metadata: run_metadata: 18 rows where technology = "bulk" and tissue

18 rows where technology = "bulk" and tissue_curation = "Blood"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	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.study_ref	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.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	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
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

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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");;