{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where technology = \"bulk\", tissue_curation = \"Blood\" and tissue_curation_coarse = \"Hematopoietic System\"", "rows": [[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.", null, null, null, "vein endothelium cells  Day5 rep2", "GSM7899809", null, "source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing", "vein endothelium cells  Day5 rep2", "Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value\u226420 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built  and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with \u201c rna strandness RF\u201d and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region  a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations  using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r  project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Caudal hematopoietic tissue", null, "Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer\u2019s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.", null, "tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP471831", null, "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, null, null, 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", null, "China", "2023-11-14", "Larval", "Larval", "Blood", "Hematopoietic System"], [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.", null, null, null, "vein endothelium cells  Day5 rep1", "GSM7899808", null, "source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing", "vein endothelium cells  Day5 rep1", "Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value\u226420 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built  and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with \u201c rna strandness RF\u201d and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region  a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations  using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r  project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Caudal hematopoietic tissue", null, "Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer\u2019s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.", null, "tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment", "GSM7899808", "GSM7899808: vein endothelium cells  Day5 rep1; Danio rerio; RNA Seq", "GSM7899808 r1", "GSM7899808", "1", "Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP471831", null, "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, null, null, 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", null, "China", "2023-11-14", "Larval", "Larval", "Blood", "Hematopoietic System"], [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.", null, null, null, "non vein endothelium cells  Control  Day5 rep2", "GSM7899807", null, "source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing", "non vein endothelium cells  Control  Day5 rep2", "Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value\u226420 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built  and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with \u201c rna strandness RF\u201d and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region  a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations  using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r  project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Caudal hematopoietic tissue", null, "Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer\u2019s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.", null, "tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment", "GSM7899807", "GSM7899807: non vein endothelium cells  Control  Day5 rep2; Danio rerio; RNA Seq", "GSM7899807 r1", "GSM7899807", "1", "Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP471831", null, "loader:fastq load.py", "non-vein_endothelium_cells-2_1.fq.gz non-vein_endothelium_cells-2_2.fq.gz", "fastq fastq", 9363942600.0, 31213142.0, "GSM7899807 r1", "0:150 1:150", "A:2523111369;C:2155598161;G:2171776473;T:2513164552;N:292045", 150, 150, null, null, 2523111369, 2155598161, 2171776473, 2513164552, 292045, "SRX22524050", "SRS19535495", "SRA1750986", "South China University of Technology", "South China University of Technology", 2, 0.93879, 0.93706, 0.10971, 0.10945, 0.76721, 0.76737, 0.51346, 0.51513, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2023-11-14", "Larval", "Larval", "Blood", "Hematopoietic System"], [28905, "SRR26827535", "SRX22524049", "SRS19535494", "SRP471831", "PRJNA1040223", "The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish", "GSE247730", "Transcriptome Analysis", "Neutrophils and erythrocytes are vital to the immune system and oxygen transport  respectively. However  the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research  zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study  we showed that erythrocytes predominantly reside inside the blood vessels of the CHT  while neutrophils stay outside. Ectopic vascular endothelium  induced by Bone Morphogenetic Protein 2bBmp2b overexpression  attracts both cell types  with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter  which is specifically expressed in vein  lymphatic vessels and CHT vein endothelial cells  rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.", null, null, null, "non vein endothelium cells  Control  Day5 rep1", "GSM7899806", null, "source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing", "non vein endothelium cells  Control  Day5 rep1", "Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value\u226420 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built  and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with \u201c rna strandness RF\u201d and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region  a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations  using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r  project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Caudal hematopoietic tissue", null, "Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer\u2019s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.", null, "tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment", "GSM7899806", "GSM7899806: non vein endothelium cells  Control  Day5 rep1; Danio rerio; RNA Seq", "GSM7899806 r1", "GSM7899806", "1", "Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP471831", null, "loader:fastq load.py", "non-vein_endothelium_cells-1_1.fq.gz non-vein_endothelium_cells-1_2.fq.gz", "fastq fastq", 8396176800.0, 27987256.0, "GSM7899806 r1", "0:150 1:150", "A:2190594419;C:1990596503;G:2019391921;T:2194713332;N:880625", 150, 150, null, null, 2190594419, 1990596503, 2019391921, 2194713332, 880625, "SRX22524049", "SRS19535494", "SRA1750986", "South China University of Technology", "South China University of Technology", 2, 0.94508, 0.94385, 0.0967, 0.09697, 0.77642, 0.77632, 0.49896, 0.49962, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2023-11-14", "Larval", "Larval", "Blood", "Hematopoietic System"], [30018, "SRR27988043", "SRX23641260", "SRS20476222", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.", null, null, null, "hamp /   36 hpf blood", "zebrafish hamp /  36 hpf blood replicate 3", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:hamp knockdown|sample type:tissue sample|treatment:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  hamp /   36 hpf blood  replicate 3", "B 6", "B 6", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "KO-3_R2_001.fastq.gz KO-3_R1_001.fastq.gz", "fastq fastq", 8752665900.0, 29175553.0, "KO 3 R1 001.fastq.gz", "0:150 1:150", "A:2204170575;C:2174083961;G:2224694970;T:2149603712;N:112682", 150, 150, null, null, 2204170575, 2174083961, 2224694970, 2149603712, 112682, "SRX23641260", "SRS20476222", "SRA1803422", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.91553, 0.91645, 0.01276, 0.01288, 0.85884, 0.85839, 0.35101, 0.40996, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-02-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [30019, "SRR27988044", "SRX23641259", "SRS20476221", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.", null, null, null, "hamp /   36 hpf blood", "zebrafish hamp /  36 hpf blood replicate 2", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:hamp knockdown|sample type:tissue sample|treatment:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  hamp /   36 hpf blood  replicate 2", "B 5", "B 5", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "KO-2_R1_001.fastq.gz KO-2_R2_001.fastq.gz", "fastq fastq", 8060498700.0, 26868329.0, "KO 2 R1 001.fastq.gz", "0:150 1:150", "A:2045797336;C:1985847523;G:2035528018;T:1993222840;N:102983", 150, 150, null, null, 2045797336, 1985847523, 2035528018, 1993222840, 102983, "SRX23641259", "SRS20476221", "SRA1803422", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.9213, 0.92027, 0.0167, 0.01676, 0.8242, 0.82475, 0.41081, 0.41111, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-02-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [30020, "SRR27988045", "SRX23641258", "SRS20476220", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.", null, null, null, "hamp /   36 hpf blood", "zebrafish hamp /  36 hpf blood replicate 1", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:hamp knockdown|sample type:tissue sample|treatment:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  hamp /   36 hpf blood  replicate 1", "B 4", "B 4", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "KO-1_R1_001.fastq.gz KO-1_R2_001.fastq.gz", "fastq fastq", 8707637700.0, 29025459.0, "KO 1 R1 001.fastq.gz", "0:150 1:150", "A:2222026435;C:2133480283;G:2182087972;T:2169932447;N:110563", 150, 150, null, null, 2222026435, 2133480283, 2182087972, 2169932447, 110563, "SRX23641258", "SRS20476220", "SRA1803422", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.91531, 0.91359, 0.02185, 0.0221, 0.81213, 0.8128, 0.37868, 0.42351, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-02-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [30021, "SRR27988046", "SRX23641257", "SRS20476219", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.", null, null, null, "wild type 36 hpf blood", "zebrafish wild type 36 hpf blood replicate 3", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:wild type|sample type:tissue sample|treatment:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  wild type  36 hpf blood  replicate 3", "B 3", "B 3", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT-3_R1_001.fastq.gz WT-3_R2_001.fastq.gz", "fastq fastq", 8829371400.0, 29431238.0, "WT 3 R1 001.fastq.gz", "0:150 1:150", "A:2278837675;C:2141723937;G:2193442375;T:2215253519;N:113894", 150, 150, null, null, 2278837675, 2141723937, 2193442375, 2215253519, 113894, "SRX23641257", "SRS20476219", "SRA1803422", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.90531, 0.9043, 0.03015, 0.03017, 0.8101, 0.8112, 0.43085, 0.43002, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-02-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [30022, "SRR27988047", "SRX23641256", "SRS20476218", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.", null, null, null, "wild type 36 hpf blood", "zebrafish wild type 36 hpf blood replicate 2", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:wild type|sample type:tissue sample|treatment:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  wild type  36 hpf blood  replicate 2", "B 2", "B 2", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT-2_R1_001.fastq.gz WT-2_R2_001.fastq.gz", "fastq fastq", 7365643800.0, 24552146.0, "WT 2 R1 001.fastq.gz", "0:150 1:150", "A:1867985067;C:1819016430;G:1870006707;T:1808540769;N:94827", 150, 150, null, null, 1867985067, 1819016430, 1870006707, 1808540769, 94827, "SRX23641256", "SRS20476218", "SRA1803422", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.90612, 0.90536, 0.01714, 0.01746, 0.88109, 0.88156, 0.32469, 0.39232, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-02-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [30023, "SRR27988048", "SRX23641255", "SRS20476217", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.", null, null, null, "wild type 36 hpf blood", "zebrafish wild type 36 hpf blood replicate 1", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:wild type|sample type:tissue sample|treatment:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  wild type  36 hpf blood  replicate 1", "B 1", "B 1", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT-1_R1_001.fastq.gz WT-1_R2_001.fastq.gz", "fastq fastq", 8631863400.0, 28772878.0, "WT 1 R1 001.fastq.gz", "0:150 1:150", "A:2186212554;C:2135990723;G:2179142081;T:2130408485;N:109557", 150, 150, null, null, 2186212554, 2135990723, 2179142081, 2130408485, 109557, "SRX23641255", "SRS20476217", "SRA1803422", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.90461, 0.90281, 0.01388, 0.01365, 0.83871, 0.83895, 0.36511, 0.41074, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-02-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [62955, "SRR13519935", "SRX9930983", "SRS8106457", "SRP303120", "PRJNA694557", "Slc20a1b is essential for hematopoietic stem/progenitor cell expansion in zebrafish", "GSE165415", "Transcriptome Analysis", "Hematopoietic stem and progenitor cells HSPCs are able to self renew and can give rise to all blood lineages throughout their lifetime  yet the mechanisms regulating HSPC development have yet to be discovered. In this study  we characterized a hematopoiesis defective zebrafish mutant line named smu07  which was obtained from our previous forward genetic screening  and found the HSPC expansion deficiency in the mutant. Positional cloning identified that slc20a1b  which encodes a sodium phosphate cotransporter  contributed to the smu07 blood phenotype. Further analysis demonstrated that mutation of slc20a1b affects HSPC expansion through cell cycle arrest at G2/M phases in a cell autonomous manner. Our study shows that slc20a1b is a vital regulator for HSPC proliferation in zebrafish early hematopoiesis and provides valuable insights into HSPC development. Overall design: A mini bulk RNA Seq analysis to compare the expression profiles of wild type HSPCs and smu07 mutant HSPCs", null, "pubmed:33751369", null, "Mutant HSPCs sample2", "GSM5033015", null, "tissue:Hematopoietic Stem/Progenitor Cell|strain:AB|genotype:Smu07 mutant|age:4 dpf|facs gate:cd41:eGFP low", "Mutant HSPCs sample2", "Clean fastq files were applied to FASTQC for quality control. post quality control  the clean reads were mapped to the zebrafish GRCz11 reference genome using STAR. The mapped reads were then counted using FeatureCounts from Rsubread. The counts matrix was applied to DESeq2 for normalization  differentially expressed genes identification  and sample to sample distance analysis. GO terms enrichment was performed using the online resource Metascape. Genome build: GRCz11 Supplementary files format and content: Normalized counts TPM matrix", "Hematopoietic Stem/Progenitor Cell", "The embryos underwent no further treatment.", "The 4 dpf larvae were grind and enzyme digested into single cells. The cells were then applied to FACS to sort the HSPCs. Approximately 500  cells from each group were collected and applied to the Discover sc WTA v2 kit Vazyme  N711 03 for cell lysis  reverse transcription  amplification  and library construction.", "Zebrafish embroys were maintained in egg water in 28 \u00b0C till 4 dpf for sacrification.", "strain:AB|genotype:Smu07 mutant|age:4 dpf|facs gate:cd41:eGFP low", "GSM5033015", "GSM5033015: Mutant HSPCs sample2; Danio rerio; RNA Seq", "GSM5033015", null, "1", "The 4 dpf larvae were grind and enzyme digested into single cells. The cells were then applied to FACS to sort the HSPCs. Approximately 500  cells from each group were collected and applied to the Discover sc WTA v2 kit Vazyme  N711 03 for cell lysis  reverse transcription  amplification  and library construction.", "GEO Accession:GSM5033015", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303120", null, null, "mut_s2_1.fq.gz mut_s2_2.fq.gz", "fastq fastq", 26776953600.0, 89256512.0, "GSM5033015 r1", "0:150 1:150", "A:6950803865;C:6328522725;G:6423534554;T:7073865657;N:226799", 150, 150, null, null, 6950803865, 6328522725, 6423534554, 7073865657, 226799, "SRX9930983", "SRS8106457", "SRA1187446", "GEO", "South China University of Technology", 2, 0.94573, 0.94677, 0.11184, 0.11217, 0.77546, 0.77644, 0.55902, 0.56264, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-25", "Larval", "Larval", "Blood", "Hematopoietic System"], [62956, "SRR13519934", "SRX9930982", "SRS8106456", "SRP303120", "PRJNA694557", "Slc20a1b is essential for hematopoietic stem/progenitor cell expansion in zebrafish", "GSE165415", "Transcriptome Analysis", "Hematopoietic stem and progenitor cells HSPCs are able to self renew and can give rise to all blood lineages throughout their lifetime  yet the mechanisms regulating HSPC development have yet to be discovered. In this study  we characterized a hematopoiesis defective zebrafish mutant line named smu07  which was obtained from our previous forward genetic screening  and found the HSPC expansion deficiency in the mutant. Positional cloning identified that slc20a1b  which encodes a sodium phosphate cotransporter  contributed to the smu07 blood phenotype. Further analysis demonstrated that mutation of slc20a1b affects HSPC expansion through cell cycle arrest at G2/M phases in a cell autonomous manner. Our study shows that slc20a1b is a vital regulator for HSPC proliferation in zebrafish early hematopoiesis and provides valuable insights into HSPC development. Overall design: A mini bulk RNA Seq analysis to compare the expression profiles of wild type HSPCs and smu07 mutant HSPCs", null, "pubmed:33751369", null, "Mutant HSPCs sample1", "GSM5033014", null, "tissue:Hematopoietic Stem/Progenitor Cell|strain:AB|genotype:Smu07 mutant|age:4 dpf|facs gate:cd41:eGFP low", "Mutant HSPCs sample1", "Clean fastq files were applied to FASTQC for quality control. post quality control  the clean reads were mapped to the zebrafish GRCz11 reference genome using STAR. The mapped reads were then counted using FeatureCounts from Rsubread. The counts matrix was applied to DESeq2 for normalization  differentially expressed genes identification  and sample to sample distance analysis. GO terms enrichment was performed using the online resource Metascape. Genome build: GRCz11 Supplementary files format and content: Normalized counts TPM matrix", "Hematopoietic Stem/Progenitor Cell", "The embryos underwent no further treatment.", "The 4 dpf larvae were grind and enzyme digested into single cells. The cells were then applied to FACS to sort the HSPCs. Approximately 500  cells from each group were collected and applied to the Discover sc WTA v2 kit Vazyme  N711 03 for cell lysis  reverse transcription  amplification  and library construction.", "Zebrafish embroys were maintained in egg water in 28 \u00b0C till 4 dpf for sacrification.", "strain:AB|genotype:Smu07 mutant|age:4 dpf|facs gate:cd41:eGFP low", "GSM5033014", "GSM5033014: Mutant HSPCs sample1; Danio rerio; RNA Seq", "GSM5033014", null, "1", "The 4 dpf larvae were grind and enzyme digested into single cells. The cells were then applied to FACS to sort the HSPCs. Approximately 500  cells from each group were collected and applied to the Discover sc WTA v2 kit Vazyme  N711 03 for cell lysis  reverse transcription  amplification  and library construction.", "GEO Accession:GSM5033014", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303120", null, null, "mut_s1_1.fq.gz mut_s1_2.fq.gz", "fastq fastq", 22228055400.0, 74093518.0, "GSM5033014 r1", "0:150 1:150", "A:5829080820;C:5209630175;G:5237139228;T:5951411290;N:793887", 150, 150, null, null, 5829080820, 5209630175, 5237139228, 5951411290, 793887, "SRX9930982", "SRS8106456", "SRA1187446", "GEO", "South China University of Technology", 2, 0.94324, 0.94335, 0.10823, 0.1086, 0.7713, 0.77118, 0.57437, 0.5727, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-25", "Larval", "Larval", "Blood", "Hematopoietic System"], [62957, "SRR13519933", "SRX9930981", "SRS8106455", "SRP303120", "PRJNA694557", "Slc20a1b is essential for hematopoietic stem/progenitor cell expansion in zebrafish", "GSE165415", "Transcriptome Analysis", "Hematopoietic stem and progenitor cells HSPCs are able to self renew and can give rise to all blood lineages throughout their lifetime  yet the mechanisms regulating HSPC development have yet to be discovered. In this study  we characterized a hematopoiesis defective zebrafish mutant line named smu07  which was obtained from our previous forward genetic screening  and found the HSPC expansion deficiency in the mutant. Positional cloning identified that slc20a1b  which encodes a sodium phosphate cotransporter  contributed to the smu07 blood phenotype. Further analysis demonstrated that mutation of slc20a1b affects HSPC expansion through cell cycle arrest at G2/M phases in a cell autonomous manner. Our study shows that slc20a1b is a vital regulator for HSPC proliferation in zebrafish early hematopoiesis and provides valuable insights into HSPC development. Overall design: A mini bulk RNA Seq analysis to compare the expression profiles of wild type HSPCs and smu07 mutant HSPCs", null, "pubmed:33751369", null, "Sibling HSPCs sample2", "GSM5033013", null, "tissue:Hematopoietic Stem/Progenitor Cell|strain:AB|genotype:Sibling|age:4 dpf|facs gate:cd41:eGFP low", "Sibling HSPCs sample2", "Clean fastq files were applied to FASTQC for quality control. post quality control  the clean reads were mapped to the zebrafish GRCz11 reference genome using STAR. The mapped reads were then counted using FeatureCounts from Rsubread. The counts matrix was applied to DESeq2 for normalization  differentially expressed genes identification  and sample to sample distance analysis. GO terms enrichment was performed using the online resource Metascape. Genome build: GRCz11 Supplementary files format and content: Normalized counts TPM matrix", "Hematopoietic Stem/Progenitor Cell", "The embryos underwent no further treatment.", "The 4 dpf larvae were grind and enzyme digested into single cells. The cells were then applied to FACS to sort the HSPCs. Approximately 500  cells from each group were collected and applied to the Discover sc WTA v2 kit Vazyme  N711 03 for cell lysis  reverse transcription  amplification  and library construction.", "Zebrafish embroys were maintained in egg water in 28 \u00b0C till 4 dpf for sacrification.", "strain:AB|genotype:Sibling|age:4 dpf|facs gate:cd41:eGFP low", "GSM5033013", "GSM5033013: Sibling HSPCs sample2; Danio rerio; RNA Seq", "GSM5033013", null, "1", "The 4 dpf larvae were grind and enzyme digested into single cells. The cells were then applied to FACS to sort the HSPCs. Approximately 500  cells from each group were collected and applied to the Discover sc WTA v2 kit Vazyme  N711 03 for cell lysis  reverse transcription  amplification  and library construction.", "GEO Accession:GSM5033013", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303120", null, null, "sib_s2_1.fq.gz sib_s2_2.fq.gz", "fastq fastq", 18434286000.0, 61447620.0, "GSM5033013 r1", "0:150 1:150", "A:4750576966;C:4455099026;G:4347017589;T:4881140912;N:451507", 150, 150, null, null, 4750576966, 4455099026, 4347017589, 4881140912, 451507, "SRX9930981", "SRS8106455", "SRA1187446", "GEO", "South China University of Technology", 2, 0.95734, 0.95687, 0.07293, 0.07264, 0.77863, 0.77808, 0.53586, 0.5353, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-25", "Larval", "Larval", "Blood", "Hematopoietic System"], [62958, "SRR13519932", "SRX9930980", "SRS8106454", "SRP303120", "PRJNA694557", "Slc20a1b is essential for hematopoietic stem/progenitor cell expansion in zebrafish", "GSE165415", "Transcriptome Analysis", "Hematopoietic stem and progenitor cells HSPCs are able to self renew and can give rise to all blood lineages throughout their lifetime  yet the mechanisms regulating HSPC development have yet to be discovered. In this study  we characterized a hematopoiesis defective zebrafish mutant line named smu07  which was obtained from our previous forward genetic screening  and found the HSPC expansion deficiency in the mutant. Positional cloning identified that slc20a1b  which encodes a sodium phosphate cotransporter  contributed to the smu07 blood phenotype. Further analysis demonstrated that mutation of slc20a1b affects HSPC expansion through cell cycle arrest at G2/M phases in a cell autonomous manner. Our study shows that slc20a1b is a vital regulator for HSPC proliferation in zebrafish early hematopoiesis and provides valuable insights into HSPC development. Overall design: A mini bulk RNA Seq analysis to compare the expression profiles of wild type HSPCs and smu07 mutant HSPCs", null, "pubmed:33751369", null, "Sibling HSPCs sample1", "GSM5033012", null, "tissue:Hematopoietic Stem/Progenitor Cell|strain:AB|genotype:Sibling|age:4 dpf|facs gate:cd41:eGFP low", "Sibling HSPCs sample1", "Clean fastq files were applied to FASTQC for quality control. post quality control  the clean reads were mapped to the zebrafish GRCz11 reference genome using STAR. The mapped reads were then counted using FeatureCounts from Rsubread. The counts matrix was applied to DESeq2 for normalization  differentially expressed genes identification  and sample to sample distance analysis. GO terms enrichment was performed using the online resource Metascape. Genome build: GRCz11 Supplementary files format and content: Normalized counts TPM matrix", "Hematopoietic Stem/Progenitor Cell", "The embryos underwent no further treatment.", "The 4 dpf larvae were grind and enzyme digested into single cells. The cells were then applied to FACS to sort the HSPCs. Approximately 500  cells from each group were collected and applied to the Discover sc WTA v2 kit Vazyme  N711 03 for cell lysis  reverse transcription  amplification  and library construction.", "Zebrafish embroys were maintained in egg water in 28 \u00b0C till 4 dpf for sacrification.", "strain:AB|genotype:Sibling|age:4 dpf|facs gate:cd41:eGFP low", "GSM5033012", "GSM5033012: Sibling HSPCs sample1; Danio rerio; RNA Seq", "GSM5033012", null, "1", "The 4 dpf larvae were grind and enzyme digested into single cells. The cells were then applied to FACS to sort the HSPCs. Approximately 500  cells from each group were collected and applied to the Discover sc WTA v2 kit Vazyme  N711 03 for cell lysis  reverse transcription  amplification  and library construction.", "GEO Accession:GSM5033012", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303120", null, null, "sib_s1_1.fq.gz sib_s1_2.fq.gz", "fastq fastq", 16659472500.0, 55531575.0, "GSM5033012 r1", "0:150 1:150", "A:4292010846;C:4032689463;G:3921477069;T:4412886880;N:408242", 150, 150, null, null, 4292010846, 4032689463, 3921477069, 4412886880, 408242, "SRX9930980", "SRS8106454", "SRA1187446", "GEO", "South China University of Technology", 2, 0.95812, 0.9589, 0.0691, 0.0693, 0.77944, 0.77875, 0.52349, 0.53349, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2021-01-25", "Larval", "Larval", "Blood", "Hematopoietic System"], [76522, "SRR24999166", "SRX20755041", "SRS18043618", "SRP445421", "PRJNA986547", "Znf687 recruits Brd4 Smrt complex  to regulate gfi1aa expression   during neutrophil development", "GSE235609", "Transcriptome Analysis", "Neutrophils are key component of the innate immune system in vertebrates. Diverse transcription factors and cofactors act in a well coordinated manner to ensure proper neutrophil development. Dysregulation of the transcriptional program triggering neutrophil differentiation is associated with various human hematologic disorders such as neutropenia  neutrophilia  and leukemia. In the current study we show the zinc finger protein Znf687 is a lineage specific transcription factor  whose deficiency leads to an impaired neutrophil development in zebrafish. Mechanistically  Znf687 functions as a negative regulator of gfi1aa  a pivotal modulator in terminal granulopoiesis  to regulate neutrophil maturation. Moreover  we found BRD4  an important epigenetic regulator  interacts with ZNF687 in neutrophils. Deficiency of brd4 results in similar defective neutrophil development as observed in znf687 mutant zebrafish. Biochemical and genetic analyses further reveal that instead of serving as a canonical transcriptional coactivator  Brd4 directly interacts and bridges Znf687 and Smrt nuclear corepressor on gfi1aa gene's promoter to exert transcription repression. Overall  our work not only indicates Znf687 and Brd4 are reciprocally required in promoting granulopoiesis  but also provides new insights into the role of the two crucial regulators in transcriptional repression. Overall design: We found that Znf687 served as a transcription repressor.we speculated that the aberrant upregulation of certain downstream target of Znf687 would be responsible for the defective neutrophil differentiation. Then RNA sequencing RNA seq analyses were conducted in the remaining mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", null, "pubmed:38326409", null, "Tgmpx:eGFP 2", "GSM7506191", null, "source name:hematopoietic|tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:WT|treatment:control|geo loc name:missing|collection date:missing", "Tgmpx:eGFP 2", "We filter the low quality reads More than 20% of the bases qualities are lower than 10  reads with adaptors and reads with unknown bases N bases more than 5% to get the clean reads. We use fastp to filter. We use HISATv2.0.4 to do the mapping step. We mapped clean reads to reference using Bowtie2v2.2.6   and then calculate gene expression level with RSEMv1.2.12. Then  we calculate pearson correlation between all samples using cor  perform hierarchical clustering between all samples using hclust  perform PCA analysis with all samples using princomp  and draw the diagrams with ggplot2 with fuctions of R. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "hematopoietic", "mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", "RNA was extracted from sorted cells using RNeasy Micro Qiagen  Manchester  UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co.  Ltd.  Nanjing  China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer\u2019s instructions.", "Wild type zebrafish without xxx were used as blank to determine the background values in GFP controls.", "tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:WT|treatment:control", "GSM7506191", "GSM7506191: Tgmpx:eGFP 2; Danio rerio; RNA Seq", "GSM7506191 r1", "GSM7506191", "1", "RNA was extracted from sorted cells using RNeasy Micro Qiagen  Manchester  UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co.  Ltd.  Nanjing  China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP445421", null, null, "R21136162-qtsw-z003-mpx-11-11_combined_R1.fastq.gz R21136162-qtsw-z003-mpx-11-11_combined_R2.fastq.gz", "fastq fastq", 6391196700.0, 21303989.0, "GSM7506191 r1", "0:150 1:150", "A:1663138882;C:1355987073;G:1750924104;T:1621100160;N:46481", 150, 150, null, null, 1663138882, 1355987073, 1750924104, 1621100160, 46481, "SRX20755041", "SRS18043618", "SRA1660768", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", 2, 0.94347, 0.94088, 0.10896, 0.10794, 0.69522, 0.69824, 0.48646, 0.48484, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2023-06-22", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [76523, "SRR24999167", "SRX20755040", "SRS18043617", "SRP445421", "PRJNA986547", "Znf687 recruits Brd4 Smrt complex  to regulate gfi1aa expression   during neutrophil development", "GSE235609", "Transcriptome Analysis", "Neutrophils are key component of the innate immune system in vertebrates. Diverse transcription factors and cofactors act in a well coordinated manner to ensure proper neutrophil development. Dysregulation of the transcriptional program triggering neutrophil differentiation is associated with various human hematologic disorders such as neutropenia  neutrophilia  and leukemia. In the current study we show the zinc finger protein Znf687 is a lineage specific transcription factor  whose deficiency leads to an impaired neutrophil development in zebrafish. Mechanistically  Znf687 functions as a negative regulator of gfi1aa  a pivotal modulator in terminal granulopoiesis  to regulate neutrophil maturation. Moreover  we found BRD4  an important epigenetic regulator  interacts with ZNF687 in neutrophils. Deficiency of brd4 results in similar defective neutrophil development as observed in znf687 mutant zebrafish. Biochemical and genetic analyses further reveal that instead of serving as a canonical transcriptional coactivator  Brd4 directly interacts and bridges Znf687 and Smrt nuclear corepressor on gfi1aa gene's promoter to exert transcription repression. Overall  our work not only indicates Znf687 and Brd4 are reciprocally required in promoting granulopoiesis  but also provides new insights into the role of the two crucial regulators in transcriptional repression. Overall design: We found that Znf687 served as a transcription repressor.we speculated that the aberrant upregulation of certain downstream target of Znf687 would be responsible for the defective neutrophil differentiation. Then RNA sequencing RNA seq analyses were conducted in the remaining mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", null, "pubmed:38326409", null, "Tgmpx:eGFP larvae injected with znf687a MO 1", "GSM7506192", null, "source name:hematopoietic|tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:znf687a knowdown|treatment:znf687a MO|geo loc name:missing|collection date:missing", "Tgmpx:eGFP larvae injected with znf687a MO 1", "We filter the low quality reads More than 20% of the bases qualities are lower than 10  reads with adaptors and reads with unknown bases N bases more than 5% to get the clean reads. We use fastp to filter. We use HISATv2.0.4 to do the mapping step. We mapped clean reads to reference using Bowtie2v2.2.6   and then calculate gene expression level with RSEMv1.2.12. Then  we calculate pearson correlation between all samples using cor  perform hierarchical clustering between all samples using hclust  perform PCA analysis with all samples using princomp  and draw the diagrams with ggplot2 with fuctions of R. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "hematopoietic", "mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", "RNA was extracted from sorted cells using RNeasy Micro Qiagen  Manchester  UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co.  Ltd.  Nanjing  China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer\u2019s instructions.", "Wild type zebrafish without xxx were used as blank to determine the background values in GFP controls.", "tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:znf687a knowdown|treatment:znf687a  MO", "GSM7506192", "GSM7506192: Tgmpx:eGFP larvae injected with znf687a MO 1; Danio rerio; RNA Seq", "GSM7506192 r1", "GSM7506192", "1", "RNA was extracted from sorted cells using RNeasy Micro Qiagen  Manchester  UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co.  Ltd.  Nanjing  China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP445421", null, null, "R21136162-qtsw-z003-mo-11-10_combined_R2.fastq.gz R21136162-qtsw-z003-mo-11-10_combined_R1.fastq.gz", "fastq fastq", 5474240400.0, 18247468.0, "GSM7506192 r1", "0:150 1:150", "A:1344187663;C:1136523926;G:1697034586;T:1296453731;N:40494", 150, 150, null, null, 1344187663, 1136523926, 1697034586, 1296453731, 40494, "SRX20755040", "SRS18043617", "SRA1660768", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", 2, 0.85041, 0.8461, 0.08081, 0.07986, 0.74328, 0.746, 0.48356, 0.47751, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2023-06-22", "Multi-stage", "Multi-stage", "Blood", "Hematopoietic System"], [76524, "SRR24999168", "SRX20755039", "SRS18043616", "SRP445421", "PRJNA986547", "Znf687 recruits Brd4 Smrt complex  to regulate gfi1aa expression   during neutrophil development", "GSE235609", "Transcriptome Analysis", "Neutrophils are key component of the innate immune system in vertebrates. Diverse transcription factors and cofactors act in a well coordinated manner to ensure proper neutrophil development. Dysregulation of the transcriptional program triggering neutrophil differentiation is associated with various human hematologic disorders such as neutropenia  neutrophilia  and leukemia. In the current study we show the zinc finger protein Znf687 is a lineage specific transcription factor  whose deficiency leads to an impaired neutrophil development in zebrafish. Mechanistically  Znf687 functions as a negative regulator of gfi1aa  a pivotal modulator in terminal granulopoiesis  to regulate neutrophil maturation. Moreover  we found BRD4  an important epigenetic regulator  interacts with ZNF687 in neutrophils. Deficiency of brd4 results in similar defective neutrophil development as observed in znf687 mutant zebrafish. Biochemical and genetic analyses further reveal that instead of serving as a canonical transcriptional coactivator  Brd4 directly interacts and bridges Znf687 and Smrt nuclear corepressor on gfi1aa gene's promoter to exert transcription repression. Overall  our work not only indicates Znf687 and Brd4 are reciprocally required in promoting granulopoiesis  but also provides new insights into the role of the two crucial regulators in transcriptional repression. Overall design: We found that Znf687 served as a transcription repressor.we speculated that the aberrant upregulation of certain downstream target of Znf687 would be responsible for the defective neutrophil differentiation. Then RNA sequencing RNA seq analyses were conducted in the remaining mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", null, "pubmed:38326409", null, "Tgmpx:eGFP larvae injected with znf687a MO 2", "GSM7506193", null, "source name:hematopoietic|tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:znf687a knowdown|treatment:znf7687a MO|geo loc name:missing|collection date:missing", "Tgmpx:eGFP larvae injected with znf687a MO 2", "We filter the low quality reads More than 20% of the bases qualities are lower than 10  reads with adaptors and reads with unknown bases N bases more than 5% to get the clean reads. We use fastp to filter. We use HISATv2.0.4 to do the mapping step. We mapped clean reads to reference using Bowtie2v2.2.6   and then calculate gene expression level with RSEMv1.2.12. Then  we calculate pearson correlation between all samples using cor  perform hierarchical clustering between all samples using hclust  perform PCA analysis with all samples using princomp  and draw the diagrams with ggplot2 with fuctions of R. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "hematopoietic", "mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", "RNA was extracted from sorted cells using RNeasy Micro Qiagen  Manchester  UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co.  Ltd.  Nanjing  China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer\u2019s instructions.", "Wild type zebrafish without xxx were used as blank to determine the background values in GFP controls.", "tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:znf687a knowdown|treatment:znf7687a MO", "GSM7506193", "GSM7506193: Tgmpx:eGFP larvae injected with znf687a MO 2; Danio rerio; RNA Seq", "GSM7506193 r1", "GSM7506193", "1", "RNA was extracted from sorted cells using RNeasy Micro Qiagen  Manchester  UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co.  Ltd.  Nanjing  China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP445421", null, null, "R21136162-qtsw-z003-mo-11-11_combined_R2.fastq.gz R21136162-qtsw-z003-mo-11-11_combined_R1.fastq.gz", "fastq fastq", 7189581900.0, 23965273.0, "GSM7506193 r1", "0:150 1:150", "A:1383671914;C:1160994305;G:3299098586;T:1345763504;N:53591", 150, 150, null, null, 1383671914, 1160994305, 3299098586, 1345763504, 53591, "SRX20755039", "SRS18043616", "SRA1660768", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", 2, 0.89402, 0.8908, 0.09186, 0.09076, 0.76307, 0.76473, 0.51884, 0.5204, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2023-06-22", "Multi-stage", "Multi-stage", "Blood", "Hematopoietic System"], [76525, "SRR24999169", "SRX20755038", "SRS18043615", "SRP445421", "PRJNA986547", "Znf687 recruits Brd4 Smrt complex  to regulate gfi1aa expression   during neutrophil development", "GSE235609", "Transcriptome Analysis", "Neutrophils are key component of the innate immune system in vertebrates. Diverse transcription factors and cofactors act in a well coordinated manner to ensure proper neutrophil development. Dysregulation of the transcriptional program triggering neutrophil differentiation is associated with various human hematologic disorders such as neutropenia  neutrophilia  and leukemia. In the current study we show the zinc finger protein Znf687 is a lineage specific transcription factor  whose deficiency leads to an impaired neutrophil development in zebrafish. Mechanistically  Znf687 functions as a negative regulator of gfi1aa  a pivotal modulator in terminal granulopoiesis  to regulate neutrophil maturation. Moreover  we found BRD4  an important epigenetic regulator  interacts with ZNF687 in neutrophils. Deficiency of brd4 results in similar defective neutrophil development as observed in znf687 mutant zebrafish. Biochemical and genetic analyses further reveal that instead of serving as a canonical transcriptional coactivator  Brd4 directly interacts and bridges Znf687 and Smrt nuclear corepressor on gfi1aa gene's promoter to exert transcription repression. Overall  our work not only indicates Znf687 and Brd4 are reciprocally required in promoting granulopoiesis  but also provides new insights into the role of the two crucial regulators in transcriptional repression. Overall design: We found that Znf687 served as a transcription repressor.we speculated that the aberrant upregulation of certain downstream target of Znf687 would be responsible for the defective neutrophil differentiation. Then RNA sequencing RNA seq analyses were conducted in the remaining mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", null, "pubmed:38326409", null, "Tgmpx:eGFP 1", "GSM7506190", null, "source name:hematopoietic|tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:WT|treatment:control|geo loc name:missing|collection date:missing", "Tgmpx:eGFP 1", "We filter the low quality reads More than 20% of the bases qualities are lower than 10  reads with adaptors and reads with unknown bases N bases more than 5% to get the clean reads. We use fastp to filter. We use HISATv2.0.4 to do the mapping step. We mapped clean reads to reference using Bowtie2v2.2.6   and then calculate gene expression level with RSEMv1.2.12. Then  we calculate pearson correlation between all samples using cor  perform hierarchical clustering between all samples using hclust  perform PCA analysis with all samples using princomp  and draw the diagrams with ggplot2 with fuctions of R. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "hematopoietic", "mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", "RNA was extracted from sorted cells using RNeasy Micro Qiagen  Manchester  UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co.  Ltd.  Nanjing  China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer\u2019s instructions.", "Wild type zebrafish without xxx were used as blank to determine the background values in GFP controls.", "tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:WT|treatment:control", "GSM7506190", "GSM7506190: Tgmpx:eGFP 1; Danio rerio; RNA Seq", "GSM7506190 r1", "GSM7506190", "1", "RNA was extracted from sorted cells using RNeasy Micro Qiagen  Manchester  UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co.  Ltd.  Nanjing  China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP445421", null, null, "R21136162-qtsw-z003-mpx-11-10_combined_R2.fastq.gz R21136162-qtsw-z003-mpx-11-10_combined_R1.fastq.gz", "fastq fastq", 7364874300.0, 24549581.0, "GSM7506190 r1", "0:150 1:150", "A:1988715009;C:1657810285;G:1778472191;T:1939822538;N:54277", 150, 150, null, null, 1988715009, 1657810285, 1778472191, 1939822538, 54277, "SRX20755038", "SRS18043615", "SRA1660768", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", 2, 0.94842, 0.94741, 0.10807, 0.10703, 0.69451, 0.69552, 0.4957, 0.49509, 150, 150, "B", "B", "biological fallback assumption", 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"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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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], 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