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53 rows where experiment.library_selection = "cDNA", technology = "bulk" and tissue_curation_coarse = "Hematopoietic System"

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devstage_curation 5

devstage_curation_coarse 4

tissue_curation 2

tissue_curation_coarse 1

  • Hematopoietic System · 53 ✖

technology 1

  • bulk · 53 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • cDNA · 53 ✖

experiment.library_layout 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
28902 28902 SRR26827532 SRX22524052 SRS19535497 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.       vein endothelium cells Day5 rep2 GSM7899809   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≤20 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 “ rna strandness RF” 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   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.   tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment GSM7899809 GSM7899809: vein endothelium cells Day5 rep2; Danio rerio; RNA Seq GSM7899809 r1 GSM7899809 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471831   loader:fastq load.py vein_endothelium_cells-2_1.fq.gz vein_endothelium_cells-2_2.fq.gz fastq fastq 9110989800.0 30369966.0 GSM7899809 r1 0:150 1:150 A:2454542720;C:2090617752;G:2126374129;T:2439172440;N:282759 150 150     2454542720 2090617752 2126374129 2439172440 282759 SRX22524052 SRS19535497 SRA1750986 South China University of Technology South China University of Technology 2 0.89413 0.89048 0.1507 0.14922 0.78466 0.78496 0.5263 0.5335 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   China 2023-11-14 Larval Larval Blood Hematopoietic System
28903 28903 SRR26827533 SRX22524051 SRS19535496 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.       vein endothelium cells Day5 rep1 GSM7899808   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≤20 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 “ rna strandness RF” 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   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.   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. Guangzhou China.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471831   loader:fastq load.py vein_endothelium_cells-1_2.fq.gz vein_endothelium_cells-1_1.fq.gz fastq fastq 8585973300.0 28619911.0 GSM7899808 r1 0:150 1:150 A:2253650188;C:2015841518;G:2037568162;T:2278266858;N:646574 150 150     2253650188 2015841518 2037568162 2278266858 646574 SRX22524051 SRS19535496 SRA1750986 South China University of Technology South China University of Technology 2 0.8876 0.88392 0.14777 0.14719 0.78969 0.79038 0.53142 0.53136 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   China 2023-11-14 Larval Larval Blood Hematopoietic System
28904 28904 SRR26827534 SRX22524050 SRS19535495 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.       non vein endothelium cells Control Day5 rep2 GSM7899807   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≤20 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 “ rna strandness RF” 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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471831   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     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   China 2023-11-14 Larval Larval Blood Hematopoietic System
28905 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.       non vein endothelium cells Control Day5 rep1 GSM7899806   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≤20 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 “ rna strandness RF” 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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471831   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     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   China 2023-11-14 Larval Larval Blood Hematopoietic System
30018 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.       hamp / 36 hpf blood zebrafish hamp / 36 hpf blood replicate 3   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                 RNA seq hamp / 36 hpf blood replicate 3 B 6 B 6 bulk RNA seq     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     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     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   China 2024-02-16 Pharyngula Embryo Blood Hematopoietic System
30019 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.       hamp / 36 hpf blood zebrafish hamp / 36 hpf blood replicate 2   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                 RNA seq hamp / 36 hpf blood replicate 2 B 5 B 5 bulk RNA seq     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     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     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   China 2024-02-16 Pharyngula Embryo Blood Hematopoietic System
30020 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.       hamp / 36 hpf blood zebrafish hamp / 36 hpf blood replicate 1   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                 RNA seq hamp / 36 hpf blood replicate 1 B 4 B 4 bulk RNA seq     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     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     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   China 2024-02-16 Pharyngula Embryo Blood Hematopoietic System
30021 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.       wild type 36 hpf blood zebrafish wild type 36 hpf blood replicate 3   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                 RNA seq wild type 36 hpf blood replicate 3 B 3 B 3 bulk RNA seq     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     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     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   China 2024-02-16 Pharyngula Embryo Blood Hematopoietic System
30022 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.       wild type 36 hpf blood zebrafish wild type 36 hpf blood replicate 2   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                 RNA seq wild type 36 hpf blood replicate 2 B 2 B 2 bulk RNA seq     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     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     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   China 2024-02-16 Pharyngula Embryo Blood Hematopoietic System
30023 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.       wild type 36 hpf blood zebrafish wild type 36 hpf blood replicate 1   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                 RNA seq wild type 36 hpf blood replicate 1 B 1 B 1 bulk RNA seq     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     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     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   China 2024-02-16 Pharyngula Embryo Blood Hematopoietic System
33158 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 …       Dr thymus foxn1 / rep3 GSM8392364   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP519440     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     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   Germany 2024-07-11 Undetermined Undetermined Thymus Hematopoietic System
33159 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 …       Dr thymus foxn1 / rep2 GSM8392363   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP519440     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     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   Germany 2024-07-11 Undetermined Undetermined Thymus Hematopoietic System
33160 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 …       Dr thymus foxn1 / rep1 GSM8392362   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP519440     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     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   Germany 2024-07-11 Undetermined Undetermined Thymus Hematopoietic System
33161 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 …       Dr thymus foxn1+/+ rep3 GSM8392361   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP519440     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     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   Germany 2024-07-11 Undetermined Undetermined Thymus Hematopoietic System
33162 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 …       Dr thymus foxn1+/+ rep2 GSM8392360   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP519440     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     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   Germany 2024-07-11 Undetermined Undetermined Thymus Hematopoietic System
33163 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 …       Dr thymus foxn1+/+ rep1 GSM8392359   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP519440     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     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   Germany 2024-07-11 Undetermined Undetermined Thymus Hematopoietic System
62955 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   pubmed:33751369   Mutant HSPCs sample2 GSM5033015   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 °C 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   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   SRP303120     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     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   China 2021-01-25 Larval Larval Blood Hematopoietic System
62956 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   pubmed:33751369   Mutant HSPCs sample1 GSM5033014   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 °C 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   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   SRP303120     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     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   China 2021-01-25 Larval Larval Blood Hematopoietic System
62957 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   pubmed:33751369   Sibling HSPCs sample2 GSM5033013   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 °C 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   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   SRP303120     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     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   China 2021-01-25 Larval Larval Blood Hematopoietic System
62958 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   pubmed:33751369   Sibling HSPCs sample1 GSM5033012   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 °C 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   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   SRP303120     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     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   China 2021-01-25 Larval Larval Blood Hematopoietic System
76522 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.   pubmed:38326409   Tgmpx:eGFP 2 GSM7506191   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 μg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS® 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. 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 μg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS® 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP445421     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     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   China 2023-06-22 Hatching Embryo Blood Hematopoietic System
76523 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.   pubmed:38326409   Tgmpx:eGFP larvae injected with znf687a MO 1 GSM7506192   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 μg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS® 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. 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 μg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS® 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP445421     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     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   China 2023-06-22 Multi-stage Multi-stage Blood Hematopoietic System
76524 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.   pubmed:38326409   Tgmpx:eGFP larvae injected with znf687a MO 2 GSM7506193   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 μg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS® 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. 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 μg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS® 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP445421     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     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   China 2023-06-22 Multi-stage Multi-stage Blood Hematopoietic System
76525 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.   pubmed:38326409   Tgmpx:eGFP 1 GSM7506190   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 μg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS® 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. 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 μg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS® 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP445421     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     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   China 2023-06-22 Hatching Embryo Blood Hematopoietic System
76641 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus lckmCherry cd79aGFP Population T4 Sample 53 GSM7595974   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76642 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus lckmCherry cd79aGFP Population T4 Sample 52 GSM7595973   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76643 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus lckmCherry cd79aGFP Population T4 Sample 51 GSM7595972   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76644 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus lckmCherry cd79aGFP Population T2 Sample 50 GSM7595971   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76645 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus lckmCherry cd79aGFP Population T2 Sample 49 GSM7595970   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76646 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus lckmCherry cd79aGFP Population T2 Sample 48 GSM7595969   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76647 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus lckmCherry cd79aGFP Population T1 Sample 47 GSM7595968   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76648 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus lckmCherry cd79aGFP Population T1 Sample 46 GSM7595967   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76649 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus lckmCherry cd79aGFP Population T1 Sample 45 GSM7595966   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76657 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus rag2RFP cd79aGFP Population T4 Sample 35 GSM7595958   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76658 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus rag2RFP cd79aGFP Population T4 Sample 34 GSM7595957   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76659 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus rag2RFP cd79aGFP Population T4 Sample 33 GSM7595956   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76660 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus rag2RFP cd79aGFP Population T3 Sample 32 GSM7595955   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76661 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus rag2RFP cd79aGFP Population T3 Sample 31 GSM7595954   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76662 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus rag2RFP cd79aGFP Population T3 Sample 30 GSM7595953   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76663 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus rag2RFP cd79aGFP Population T2 Sample 29 GSM7595952   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76664 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus rag2RFP cd79aGFP Population T2 Sample 28 GSM7595951   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76665 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus rag2RFP cd79aGFP Population T2 Sample 27 GSM7595950   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76666 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus rag2RFP cd79aGFP Population T1 Sample 26 GSM7595949   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76667 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus rag2RFP cd79aGFP Population T1 Sample 25 GSM7595948   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76668 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus rag2RFP cd79aGFP Population T1 Sample 24 GSM7595947   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76672 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus lckmCherry cd79bGFP Population T4 Sample 20 GSM7595943   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76673 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus lckmCherry cd79bGFP Population T4 Sample 19 GSM7595942   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76685 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus rag2RFP cd79bGFP Population T4 Sample 6 GSM7595930   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76686 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus rag2RFP cd79bGFP Population T4 Sample 5 GSM7595929   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76687 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus rag2RFP cd79bGFP Population T4 Sample 4 GSM7595928   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76688 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus rag2RFP cd79bGFP Population T1 Sample 3 GSM7595927   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76689 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus rag2RFP cd79bGFP Population T1 Sample 2 GSM7595926   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System
76690 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 × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Thymus rag2RFP cd79bGFP Population T1 Sample 1 GSM7595925   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   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue: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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   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     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   United States 2023-07-12 Undetermined Undetermined Thymus Hematopoietic System

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