63359, 0.63884, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76647, "SRR25247904", "SRX20994103", "SRS18268511", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus lckmCherry cd79aGFP Population T1 Sample 47", "GSM7595968", null, "source name:Thymus|tissue:Thymus|cell type:T State III|genotype:lckmCherry cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus lckmCherry cd79aGFP Population T1 Sample 47", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:T State III|genotype:lckmCherry cd79aGFP|treatment:NA", "GSM7595968", "GSM7595968: Thymus lckmCherry cd79aGFP Population T1 Sample 47; Danio rerio; RNA Seq", "GSM7595968 r1", "GSM7595968", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "47_S59_R1_001.fastq.gz 47_S59_R2_001.fastq.gz", "fastq fastq", 8746939552.0, 28963376.0, "GSM7595968 r1", "0:151 1:151", "A:2581719668;C:1603400764;G:1776556616;T:2785228356;N:34148", 151, 151, null, null, 2581719668, 1603400764, 1776556616, 2785228356, 34148, "SRX20994103", "SRS18268511", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.74197, 0.56047, 0.10187, 0.099, 0.88481, 0.93701, 0.67376, 0.69505, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76648, "SRR25247906", "SRX20994102", "SRS18268509", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus lckmCherry cd79aGFP Population T1 Sample 46", "GSM7595967", null, "source name:Thymus|tissue:Thymus|cell type:T State III|genotype:lckmCherry cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus lckmCherry cd79aGFP Population T1 Sample 46", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:T State III|genotype:lckmCherry cd79aGFP|treatment:NA", "GSM7595967", "GSM7595967: Thymus lckmCherry cd79aGFP Population T1 Sample 46; Danio rerio; RNA Seq", "GSM7595967 r1", "GSM7595967", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "46_S58_R2_001.fastq.gz 46_S58_R1_001.fastq.gz", "fastq fastq", 11602233886.0, 38417993.0, "GSM7595967 r1", "0:151 1:151", "A:3413897763;C:2146046716;G:2373195191;T:3669047894;N:46322", 151, 151, null, null, 3413897763, 2146046716, 2373195191, 3669047894, 46322, "SRX20994102", "SRS18268509", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.72323, 0.53899, 0.12972, 0.13114, 0.88458, 0.93959, 0.69874, 0.72809, 151, 151, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76649, "SRR25247907", "SRX20994101", "SRS18268508", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus lckmCherry cd79aGFP Population T1 Sample 45", "GSM7595966", null, "source name:Thymus|tissue:Thymus|cell type:T State III|genotype:lckmCherry cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus lckmCherry cd79aGFP Population T1 Sample 45", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:T State III|genotype:lckmCherry cd79aGFP|treatment:NA", "GSM7595966", "GSM7595966: Thymus lckmCherry cd79aGFP Population T1 Sample 45; Danio rerio; RNA Seq", "GSM7595966 r1", "GSM7595966", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "45_S57_R1_001.fastq.gz 45_S57_R2_001.fastq.gz", "fastq fastq", 8407299480.0, 27838740.0, "GSM7595966 r1", "0:151 1:151", "A:2458010874;C:1568377940;G:1764963889;T:2615913460;N:33317", 151, 151, null, null, 2458010874, 1568377940, 1764963889, 2615913460, 33317, "SRX20994101", "SRS18268508", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.73863, 0.56362, 0.11999, 0.10773, 0.89501, 0.94418, 0.66398, 0.67575, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76657, "SRR25247915", "SRX20994093", "SRS18268500", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus rag2RFP cd79aGFP Population T4 Sample 35", "GSM7595958", null, "source name:Thymus|tissue:Thymus|cell type:Thymic B|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus rag2RFP cd79aGFP Population T4 Sample 35", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:Thymic B|genotype:rag2RFP cd79aGFP|treatment:NA", "GSM7595958", "GSM7595958: Thymus rag2RFP cd79aGFP Population T4 Sample 35; Danio rerio; RNA Seq", "GSM7595958 r1", "GSM7595958", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "35_S47_R2_001.fastq.gz 35_S47_R1_001.fastq.gz", "fastq fastq", 7950117082.0, 26324891.0, "GSM7595958 r1", "0:151 1:151", "A:2332817459;C:1484005026;G:1661277987;T:2471985200;N:31410", 151, 151, null, null, 2332817459, 1484005026, 1661277987, 2471985200, 31410, "SRX20994093", "SRS18268500", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.70931, 0.52058, 0.10349, 0.10014, 0.90481, 0.94809, 0.71184, 0.74817, 151, 151, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76658, "SRR25247916", "SRX20994092", "SRS18268498", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus rag2RFP cd79aGFP Population T4 Sample 34", "GSM7595957", null, "source name:Thymus|tissue:Thymus|cell type:Thymic B|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus rag2RFP cd79aGFP Population T4 Sample 34", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:Thymic B|genotype:rag2RFP cd79aGFP|treatment:NA", "GSM7595957", "GSM7595957: Thymus rag2RFP cd79aGFP Population T4 Sample 34; Danio rerio; RNA Seq", "GSM7595957 r1", "GSM7595957", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "34_S46_R2_001.fastq.gz 34_S46_R1_001.fastq.gz", "fastq fastq", 7966171704.0, 26378052.0, "GSM7595957 r1", "0:151 1:151", "A:2329420986;C:1477961313;G:1664561539;T:2494196526;N:31340", 151, 151, null, null, 2329420986, 1477961313, 1664561539, 2494196526, 31340, "SRX20994092", "SRS18268498", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.71845, 0.50928, 0.0957, 0.09999, 0.90384, 0.95312, 0.74113, 0.75866, 151, 151, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76659, "SRR25247917", "SRX20994091", "SRS18268499", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus rag2RFP cd79aGFP Population T4 Sample 33", "GSM7595956", null, "source name:Thymus|tissue:Thymus|cell type:Thymic B|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus rag2RFP cd79aGFP Population T4 Sample 33", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:Thymic B|genotype:rag2RFP cd79aGFP|treatment:NA", "GSM7595956", "GSM7595956: Thymus rag2RFP cd79aGFP Population T4 Sample 33; Danio rerio; RNA Seq", "GSM7595956 r1", "GSM7595956", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "33_S45_R1_001.fastq.gz 33_S45_R2_001.fastq.gz", "fastq fastq", 8314572796.0, 27531698.0, "GSM7595956 r1", "0:151 1:151", "A:2452587590;C:1535172003;G:1743148608;T:2583631469;N:33126", 151, 151, null, null, 2452587590, 1535172003, 1743148608, 2583631469, 33126, "SRX20994091", "SRS18268499", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.62571, 0.44431, 0.112, 0.09476, 0.91405, 0.9487, 0.71132, 0.74047, 151, 151, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76660, "SRR25247918", "SRX20994090", "SRS18268497", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus rag2RFP cd79aGFP Population T3 Sample 32", "GSM7595955", null, "source name:Thymus|tissue:Thymus|cell type:T Stage I|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus rag2RFP cd79aGFP Population T3 Sample 32", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:T Stage I|genotype:rag2RFP cd79aGFP|treatment:NA", "GSM7595955", "GSM7595955: Thymus rag2RFP cd79aGFP Population T3 Sample 32; Danio rerio; RNA Seq", "GSM7595955 r1", "GSM7595955", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "32_S44_R1_001.fastq.gz 32_S44_R2_001.fastq.gz", "fastq fastq", 10270435026.0, 34008063.0, "GSM7595955 r1", "0:151 1:151", "A:3072285253;C:1829169076;G:2174184861;T:3194754612;N:41224", 151, 151, null, null, 3072285253, 1829169076, 2174184861, 3194754612, 41224, "SRX20994090", "SRS18268497", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.68076, 0.52889, 0.18916, 0.16273, 0.87144, 0.9303, 0.5977, 0.60526, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76661, "SRR25247919", "SRX20994089", "SRS18268496", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus rag2RFP cd79aGFP Population T3 Sample 31", "GSM7595954", null, "source name:Thymus|tissue:Thymus|cell type:T Stage I|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus rag2RFP cd79aGFP Population T3 Sample 31", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:T Stage I|genotype:rag2RFP cd79aGFP|treatment:NA", "GSM7595954", "GSM7595954: Thymus rag2RFP cd79aGFP Population T3 Sample 31; Danio rerio; RNA Seq", "GSM7595954 r1", "GSM7595954", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "31_S43_R1_001.fastq.gz 31_S43_R2_001.fastq.gz", "fastq fastq", 8576339752.0, 28398476.0, "GSM7595954 r1", "0:151 1:151", "A:2575134911;C:1518644685;G:1746645548;T:2735880553;N:34055", 151, 151, null, null, 2575134911, 1518644685, 1746645548, 2735880553, 34055, "SRX20994089", "SRS18268496", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.75636, 0.6119, 0.26758, 0.23065, 0.86801, 0.92807, 0.60587, 0.61722, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76662, "SRR25247920", "SRX20994088", "SRS18268495", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus rag2RFP cd79aGFP Population T3 Sample 30", "GSM7595953", null, "source name:Thymus|tissue:Thymus|cell type:T Stage I|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus rag2RFP cd79aGFP Population T3 Sample 30", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:T Stage I|genotype:rag2RFP cd79aGFP|treatment:NA", "GSM7595953", "GSM7595953: Thymus rag2RFP cd79aGFP Population T3 Sample 30; Danio rerio; RNA Seq", "GSM7595953 r1", "GSM7595953", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "30_S42_R1_001.fastq.gz 30_S42_R2_001.fastq.gz", "fastq fastq", 10957925040.0, 36284520.0, "GSM7595953 r1", "0:151 1:151", "A:3260030485;C:1943181567;G:2272932117;T:3481737311;N:43560", 151, 151, null, null, 3260030485, 1943181567, 2272932117, 3481737311, 43560, "SRX20994088", "SRS18268495", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.75404, 0.62746, 0.32062, 0.27288, 0.87588, 0.93123, 0.63498, 0.66153, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76663, "SRR25247921", "SRX20994087", "SRS18268494", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus rag2RFP cd79aGFP Population T2 Sample 29", "GSM7595952", null, "source name:Thymus|tissue:Thymus|cell type:T Stage I|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus rag2RFP cd79aGFP Population T2 Sample 29", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:T Stage I|genotype:rag2RFP cd79aGFP|treatment:NA", "GSM7595952", "GSM7595952: Thymus rag2RFP cd79aGFP Population T2 Sample 29; Danio rerio; RNA Seq", "GSM7595952 r1", "GSM7595952", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "29_S41_R1_001.fastq.gz 29_S41_R2_001.fastq.gz", "fastq fastq", 10621822898.0, 35171599.0, "GSM7595952 r1", "0:151 1:151", "A:3115594114;C:1963383687;G:2242332489;T:3300470381;N:42227", 151, 151, null, null, 3115594114, 1963383687, 2242332489, 3300470381, 42227, "SRX20994087", "SRS18268494", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.71819, 0.58604, 0.20876, 0.18902, 0.88554, 0.93482, 0.62188, 0.63983, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76664, "SRR25247922", "SRX20994086", "SRS18268492", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus rag2RFP cd79aGFP Population T2 Sample 28", "GSM7595951", null, "source name:Thymus|tissue:Thymus|cell type:T Stage I|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus rag2RFP cd79aGFP Population T2 Sample 28", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:T Stage I|genotype:rag2RFP cd79aGFP|treatment:NA", "GSM7595951", "GSM7595951: Thymus rag2RFP cd79aGFP Population T2 Sample 28; Danio rerio; RNA Seq", "GSM7595951 r1", "GSM7595951", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "28_S40_R2_001.fastq.gz 28_S40_R1_001.fastq.gz", "fastq fastq", 8727889694.0, 28900297.0, "GSM7595951 r1", "0:151 1:151", "A:2547391532;C:1595452476;G:1834559014;T:2750452130;N:34542", 151, 151, null, null, 2547391532, 1595452476, 1834559014, 2750452130, 34542, "SRX20994086", "SRS18268492", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.74557, 0.58372, 0.26466, 0.23691, 0.88623, 0.93344, 0.65795, 0.66615, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76665, "SRR25247923", "SRX20994085", "SRS18268493", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus rag2RFP cd79aGFP Population T2 Sample 27", "GSM7595950", null, "source name:Thymus|tissue:Thymus|cell type:T Stage I|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus rag2RFP cd79aGFP Population T2 Sample 27", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:T Stage I|genotype:rag2RFP cd79aGFP|treatment:NA", "GSM7595950", "GSM7595950: Thymus rag2RFP cd79aGFP Population T2 Sample 27; Danio rerio; RNA Seq", "GSM7595950 r1", "GSM7595950", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "27_S39_R1_001.fastq.gz 27_S39_R2_001.fastq.gz", "fastq fastq", 9477428024.0, 31382212.0, "GSM7595950 r1", "0:151 1:151", "A:2824829196;C:1691241542;G:1990496690;T:2970823258;N:37338", 151, 151, null, null, 2824829196, 1691241542, 1990496690, 2970823258, 37338, "SRX20994085", "SRS18268493", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.72602, 0.56304, 0.29776, 0.23812, 0.89021, 0.93888, 0.62393, 0.62679, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76666, "SRR25247924", "SRX20994084", "SRS18268491", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus rag2RFP cd79aGFP Population T1 Sample 26", "GSM7595949", null, "source name:Thymus|tissue:Thymus|cell type:T Stage II|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus rag2RFP cd79aGFP Population T1 Sample 26", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:T Stage II|genotype:rag2RFP cd79aGFP|treatment:NA", "GSM7595949", "GSM7595949: Thymus rag2RFP cd79aGFP Population T1 Sample 26; Danio rerio; RNA Seq", "GSM7595949 r1", "GSM7595949", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "26_S38_R1_001.fastq.gz 26_S38_R2_001.fastq.gz", "fastq fastq", 9995699586.0, 33098343.0, "GSM7595949 r1", "0:151 1:151", "A:2895036004;C:1859983984;G:2130779126;T:3109860999;N:39473", 151, 151, null, null, 2895036004, 1859983984, 2130779126, 3109860999, 39473, "SRX20994084", "SRS18268491", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.71196, 0.53328, 0.13463, 0.12387, 0.8761, 0.93111, 0.60964, 0.62685, 151, 151, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76667, "SRR25247928", "SRX20994083", "SRS18268490", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus rag2RFP cd79aGFP Population T1 Sample 25", "GSM7595948", null, "source name:Thymus|tissue:Thymus|cell type:T Stage II|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus rag2RFP cd79aGFP Population T1 Sample 25", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:T Stage II|genotype:rag2RFP cd79aGFP|treatment:NA", "GSM7595948", "GSM7595948: Thymus rag2RFP cd79aGFP Population T1 Sample 25; Danio rerio; RNA Seq", "GSM7595948 r1", "GSM7595948", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "25_S37_R1_001.fastq.gz 25_S37_R2_001.fastq.gz", "fastq fastq", 8574030660.0, 28390830.0, "GSM7595948 r1", "0:151 1:151", "A:2488813358;C:1589002672;G:1801315676;T:2694865137;N:33817", 151, 151, null, null, 2488813358, 1589002672, 1801315676, 2694865137, 33817, "SRX20994083", "SRS18268490", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.76128, 0.60104, 0.2036, 0.19091, 0.86896, 0.92368, 0.63325, 0.64052, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76668, "SRR25247925", "SRX20994082", "SRS18268489", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus rag2RFP cd79aGFP Population T1 Sample 24", "GSM7595947", null, "source name:Thymus|tissue:Thymus|cell type:T Stage II|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus rag2RFP cd79aGFP Population T1 Sample 24", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:T Stage II|genotype:rag2RFP cd79aGFP|treatment:NA", "GSM7595947", "GSM7595947: Thymus rag2RFP cd79aGFP Population T1 Sample 24; Danio rerio; RNA Seq", "GSM7595947 r1", "GSM7595947", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "24_S36_R1_001.fastq.gz 24_S36_R2_001.fastq.gz", "fastq fastq", 10245271178.0, 33924739.0, "GSM7595947 r1", "0:151 1:151", "A:3027828661;C:1881531100;G:2109776614;T:3226094586;N:40217", 151, 151, null, null, 3027828661, 1881531100, 2109776614, 3226094586, 40217, "SRX20994082", "SRS18268489", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.74318, 0.57154, 0.19699, 0.18085, 0.87008, 0.92683, 0.60011, 0.60753, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76672, "SRR25247930", "SRX20994078", "SRS18268485", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus lckmCherry cd79bGFP Population T4 Sample 20", "GSM7595943", null, "source name:Thymus|tissue:Thymus|cell type:Thymic B|genotype:lckmCherry cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus lckmCherry cd79bGFP Population T4 Sample 20", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:Thymic B|genotype:lckmCherry cd79bGFP|treatment:NA", "GSM7595943", "GSM7595943: Thymus lckmCherry cd79bGFP Population T4 Sample 20; Danio rerio; RNA Seq", "GSM7595943 r1", "GSM7595943", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "20_S32_R1_001.fastq.gz 20_S32_R2_001.fastq.gz", "fastq fastq", 7357232796.0, 24361698.0, "GSM7595943 r1", "0:151 1:151", "A:2156745950;C:1361406858;G:1502397402;T:2336653301;N:29285", 151, 151, null, null, 2156745950, 1361406858, 1502397402, 2336653301, 29285, "SRX20994078", "SRS18268485", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.76466, 0.59032, 0.13633, 0.14407, 0.89457, 0.94126, 0.70613, 0.73475, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76673, "SRR25247931", "SRX20994077", "SRS18268484", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus lckmCherry cd79bGFP Population T4 Sample 19", "GSM7595942", null, "source name:Thymus|tissue:Thymus|cell type:Thymic B|genotype:lckmCherry cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus lckmCherry cd79bGFP Population T4 Sample 19", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:Thymic B|genotype:lckmCherry cd79bGFP|treatment:NA", "GSM7595942", "GSM7595942: Thymus lckmCherry cd79bGFP Population T4 Sample 19; Danio rerio; RNA Seq", "GSM7595942 r1", "GSM7595942", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "19_S31_R1_001.fastq.gz 19_S31_R2_001.fastq.gz", "fastq fastq", 7835569992.0, 25945596.0, "GSM7595942 r1", "0:151 1:151", "A:2285864595;C:1463161267;G:1656089782;T:2430423318;N:31030", 151, 151, null, null, 2285864595, 1463161267, 1656089782, 2430423318, 31030, "SRX20994077", "SRS18268484", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.68242, 0.50364, 0.13384, 0.12452, 0.91192, 0.94803, 0.71089, 0.72547, 151, 151, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76685, "SRR25247942", "SRX20994065", "SRS18268472", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus rag2RFP cd79bGFP Population T4 Sample 6", "GSM7595930", null, "source name:Thymus|tissue:Thymus|cell type:Thymic B|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus rag2RFP cd79bGFP Population T4 Sample 6", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:Thymic B|genotype:rag2RFP cd79bGFP|treatment:NA", "GSM7595930", "GSM7595930: Thymus rag2RFP cd79bGFP Population T4 Sample 6; Danio rerio; RNA Seq", "GSM7595930 r1", "GSM7595930", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "6_S18_R1_001.fastq.gz 6_S18_R2_001.fastq.gz", "fastq fastq", 8390217454.0, 27782177.0, "GSM7595930 r1", "0:151 1:151", "A:2421221360;C:1601232886;G:1787641759;T:2580087936;N:33513", 151, 151, null, null, 2421221360, 1601232886, 1787641759, 2580087936, 33513, "SRX20994065", "SRS18268472", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.69069, 0.52877, 0.14308, 0.13948, 0.91693, 0.94724, 0.72517, 0.38475, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76686, "SRR25247943", "SRX20994064", "SRS18268471", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus rag2RFP cd79bGFP Population T4 Sample 5", "GSM7595929", null, "source name:Thymus|tissue:Thymus|cell type:Thymic B|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus rag2RFP cd79bGFP Population T4 Sample 5", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:Thymic B|genotype:rag2RFP cd79bGFP|treatment:NA", "GSM7595929", "GSM7595929: Thymus rag2RFP cd79bGFP Population T4 Sample 5; Danio rerio; RNA Seq", "GSM7595929 r1", "GSM7595929", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "5_S17_R1_001.fastq.gz 5_S17_R2_001.fastq.gz", "fastq fastq", 8158834114.0, 27016007.0, "GSM7595929 r1", "0:151 1:151", "A:2339327280;C:1558094669;G:1747369217;T:2514010546;N:32402", 151, 151, null, null, 2339327280, 1558094669, 1747369217, 2514010546, 32402, "SRX20994064", "SRS18268471", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.65335, 0.48523, 0.15841, 0.15278, 0.92368, 0.95177, 0.6743, 0.67965, 151, 151, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76687, "SRR25247945", "SRX20994063", "SRS18268470", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus rag2RFP cd79bGFP Population T4 Sample 4", "GSM7595928", null, "source name:Thymus|tissue:Thymus|cell type:Thymic B|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus rag2RFP cd79bGFP Population T4 Sample 4", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:Thymic B|genotype:rag2RFP cd79bGFP|treatment:NA", "GSM7595928", "GSM7595928: Thymus rag2RFP cd79bGFP Population T4 Sample 4; Danio rerio; RNA Seq", "GSM7595928 r1", "GSM7595928", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "4_S16_R1_001.fastq.gz 4_S16_R2_001.fastq.gz", "fastq fastq", 8704163064.0, 28821732.0, "GSM7595928 r1", "0:151 1:151", "A:2466210983;C:1690333059;G:1912063529;T:2635521209;N:34284", 151, 151, null, null, 2466210983, 1690333059, 1912063529, 2635521209, 34284, "SRX20994063", "SRS18268470", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.54845, 0.35725, 0.13255, 0.1049, 0.9445, 0.96327, 0.66031, 0.66937, 151, 151, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76688, "SRR25247946", "SRX20994062", "SRS18268469", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus rag2RFP cd79bGFP Population T1 Sample 3", "GSM7595927", null, "source name:Thymus|tissue:Thymus|cell type:T Stage II|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus rag2RFP cd79bGFP Population T1 Sample 3", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:T Stage II|genotype:rag2RFP cd79bGFP|treatment:NA", "GSM7595927", "GSM7595927: Thymus rag2RFP cd79bGFP Population T1 Sample 3; Danio rerio; RNA Seq", "GSM7595927 r1", "GSM7595927", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "3_S15_R1_001.fastq.gz 3_S15_R2_001.fastq.gz", "fastq fastq", 9629450294.0, 31885597.0, "GSM7595927 r1", "0:151 1:151", "A:2813374436;C:1804435410;G:2009975925;T:3001626142;N:38381", 151, 151, null, null, 2813374436, 1804435410, 2009975925, 3001626142, 38381, "SRX20994062", "SRS18268469", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.6865, 0.47098, 0.18726, 0.14724, 0.88349, 0.93563, 0.63844, 0.65717, 151, 151, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76689, "SRR25247947", "SRX20994061", "SRS18268468", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus rag2RFP cd79bGFP Population T1 Sample 2", "GSM7595926", null, "source name:Thymus|tissue:Thymus|cell type:T Stage II|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus rag2RFP cd79bGFP Population T1 Sample 2", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:T Stage II|genotype:rag2RFP cd79bGFP|treatment:NA", "GSM7595926", "GSM7595926: Thymus rag2RFP cd79bGFP Population T1 Sample 2; Danio rerio; RNA Seq", "GSM7595926 r1", "GSM7595926", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "2_S14_R1_001.fastq.gz 2_S14_R2_001.fastq.gz", "fastq fastq", 9283788946.0, 30741023.0, "GSM7595926 r1", "0:151 1:151", "A:2741738440;C:1702138319;G:1938033936;T:2901841449;N:36802", 151, 151, null, null, 2741738440, 1702138319, 1938033936, 2901841449, 36802, "SRX20994061", "SRS18268468", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.72627, 0.59001, 0.22607, 0.20684, 0.88556, 0.93249, 0.65227, 0.66481, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [76690, "SRR25247948", "SRX20994060", "SRS18268467", "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 \u00d7 cd79a:GFP rag2:RFP \u00d7 cd79b:GFP cd79a:GFP \u00d7 lck:mCherry and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Thymus rag2RFP cd79bGFP Population T1 Sample 1", "GSM7595925", null, "source name:Thymus|tissue:Thymus|cell type:T Stage II|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing", "Thymus rag2RFP cd79bGFP Population T1 Sample 1", "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", "Thymus", null, "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\u2019 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:Thymus|cell type:T Stage II|genotype:rag2RFP cd79bGFP|treatment:NA", "GSM7595925", "GSM7595925: Thymus rag2RFP cd79bGFP Population T1 Sample 1; Danio rerio; RNA Seq", "GSM7595925 r1", "GSM7595925", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "loader:fastq load.py", "1_S13_R1_001.fastq.gz 1_S13_R2_001.fastq.gz", "fastq fastq", 9464822242.0, 31340471.0, "GSM7595925 r1", "0:151 1:151", "A:2638585573;C:1886184090;G:2274314822;T:2665699767;N:37990", 151, 151, null, null, 2638585573, 1886184090, 2274314822, 2665699767, 37990, "SRX20994060", "SRS18268467", "SRA1671790", "Pediatrics, University of Oklahoma Health Sciences Center", "Pediatrics, University of Oklahoma Health Sciences Center", 2, 0.59028, 0.41513, 0.22607, 0.21014, 0.89134, 0.94298, 0.64355, 0.60145, 151, 151, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"]], "truncated": false, "filtered_table_rows_count": 59, "expanded_columns": [], "expandable_columns": [], "columns": ["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", 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