{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", technology = \"10x\" and tissue_curation_coarse = \"Hematopoietic System\"", "rows": [[53001, "SRR12173589", "SRX8688333", "SRS6966994", "SRP213938", "PRJNA553572", "A map of cis regulatory elements and 3D genome structures in zebrafish", "GSE134055", "Other", "The zebrafish has been widely used for the study of human disease and development  as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome  however  has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects  we performed RNA seq  ATAC seq  ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall  we have identified 235 596 cis regulatory elements  which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish  human  and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore  through the analysis of Hi C data in zebrafish brain and muscle  we observed different levels of 3D genome organization  including compartment  topological associating domains TADs  and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and  embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3  RNA Seq  11 of them were examined using ATAC seq  WGBS and ChIP seq H3K9me3 and H3K9me2  and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that  for the samples GSM4661977 GSM4662088  [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.", null, "pubmed:33239788;pubmed:35649578", null, "YueLab RNA seq Blood rep2", "GSM4662086", null, "source name:YueLab RNA seq Blood|strain:Tuebingen|tissue:Blood", "YueLab RNA seq Blood rep2", "RNA seq reads were aligned to zv10 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using Bowtie2;H3K27ac  H3K4me3 ChIP seq were called using MACS2 with the following  setting: ChIP seq q value <10e 2  p value<10e 5  Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5.For the ATAC seq  the peak length were fixed to 500 bp. We only selected the peak with the most significant signal if several peaks overlap with each other in each tissue.Since the H3K9me3 and H3K9me2 makers are broad domain  we called the peak using Homer with the parameter \u201c region  size 1000\u201d  and peaks within 5 kb were merged together. HiC matrix was generated using HiC Pro WGBS data were mapped to in silico bisulfite converted zebrafish genome reference by using Bismark For the scATAC seq  the BCL files generated from sequencing were used as inputs to the 10X Genomics Cell Ranger ATAC seq pipeline; then the FASTQ files were aligned to the GRCz10 genome using BWA and the fragments with MAPQ>30 were kept for further analysis and each fragment is associated with a single cell barcode. Genome build: zv10GRCz10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged", "YueLab RNA seq Blood", null, "RNA seq: For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer\u2019s protocol. Briefly  polyA RNA was purified from 1000\u00a0ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 \u00b5L of ChIP seq lysis buffer 20 mM Tris HCl  pH 8.0  1% SDS  50 mM EDTA  1X proteinase inhibitor cocktail. Next  900 \u00b5L cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W  duty factor 5  200 per burst. Sonication time is variable  depending on tissue types. To check the chromatin fragmentation size  20 \u00b5L of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl  pH 8.0  1% SDS  1 mM EDTA at 65 \u00b0C overnight  treated with Rnase A and proteinase K and purified by phenol chloroform extraction. Input DNA was then loaded on a Lonza flash gel to make sure that the majority of DNA size distributes between 100 300 bp. To prepare antibody beads complex  3 \u00b5g of histone H3K27ac antibody Active Motif  39133 or H3K4me3 antibody EMD Millipore  07 473 was mix with 12 \u00b5L M 280 sheep anti rabbit IgG Dynabeads ThermoFisher  11203D in 150 \u00b5L of 5 mg/mL BSA/1X PBS buffer  with rotation at 4 \u00b0C for 3 h. post incubation  antibody beads complex was washed once with BSA/1X PBS buffer. About 200 \u00b5g chromatin was used per IP. Equal volume of master mix 1X TE  2% Triton X 100  0.2% sodium deoxycholate  2X proteinase inhibitor cocktail was mixed with 200 \u00b5g chromatin and then incubated with antibody beads complex overnight with rotation. The next morning  the beads were washed 5 times with cold RIPA wash buffer 20 mM Tris HCl  pH 8.0  1% NP 40  0.7% sodium deoxycholate  500 mM LiCl  1 mM EDTA  1X proteinase inhibitor cocktail. Then the chromatin bound on the beads was eluted by 150 \u00b5L of elution buffer at 65 \u00b0C for 30 min. ChIP seq: To prepare the library  eluted chromatin was reverse crosslinked and purified by phenol chloroform extraction. Then DNA was end repaired by END IT DNA end repair kit Epicentre  ER81050 according to kit\u2019s protocol  added A using Klenow  fragment 3\u2019 >5\u2019 exo  NEB  M0212S  ligated with Illumina TruSeq adaptor Illumina  FC 121 3001 and subsequently amplified by PCR Roche  kk2601. The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit Agilent. The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp. ATAC seq: Tuebingen adult tissues were ground in liquid nitrogen resuspended in 1 mL of lysis buffer 1X PBS  0.2% NP 40  5% BSA  1 mM DTT  protease inhibitors  followed by incubation at  4 \u00b0C for 10 min on an overhead shaker. post that  lysate was filtered through 40 \uf06dm cell strainer and nuclei were collected at 1000X g for 5 min. ATAC seq: Tagmentation was performed immediately according to ATAC seq protocol reported previouslyBuenrostro et al.  2013 Hi C: For brain tissue  two adult Tuebingen brains were slightly ground into small granules in liquid nitrogen and resuspended in 1 mL of cold hypotonic buffer 20 mM Tris HCl  pH 8.0  10 mM NaCl  20 mM EDTA. Granular brains were then dounce homogenized with loose pestle for 20 times. The top of the homogenate was carefully transferred into a new tube and fixed with 2% formaldehyde at room temperature for 10 min. 0.2 M of glycine was added to stop fixation. For muscle tissue  60 mg of Tuebingen muscle was first chopped into small pieces and digested by 0.25% trypsin at room temperature for 30 min. post neutralization with FBS  muscle cells were resuspended in cold 1X PBS and fixed with 2% of formaldehyde at room temperature for 10 min. 0.2 M glycine was then added to stop fixation. Hi C: Hi C experiments on adult zebrafish brain and muscle tissues were performed according to previously published protocolRao et al.  2014. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 100 bp high throughput sequencing using HiSeq 2500  or HiSeq 4000Illumina. WGBS: T\u00fcbingen adult tissues were dissected  and the genomic DNA was extracted using DNeasy Blood & Tissue Kit Qiagen  69504. Then 1 \u00b5g of genomic DNA of each adult tissue was subjected to bisulfite conversion using EZ DNA Methylation Gold Kits WGBS: The final libraries were prepared using the Accel NGS\u00ae Methyl Seq DNA Library Kit. scATAC seq: Single cell ATAC seq scATAC seq was performed in one female brain and one male brain  respectively  on the 10X Genomics platform. To isolate nuclei  freshly dissected single brain was transferred to 1 mL NbActiv1 medium BrainBits  NbActiv1 500 with a wide bore pipette tip to break the tissue into small pieces. Then the tissue was broken up completely using regular bore pipette tips followed by filtering through a 30 \u00b5m cell strainer. The isolated cells were spun down at 500 g for 5 min at 4 \u00b0C and then lysed in 100 \u00b5L chilled 0.1X Lysis Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA 0.01% Tween 20  0.01% NP40 and 0.001% digitonin on ice for 5 min. Then 1 mL chilled Wash Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA  0.1% Tween 20 was added to the lysed cells and cells were spun down at 500 g for 5 min at 4 \u00b0C. At last  300 \u00b5L chilled Diluted Nuclei Buffer 10x Genomics  PN 2000153/2000207 was added to resuspend the nuclei. The nuclei were filtered again using a 30 \u00b5m cell strainer before cell counting scATAC seq: Around 12 000 nuclei were used for one Tn5 tagmentation reaction  and the scATAC seq library was prepared and sequenced exactly according to the company\u2019s user guide.", "RNA seq: Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions ChIP seq  ATAC seq  Hi C and WGBS: Ault Tuebingen zebrafish were raised under standard laboratory conditions", "strain:Tuebingen|tissue:Blood", "GSM4662086", "GSM4662086: YueLab RNA seq Blood rep2; Danio rerio; RNA Seq", "GSM4662086", null, "1", "RNA seq: For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 \u00b5L of ChIP seq lysis buffer 20 mM Tris HCl  pH 8.0  1% SDS  50 mM EDTA  1X proteinase inhibitor cocktail. Next  900 \u00b5L cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W  duty factor 5  200 per burst. Sonication time is variable  depending on tissue types. To check the chromatin fragmentation size  20 \u00b5L of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl  pH 8.0  1% SDS  1 mM EDTA at 65 \u00b0C overnight  treated with Rnase A and proteinase K and purified by phenol chloroform extraction. Input DNA was then loaded on a Lonza flash gel to make sure that the majority of DNA size distributes between 100 300 bp. To prepare antibody beads complex  3 \u00b5g of histone H3K27ac antibody Active Motif  39133 or H3K4me3 antibody EMD Millipore  07 473 was mix with 12 \u00b5L M 280 sheep anti rabbit IgG Dynabeads ThermoFisher  11203D in 150 \u00b5L of 5 mg/mL BSA/1X PBS buffer  with rotation at 4 \u00b0C for 3 h. post incubation  antibody beads complex was washed once with BSA/1X PBS buffer. About 200 \u00b5g chromatin was used per IP. Equal volume of master mix 1X TE  2% Triton X 100  0.2% sodium deoxycholate  2X proteinase inhibitor cocktail was mixed with 200 \u00b5g chromatin and then incubated with antibody beads complex overnight with rotation. The next morning  the beads were washed 5 times with cold RIPA wash buffer 20 mM Tris HCl  pH 8.0  1% NP 40  0.7% sodium deoxycholate  500 mM LiCl  1 mM EDTA  1X proteinase inhibitor cocktail. Then the chromatin bound on the beads was eluted by 150 \u00b5L of elution buffer at 65 \u00b0C for 30 min. ChIP seq: To prepare the library  eluted chromatin was reverse crosslinked and purified by phenol chloroform extraction. Then DNA was end repaired by END IT DNA end repair kit Epicentre  ER81050 according to kit's protocol  added A using Klenow  fragment three prime >five prime exo  NEB  M0212S  ligated with Illumina TruSeq adaptor Illumina  FC 121 3001 and subsequently amplified by PCR Roche  kk2601. The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit Agilent. The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp. ATAC seq: Tuebingen adult tissues were ground in liquid nitrogen resuspended in 1 mL of lysis buffer 1X PBS  0.2% NP 40  5% BSA  1 mM DTT  protease inhibitors  followed by incubation at  4 \u00b0C for 10 min on an overhead shaker. post that  lysate was filtered through 40 \uf06dm cell strainer and nuclei were collected at 1000X g for 5 min. ATAC seq: Tagmentation was performed immediately according to ATAC seq protocol reported previouslyBuenrostro et al.  2013 Hi C: For brain tissue  two adult Tuebingen brains were slightly ground into small granules in liquid nitrogen and resuspended in 1 mL of cold hypotonic buffer 20 mM Tris HCl  pH 8.0  10 mM NaCl  20 mM EDTA. Granular brains were then dounce homogenized with loose pestle for 20 times. The top of the homogenate was carefully transferred into a new tube and fixed with 2% formaldehyde at room temperature for 10 min. 0.2 M of glycine was added to stop fixation. For muscle tissue  60 mg of Tuebingen muscle was first chopped into small pieces and digested by 0.25% trypsin at room temperature for 30 min. post neutralization with FBS  muscle cells were resuspended in cold 1X PBS and fixed with 2% of formaldehyde at room temperature for 10 min. 0.2 M glycine was then added to stop fixation. Hi C: Hi C experiments on adult zebrafish brain and muscle tissues were performed according to previously published protocolRao et al.  2014. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 100 bp high throughput sequencing using HiSeq 2500  or HiSeq 4000Illumina. WGBS: T\u00fcbingen adult tissues were dissected  and the genomic DNA was extracted using DNeasy Blood & Tissue Kit Qiagen  69504. Then 1 \u00b5g of genomic DNA of each adult tissue was subjected to bisulfite conversion using EZ DNA Methylation Gold Kits WGBS: The final libraries were prepared using the Accel NGS\u00ae Methyl Seq DNA Library Kit. scATAC seq: Single cell ATAC seq scATAC seq was performed in one female brain and one male brain  respectively  on the 10X Genomics platform. To isolate nuclei  freshly dissected single brain was transferred to 1 mL NbActiv1 medium BrainBits  NbActiv1 500 with a wide bore pipette tip to break the tissue into small pieces. Then the tissue was broken up completely using regular bore pipette tips followed by filtering through a 30 \u00b5m cell strainer. The isolated cells were spun down at 500 g for 5 min at 4 \u00b0C and then lysed in 100 \u00b5L chilled 0.1X Lysis Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA 0.01% Tween 20  0.01% NP40 and 0.001% digitonin on ice for 5 min. Then 1 mL chilled Wash Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA  0.1% Tween 20 was added to the lysed cells and cells were spun down at 500 g for 5 min at 4 \u00b0C. At last  300 \u00b5L chilled Diluted Nuclei Buffer 10x Genomics  PN 2000153/2000207 was added to resuspend the nuclei. The nuclei were filtered again using a 30 \u00b5m cell strainer before cell counting scATAC seq: Around 12 000 nuclei were used for one Tn5 tagmentation reaction  and the scATAC seq library was prepared and sequenced exactly according to the company's user guide.", "GEO Accession:GSM4662086", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP213938", null, null, "YueLab-RNA-seq-Blood-rep2_2.fastq.gz YueLab-RNA-seq-Blood-rep2_1.fastq.gz", "fastq fastq", 9750305560.0, 32285780.0, "GSM4662086 r1", "0:151 1:151", "A:2564237490;C:2313022617;G:2328740350;T:2544206938;N:98165", 151, 151, null, null, 2564237490, 2313022617, 2328740350, 2544206938, 98165, "SRX8688333", "SRS6966994", "SRA919194", "GEO", "Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine", 2, 0.90976, 0.90587, 0.07014, 0.06953, 0.85415, 0.85624, 0.51898, 0.51696, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "sc", "single_cell_droplet", "10x", null, "United States", "2020-07-08", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [53002, "SRR12173588", "SRX8688332", "SRS6966993", "SRP213938", "PRJNA553572", "A map of cis regulatory elements and 3D genome structures in zebrafish", "GSE134055", "Other", "The zebrafish has been widely used for the study of human disease and development  as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome  however  has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects  we performed RNA seq  ATAC seq  ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall  we have identified 235 596 cis regulatory elements  which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish  human  and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore  through the analysis of Hi C data in zebrafish brain and muscle  we observed different levels of 3D genome organization  including compartment  topological associating domains TADs  and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and  embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3  RNA Seq  11 of them were examined using ATAC seq  WGBS and ChIP seq H3K9me3 and H3K9me2  and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that  for the samples GSM4661977 GSM4662088  [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.", null, "pubmed:33239788;pubmed:35649578", null, "YueLab RNA seq Blood rep1", "GSM4662085", null, "source name:YueLab RNA seq Blood|strain:Tuebingen|tissue:Blood", "YueLab RNA seq Blood rep1", "RNA seq reads were aligned to zv10 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using Bowtie2;H3K27ac  H3K4me3 ChIP seq were called using MACS2 with the following  setting: ChIP seq q value <10e 2  p value<10e 5  Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5.For the ATAC seq  the peak length were fixed to 500 bp. We only selected the peak with the most significant signal if several peaks overlap with each other in each tissue.Since the H3K9me3 and H3K9me2 makers are broad domain  we called the peak using Homer with the parameter \u201c region  size 1000\u201d  and peaks within 5 kb were merged together. HiC matrix was generated using HiC Pro WGBS data were mapped to in silico bisulfite converted zebrafish genome reference by using Bismark For the scATAC seq  the BCL files generated from sequencing were used as inputs to the 10X Genomics Cell Ranger ATAC seq pipeline; then the FASTQ files were aligned to the GRCz10 genome using BWA and the fragments with MAPQ>30 were kept for further analysis and each fragment is associated with a single cell barcode. Genome build: zv10GRCz10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged", "YueLab RNA seq Blood", null, "RNA seq: For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer\u2019s protocol. Briefly  polyA RNA was purified from 1000\u00a0ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 \u00b5L of ChIP seq lysis buffer 20 mM Tris HCl  pH 8.0  1% SDS  50 mM EDTA  1X proteinase inhibitor cocktail. Next  900 \u00b5L cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W  duty factor 5  200 per burst. Sonication time is variable  depending on tissue types. To check the chromatin fragmentation size  20 \u00b5L of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl  pH 8.0  1% SDS  1 mM EDTA at 65 \u00b0C overnight  treated with Rnase A and proteinase K and purified by phenol chloroform extraction. Input DNA was then loaded on a Lonza flash gel to make sure that the majority of DNA size distributes between 100 300 bp. To prepare antibody beads complex  3 \u00b5g of histone H3K27ac antibody Active Motif  39133 or H3K4me3 antibody EMD Millipore  07 473 was mix with 12 \u00b5L M 280 sheep anti rabbit IgG Dynabeads ThermoFisher  11203D in 150 \u00b5L of 5 mg/mL BSA/1X PBS buffer  with rotation at 4 \u00b0C for 3 h. post incubation  antibody beads complex was washed once with BSA/1X PBS buffer. About 200 \u00b5g chromatin was used per IP. Equal volume of master mix 1X TE  2% Triton X 100  0.2% sodium deoxycholate  2X proteinase inhibitor cocktail was mixed with 200 \u00b5g chromatin and then incubated with antibody beads complex overnight with rotation. The next morning  the beads were washed 5 times with cold RIPA wash buffer 20 mM Tris HCl  pH 8.0  1% NP 40  0.7% sodium deoxycholate  500 mM LiCl  1 mM EDTA  1X proteinase inhibitor cocktail. Then the chromatin bound on the beads was eluted by 150 \u00b5L of elution buffer at 65 \u00b0C for 30 min. ChIP seq: To prepare the library  eluted chromatin was reverse crosslinked and purified by phenol chloroform extraction. Then DNA was end repaired by END IT DNA end repair kit Epicentre  ER81050 according to kit\u2019s protocol  added A using Klenow  fragment 3\u2019 >5\u2019 exo  NEB  M0212S  ligated with Illumina TruSeq adaptor Illumina  FC 121 3001 and subsequently amplified by PCR Roche  kk2601. The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit Agilent. The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp. ATAC seq: Tuebingen adult tissues were ground in liquid nitrogen resuspended in 1 mL of lysis buffer 1X PBS  0.2% NP 40  5% BSA  1 mM DTT  protease inhibitors  followed by incubation at  4 \u00b0C for 10 min on an overhead shaker. post that  lysate was filtered through 40 \uf06dm cell strainer and nuclei were collected at 1000X g for 5 min. ATAC seq: Tagmentation was performed immediately according to ATAC seq protocol reported previouslyBuenrostro et al.  2013 Hi C: For brain tissue  two adult Tuebingen brains were slightly ground into small granules in liquid nitrogen and resuspended in 1 mL of cold hypotonic buffer 20 mM Tris HCl  pH 8.0  10 mM NaCl  20 mM EDTA. Granular brains were then dounce homogenized with loose pestle for 20 times. The top of the homogenate was carefully transferred into a new tube and fixed with 2% formaldehyde at room temperature for 10 min. 0.2 M of glycine was added to stop fixation. For muscle tissue  60 mg of Tuebingen muscle was first chopped into small pieces and digested by 0.25% trypsin at room temperature for 30 min. post neutralization with FBS  muscle cells were resuspended in cold 1X PBS and fixed with 2% of formaldehyde at room temperature for 10 min. 0.2 M glycine was then added to stop fixation. Hi C: Hi C experiments on adult zebrafish brain and muscle tissues were performed according to previously published protocolRao et al.  2014. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 100 bp high throughput sequencing using HiSeq 2500  or HiSeq 4000Illumina. WGBS: T\u00fcbingen adult tissues were dissected  and the genomic DNA was extracted using DNeasy Blood & Tissue Kit Qiagen  69504. Then 1 \u00b5g of genomic DNA of each adult tissue was subjected to bisulfite conversion using EZ DNA Methylation Gold Kits WGBS: The final libraries were prepared using the Accel NGS\u00ae Methyl Seq DNA Library Kit. scATAC seq: Single cell ATAC seq scATAC seq was performed in one female brain and one male brain  respectively  on the 10X Genomics platform. To isolate nuclei  freshly dissected single brain was transferred to 1 mL NbActiv1 medium BrainBits  NbActiv1 500 with a wide bore pipette tip to break the tissue into small pieces. Then the tissue was broken up completely using regular bore pipette tips followed by filtering through a 30 \u00b5m cell strainer. The isolated cells were spun down at 500 g for 5 min at 4 \u00b0C and then lysed in 100 \u00b5L chilled 0.1X Lysis Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA 0.01% Tween 20  0.01% NP40 and 0.001% digitonin on ice for 5 min. Then 1 mL chilled Wash Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA  0.1% Tween 20 was added to the lysed cells and cells were spun down at 500 g for 5 min at 4 \u00b0C. At last  300 \u00b5L chilled Diluted Nuclei Buffer 10x Genomics  PN 2000153/2000207 was added to resuspend the nuclei. The nuclei were filtered again using a 30 \u00b5m cell strainer before cell counting scATAC seq: Around 12 000 nuclei were used for one Tn5 tagmentation reaction  and the scATAC seq library was prepared and sequenced exactly according to the company\u2019s user guide.", "RNA seq: Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions ChIP seq  ATAC seq  Hi C and WGBS: Ault Tuebingen zebrafish were raised under standard laboratory conditions", "strain:Tuebingen|tissue:Blood", "GSM4662085", "GSM4662085: YueLab RNA seq Blood rep1; Danio rerio; RNA Seq", "GSM4662085", null, "1", "RNA seq: For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 \u00b5L of ChIP seq lysis buffer 20 mM Tris HCl  pH 8.0  1% SDS  50 mM EDTA  1X proteinase inhibitor cocktail. Next  900 \u00b5L cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W  duty factor 5  200 per burst. Sonication time is variable  depending on tissue types. To check the chromatin fragmentation size  20 \u00b5L of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl  pH 8.0  1% SDS  1 mM EDTA at 65 \u00b0C overnight  treated with Rnase A and proteinase K and purified by phenol chloroform extraction. Input DNA was then loaded on a Lonza flash gel to make sure that the majority of DNA size distributes between 100 300 bp. To prepare antibody beads complex  3 \u00b5g of histone H3K27ac antibody Active Motif  39133 or H3K4me3 antibody EMD Millipore  07 473 was mix with 12 \u00b5L M 280 sheep anti rabbit IgG Dynabeads ThermoFisher  11203D in 150 \u00b5L of 5 mg/mL BSA/1X PBS buffer  with rotation at 4 \u00b0C for 3 h. post incubation  antibody beads complex was washed once with BSA/1X PBS buffer. About 200 \u00b5g chromatin was used per IP. Equal volume of master mix 1X TE  2% Triton X 100  0.2% sodium deoxycholate  2X proteinase inhibitor cocktail was mixed with 200 \u00b5g chromatin and then incubated with antibody beads complex overnight with rotation. The next morning  the beads were washed 5 times with cold RIPA wash buffer 20 mM Tris HCl  pH 8.0  1% NP 40  0.7% sodium deoxycholate  500 mM LiCl  1 mM EDTA  1X proteinase inhibitor cocktail. Then the chromatin bound on the beads was eluted by 150 \u00b5L of elution buffer at 65 \u00b0C for 30 min. ChIP seq: To prepare the library  eluted chromatin was reverse crosslinked and purified by phenol chloroform extraction. Then DNA was end repaired by END IT DNA end repair kit Epicentre  ER81050 according to kit's protocol  added A using Klenow  fragment three prime >five prime exo  NEB  M0212S  ligated with Illumina TruSeq adaptor Illumina  FC 121 3001 and subsequently amplified by PCR Roche  kk2601. The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit Agilent. The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp. ATAC seq: Tuebingen adult tissues were ground in liquid nitrogen resuspended in 1 mL of lysis buffer 1X PBS  0.2% NP 40  5% BSA  1 mM DTT  protease inhibitors  followed by incubation at  4 \u00b0C for 10 min on an overhead shaker. post that  lysate was filtered through 40 \uf06dm cell strainer and nuclei were collected at 1000X g for 5 min. ATAC seq: Tagmentation was performed immediately according to ATAC seq protocol reported previouslyBuenrostro et al.  2013 Hi C: For brain tissue  two adult Tuebingen brains were slightly ground into small granules in liquid nitrogen and resuspended in 1 mL of cold hypotonic buffer 20 mM Tris HCl  pH 8.0  10 mM NaCl  20 mM EDTA. Granular brains were then dounce homogenized with loose pestle for 20 times. The top of the homogenate was carefully transferred into a new tube and fixed with 2% formaldehyde at room temperature for 10 min. 0.2 M of glycine was added to stop fixation. For muscle tissue  60 mg of Tuebingen muscle was first chopped into small pieces and digested by 0.25% trypsin at room temperature for 30 min. post neutralization with FBS  muscle cells were resuspended in cold 1X PBS and fixed with 2% of formaldehyde at room temperature for 10 min. 0.2 M glycine was then added to stop fixation. Hi C: Hi C experiments on adult zebrafish brain and muscle tissues were performed according to previously published protocolRao et al.  2014. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 100 bp high throughput sequencing using HiSeq 2500  or HiSeq 4000Illumina. WGBS: T\u00fcbingen adult tissues were dissected  and the genomic DNA was extracted using DNeasy Blood & Tissue Kit Qiagen  69504. Then 1 \u00b5g of genomic DNA of each adult tissue was subjected to bisulfite conversion using EZ DNA Methylation Gold Kits WGBS: The final libraries were prepared using the Accel NGS\u00ae Methyl Seq DNA Library Kit. scATAC seq: Single cell ATAC seq scATAC seq was performed in one female brain and one male brain  respectively  on the 10X Genomics platform. To isolate nuclei  freshly dissected single brain was transferred to 1 mL NbActiv1 medium BrainBits  NbActiv1 500 with a wide bore pipette tip to break the tissue into small pieces. Then the tissue was broken up completely using regular bore pipette tips followed by filtering through a 30 \u00b5m cell strainer. The isolated cells were spun down at 500 g for 5 min at 4 \u00b0C and then lysed in 100 \u00b5L chilled 0.1X Lysis Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA 0.01% Tween 20  0.01% NP40 and 0.001% digitonin on ice for 5 min. Then 1 mL chilled Wash Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA  0.1% Tween 20 was added to the lysed cells and cells were spun down at 500 g for 5 min at 4 \u00b0C. At last  300 \u00b5L chilled Diluted Nuclei Buffer 10x Genomics  PN 2000153/2000207 was added to resuspend the nuclei. The nuclei were filtered again using a 30 \u00b5m cell strainer before cell counting scATAC seq: Around 12 000 nuclei were used for one Tn5 tagmentation reaction  and the scATAC seq library was prepared and sequenced exactly according to the company's user guide.", "GEO Accession:GSM4662085", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP213938", null, null, "YueLab-RNA-seq-Blood-rep1_1.fastq.gz YueLab-RNA-seq-Blood-rep1_2.fastq.gz", "fastq fastq", 10181340496.0, 33713048.0, "GSM4662085 r1", "0:151 1:151", "A:2735674306;C:2352790027;G:2376786768;T:2715986044;N:103351", 151, 151, null, null, 2735674306, 2352790027, 2376786768, 2715986044, 103351, "SRX8688332", "SRS6966993", "SRA919194", "GEO", "Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine", 2, 0.91563, 0.91373, 0.11339, 0.11315, 0.82235, 0.82266, 0.48854, 0.48669, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "sc", "single_cell_droplet", "10x", null, "United States", "2020-07-08", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [57171, "SRR11243180", "SRX7854786", "SRS6264269", "SRP251673", "PRJNA610520", "A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish", "GSE146404", "Transcriptome Analysis", "To profile the developmental landscape of fetal HSPCs and their local niche  here  by using single cell RNA sequencing  we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10\u00d7 Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.", null, "pubmed:33785593", null, "4.5 dpf CHT cells", "GSM4384818", null, "source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "4.5 dpf CHT cells", "UMI tools was used to analysis our single cell data.Firstly  in \u201cwhitelist\u201d step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI  and R2 is biological sequencing. Then in \u201cextract\u201d step we filter some low quality reads and non UMI reads with recommend parameters  so that we can use STAR to map to the reference genome. Finally  in \u201ccount\u201d step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples  measured by UMI counts", "zebrafish embryos", null, "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture\u2019s introduction.", null, "genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "GSM4384818", "GSM4384818: 4.5 dpf CHT cells; Danio rerio; RNA Seq", "GSM4384818", null, "1", "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture's introduction.", "GEO Accession:GSM4384818", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP251673", null, null, "171353H-CHT-4dpf_3_2_R1.fq.gz 171353H-CHT-4dpf_3_2_R2.fq.gz", "fastq fastq", 30131096700.0, 100436989.0, "GSM4384818 r1", "0:150 1:150", "A:6727746568;C:5761021689;G:10040248562;T:7601697440;N:382441", 150, 150, null, null, 6727746568, 5761021689, 10040248562, 7601697440, 382441, "SRX7854786", "SRS6264269", "SRA1051251", "GEO", "Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES", 2, 0.0, 0.9175, 0.0, 0.06023, 1.0, 0.84208, null, 0.51614, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-03-05", "Larval", "Larval", "Blood", "Hematopoietic System"], [57172, "SRR11243181", "SRX7854786", "SRS6264269", "SRP251673", "PRJNA610520", "A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish", "GSE146404", "Transcriptome Analysis", "To profile the developmental landscape of fetal HSPCs and their local niche  here  by using single cell RNA sequencing  we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10\u00d7 Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.", null, "pubmed:33785593", null, "4.5 dpf CHT cells", "GSM4384818", null, "source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "4.5 dpf CHT cells", "UMI tools was used to analysis our single cell data.Firstly  in \u201cwhitelist\u201d step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI  and R2 is biological sequencing. Then in \u201cextract\u201d step we filter some low quality reads and non UMI reads with recommend parameters  so that we can use STAR to map to the reference genome. Finally  in \u201ccount\u201d step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples  measured by UMI counts", "zebrafish embryos", null, "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture\u2019s introduction.", null, "genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "GSM4384818", "GSM4384818: 4.5 dpf CHT cells; Danio rerio; RNA Seq", "GSM4384818", null, "1", "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture's introduction.", "GEO Accession:GSM4384818", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP251673", null, null, "171353H-CHT-4dpf_2-2_R1.fq.gz 171353H-CHT-4dpf_2-2_R2.fq.gz", "fastq fastq", 35454747300.0, 118182491.0, "GSM4384818 r2", "0:150 1:150", "A:7924515815;C:6769046954;G:11812021964;T:8948714749;N:447818", 150, 150, null, null, 7924515815, 6769046954, 11812021964, 8948714749, 447818, "SRX7854786", "SRS6264269", "SRA1051251", "GEO", "Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES", 2, 0.0, 0.91808, 0.0, 0.05945, 1.0, 0.83938, null, 0.52604, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-03-05", "Larval", "Larval", "Blood", "Hematopoietic System"], [57173, "SRR11243182", "SRX7854786", "SRS6264269", "SRP251673", "PRJNA610520", "A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish", "GSE146404", "Transcriptome Analysis", "To profile the developmental landscape of fetal HSPCs and their local niche  here  by using single cell RNA sequencing  we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10\u00d7 Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.", null, "pubmed:33785593", null, "4.5 dpf CHT cells", "GSM4384818", null, "source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "4.5 dpf CHT cells", "UMI tools was used to analysis our single cell data.Firstly  in \u201cwhitelist\u201d step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI  and R2 is biological sequencing. Then in \u201cextract\u201d step we filter some low quality reads and non UMI reads with recommend parameters  so that we can use STAR to map to the reference genome. Finally  in \u201ccount\u201d step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples  measured by UMI counts", "zebrafish embryos", null, "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture\u2019s introduction.", null, "genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "GSM4384818", "GSM4384818: 4.5 dpf CHT cells; Danio rerio; RNA Seq", "GSM4384818", null, "1", "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture's introduction.", "GEO Accession:GSM4384818", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP251673", null, null, "171353H-CHT-4dpf_2_R1.fq.gz 171353H-CHT-4dpf_2_R2.fq.gz", "fastq fastq", 15872844300.0, 52909481.0, "GSM4384818 r3", "0:150 1:150", "A:3729663981;C:3022353413;G:5072752670;T:4047900723;N:173513", 150, 150, null, null, 3729663981, 3022353413, 5072752670, 4047900723, 173513, "SRX7854786", "SRS6264269", "SRA1051251", "GEO", "Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES", 2, 0.0, 0.92013, 0.0, 0.0618, 1.0, 0.83871, null, 0.51823, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-03-05", "Larval", "Larval", "Blood", "Hematopoietic System"], [57174, "SRR11243183", "SRX7854786", "SRS6264269", "SRP251673", "PRJNA610520", "A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish", "GSE146404", "Transcriptome Analysis", "To profile the developmental landscape of fetal HSPCs and their local niche  here  by using single cell RNA sequencing  we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10\u00d7 Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.", null, "pubmed:33785593", null, "4.5 dpf CHT cells", "GSM4384818", null, "source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "4.5 dpf CHT cells", "UMI tools was used to analysis our single cell data.Firstly  in \u201cwhitelist\u201d step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI  and R2 is biological sequencing. Then in \u201cextract\u201d step we filter some low quality reads and non UMI reads with recommend parameters  so that we can use STAR to map to the reference genome. Finally  in \u201ccount\u201d step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples  measured by UMI counts", "zebrafish embryos", null, "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture\u2019s introduction.", null, "genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "GSM4384818", "GSM4384818: 4.5 dpf CHT cells; Danio rerio; RNA Seq", "GSM4384818", null, "1", "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture's introduction.", "GEO Accession:GSM4384818", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP251673", null, null, "171353H-CHT-4dpf_1_R1.fq.gz 171353H-CHT-4dpf_1_R2.fq.gz", "fastq fastq", 17996156400.0, 59987188.0, "GSM4384818 r4", "0:150 1:150", "A:4218380165;C:3448565478;G:5754713324;T:4574296718;N:200715", 150, 150, null, null, 4218380165, 3448565478, 5754713324, 4574296718, 200715, "SRX7854786", "SRS6264269", "SRA1051251", "GEO", "Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES", 2, 0.0, 0.92379, 0.0, 0.06035, 1.0, 0.83857, null, 0.52292, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-03-05", "Larval", "Larval", "Blood", "Hematopoietic System"], [57175, "SRR11243184", "SRX7854786", "SRS6264269", "SRP251673", "PRJNA610520", "A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish", "GSE146404", "Transcriptome Analysis", "To profile the developmental landscape of fetal HSPCs and their local niche  here  by using single cell RNA sequencing  we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10\u00d7 Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.", null, "pubmed:33785593", null, "4.5 dpf CHT cells", "GSM4384818", null, "source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "4.5 dpf CHT cells", "UMI tools was used to analysis our single cell data.Firstly  in \u201cwhitelist\u201d step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI  and R2 is biological sequencing. Then in \u201cextract\u201d step we filter some low quality reads and non UMI reads with recommend parameters  so that we can use STAR to map to the reference genome. Finally  in \u201ccount\u201d step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples  measured by UMI counts", "zebrafish embryos", null, "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture\u2019s introduction.", null, "genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "GSM4384818", "GSM4384818: 4.5 dpf CHT cells; Danio rerio; RNA Seq", "GSM4384818", null, "1", "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture's introduction.", "GEO Accession:GSM4384818", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP251673", null, null, "171353H-CHT-4dpf_1-2_R1.fq.gz 171353H-CHT-4dpf_1-2_R2.fq.gz", "fastq fastq", 39542324700.0, 131807749.0, "GSM4384818 r5", "0:150 1:150", "A:8830009820;C:7582391853;G:13173552664;T:9955867355;N:503008", 150, 150, null, null, 8830009820, 7582391853, 13173552664, 9955867355, 503008, "SRX7854786", "SRS6264269", "SRA1051251", "GEO", "Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES", 2, 0.0, 0.91925, 0.0, 0.05821, 1.0, 0.83989, null, 0.50837, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-03-05", "Larval", "Larval", "Blood", "Hematopoietic System"], [57176, "SRR11243176", "SRX7854785", "SRS6264267", "SRP251673", "PRJNA610520", "A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish", "GSE146404", "Transcriptome Analysis", "To profile the developmental landscape of fetal HSPCs and their local niche  here  by using single cell RNA sequencing  we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10\u00d7 Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.", null, "pubmed:33785593", null, "3.5 dpf CHT cells", "GSM4384817", null, "source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "3.5 dpf CHT cells", "UMI tools was used to analysis our single cell data.Firstly  in \u201cwhitelist\u201d step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI  and R2 is biological sequencing. Then in \u201cextract\u201d step we filter some low quality reads and non UMI reads with recommend parameters  so that we can use STAR to map to the reference genome. Finally  in \u201ccount\u201d step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples  measured by UMI counts", "zebrafish embryos", null, "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture\u2019s introduction.", null, "genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "GSM4384817", "GSM4384817: 3.5 dpf CHT cells; Danio rerio; RNA Seq", "GSM4384817", null, "1", "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture's introduction.", "GEO Accession:GSM4384817", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP251673", null, null, "171353F_CHT-3dpf_4_R1.fq.gz 171353F_CHT-3dpf_4_R2.fq.gz", "fastq fastq", 71692100700.0, 238973669.0, "GSM4384817 r1", "0:150 1:150", "A:17020567059;C:13566816873;G:21814800469;T:19287755240;N:2161059", 150, 150, null, null, 17020567059, 13566816873, 21814800469, 19287755240, 2161059, "SRX7854785", "SRS6264267", "SRA1051251", "GEO", "Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES", 2, 0.0, 0.9088, 0.0, 0.06027, 1.0, 0.82733, null, 0.50573, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-03-05", "Larval", "Larval", "Blood", "Hematopoietic System"], [57177, "SRR11243177", "SRX7854785", "SRS6264267", "SRP251673", "PRJNA610520", "A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish", "GSE146404", "Transcriptome Analysis", "To profile the developmental landscape of fetal HSPCs and their local niche  here  by using single cell RNA sequencing  we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10\u00d7 Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.", null, "pubmed:33785593", null, "3.5 dpf CHT cells", "GSM4384817", null, "source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "3.5 dpf CHT cells", "UMI tools was used to analysis our single cell data.Firstly  in \u201cwhitelist\u201d step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI  and R2 is biological sequencing. Then in \u201cextract\u201d step we filter some low quality reads and non UMI reads with recommend parameters  so that we can use STAR to map to the reference genome. Finally  in \u201ccount\u201d step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples  measured by UMI counts", "zebrafish embryos", null, "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture\u2019s introduction.", null, "genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "GSM4384817", "GSM4384817: 3.5 dpf CHT cells; Danio rerio; RNA Seq", "GSM4384817", null, "1", "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture's introduction.", "GEO Accession:GSM4384817", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP251673", null, null, "171353F_CHT-3dpf_1_R2.fq.gz 171353F_CHT-3dpf_1_R1.fq.gz", "fastq fastq", 57793587900.0, 192645293.0, "GSM4384817 r2", "0:150 1:150", "A:13736253697;C:10912235777;G:17579141926;T:15564212842;N:1743658", 150, 150, null, null, 13736253697, 10912235777, 17579141926, 15564212842, 1743658, "SRX7854785", "SRS6264267", "SRA1051251", "GEO", "Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES", 2, 0.0, 0.90774, 0.0, 0.06058, 1.0, 0.82875, null, 0.49524, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-03-05", "Larval", "Larval", "Blood", "Hematopoietic System"], [57178, "SRR11243178", "SRX7854785", "SRS6264267", "SRP251673", "PRJNA610520", "A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish", "GSE146404", "Transcriptome Analysis", "To profile the developmental landscape of fetal HSPCs and their local niche  here  by using single cell RNA sequencing  we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10\u00d7 Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.", null, "pubmed:33785593", null, "3.5 dpf CHT cells", "GSM4384817", null, "source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "3.5 dpf CHT cells", "UMI tools was used to analysis our single cell data.Firstly  in \u201cwhitelist\u201d step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI  and R2 is biological sequencing. Then in \u201cextract\u201d step we filter some low quality reads and non UMI reads with recommend parameters  so that we can use STAR to map to the reference genome. Finally  in \u201ccount\u201d step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples  measured by UMI counts", "zebrafish embryos", null, "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture\u2019s introduction.", null, "genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "GSM4384817", "GSM4384817: 3.5 dpf CHT cells; Danio rerio; RNA Seq", "GSM4384817", null, "1", "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture's introduction.", "GEO Accession:GSM4384817", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP251673", null, null, "171353F_CHT-3dpf_3_R2.fq.gz 171353F_CHT-3dpf_3_R1.fq.gz", "fastq fastq", 63713003700.0, 212376679.0, "GSM4384817 r3", "0:150 1:150", "A:15098662178;C:12078656688;G:19421188669;T:17112576360;N:1919805", 150, 150, null, null, 15098662178, 12078656688, 19421188669, 17112576360, 1919805, "SRX7854785", "SRS6264267", "SRA1051251", "GEO", "Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES", 2, 0.0, 0.90945, 0.0, 0.06034, 1.0, 0.83149, null, 0.50559, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-03-05", "Larval", "Larval", "Blood", "Hematopoietic System"], [57179, "SRR11243179", "SRX7854785", "SRS6264267", "SRP251673", "PRJNA610520", "A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish", "GSE146404", "Transcriptome Analysis", "To profile the developmental landscape of fetal HSPCs and their local niche  here  by using single cell RNA sequencing  we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10\u00d7 Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.", null, "pubmed:33785593", null, "3.5 dpf CHT cells", "GSM4384817", null, "source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "3.5 dpf CHT cells", "UMI tools was used to analysis our single cell data.Firstly  in \u201cwhitelist\u201d step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI  and R2 is biological sequencing. Then in \u201cextract\u201d step we filter some low quality reads and non UMI reads with recommend parameters  so that we can use STAR to map to the reference genome. Finally  in \u201ccount\u201d step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples  measured by UMI counts", "zebrafish embryos", null, "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture\u2019s introduction.", null, "genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells", "GSM4384817", "GSM4384817: 3.5 dpf CHT cells; Danio rerio; RNA Seq", "GSM4384817", null, "1", "Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10\u00d7 Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10\u00d7 Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10\u00d7 Genomics  120237 following the manufacture's introduction.", "GEO Accession:GSM4384817", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP251673", null, null, "171353F_CHT-3dpf_2_R1.fq.gz 171353F_CHT-3dpf_2_R2.fq.gz", "fastq fastq", 71620433400.0, 238734778.0, "GSM4384817 r4", "0:150 1:150", "A:16843285494;C:13823957864;G:21855431757;T:19095628638;N:2129647", 150, 150, null, null, 16843285494, 13823957864, 21855431757, 19095628638, 2129647, "SRX7854785", "SRS6264267", "SRA1051251", "GEO", "Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES", 2, 0.0, 0.90995, 0.0, 0.06019, 1.0, 0.82767, null, 0.49515, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-03-05", "Larval", "Larval", "Blood", "Hematopoietic System"], [60923, "SRR12658672", "SRX9139730", "SRS7381396", "SRP282672", "PRJNA663960", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development", "GSE158099", "Transcriptome Analysis", "We used single cell RNA sequencing to investigate the expression and the heterogeneity of wild type and runx1 mutant cd41 GFPLow cd41GFP hematopoietic stem and progenitor cells at embryonic 2.5 dpf  dpf and larval stages 6  10 dpf 16 dpf. Overall design: Single cell RNA seq with FACS sorted cd41 GFPlow cells from wild type and runx1 /  at 2.5  6  10 dpf 16 dpf.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "cd41:GFPlow runx1 /  bloodless 16dpf", "GSM4792215", null, "tissue:sorted cd41:GFPlow|strain:EK|genotype/variation:runx1 /  del8  hg96 tgcd41:GFP|age:16 dpf|cell subset:sorted cd41:GFPlow", "cd41:GFPlow runx1 /  bloodless 16dpf", "Sequences from the Chromium platform were de multiplexed and aligned using CellRanger ver. 2.0.2 from 10x Genomics using custom zebrafish reference genome GRCz10 and transcript annotation reference GRCz10.87 with default parameters. Genome build: GRCz10 Supplementary files format and content: barcodes.tsv  genes.tsv  features.tsv  matrix.mtx", "sorted cd41:GFPlow", null, "Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell 3\u2019 Library & Gel Bead Kit v3. Cell lysis  cDNA preparation and library construction were prepared following the manufacturer's protocol.", null, "strain:EK|genotype/variation:runx1 /  del8  hg96 tgcd41:GFP|age:16 dpf|cell subset:sorted cd41:GFPlow", "GSM4792215", "GSM4792215: cd41:GFPlow runx1 /  bloodless 16dpf; Danio rerio; RNA Seq", "GSM4792215", null, "1", "Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell three prime Library & Gel Bead Kit v3. Cell lysis  cDNA preparation and library construction were prepared following the manufacturer's protocol.", "GEO Accession:GSM4792215", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP282672", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=SC8.EB200211 2.R1.fastq.gz   read2PairFiles=SC8.EB200211 2.R2.fastq.gz   read3PairFiles=SC8.EB200211 2.I1.fastq.gz", "SC8.EB200211_2.I1.fastq.gz SC8.EB200211_2.R1.fastq.gz SC8.EB200211_2.R2.fastq.gz", "fastq fastq fastq", 31985659032.0, 238698948.0, "GSM4792215 r1", "0:28 1:98 2:8", "A:8834796646;C:7245480386;G:7345360172;T:8558850270;N:1171558", 28, 98, 8, null, 8834796646, 7245480386, 7345360172, 8558850270, 1171558, "SRX9139730", "SRS7381396", "SRA1126726", "GEO", "NHGRI", 1, 0.93838, null, 0.0839, null, 0.7558, null, 0.51065, null, 98, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-09-16", "Larval", "Larval", "Blood", "Hematopoietic System"], [61983, "SRR13080692", "SRX9527457", "SRS7734428", "SRP293088", "PRJNA679243", "A Non Canonical Type 2 Immune Response Coordinates Tuberculous Granuloma Formation and Epithelialization", "GSE161712", "Other", "Using the zebrafish M. marinum model  we identify the basis of granuloma macrophage transformation. Single cell RNA seq analysis of zebrafish granulomas as well as analysis of M. tuberculosis infected macaques reveal that  even in the presence of robust type 1 immune responses  countervailing type 2 signals associate with macrophage epithelialization. We find that type 2 immune signaling  mediated via stat6  is absolutely required for epithelialization and granuloma formation. Overall design: Wildtype zebrafish M. marinum granuloma single cell RNAseq profile.", null, "pubmed:33761328", null, "*AB wildtype zebrafish M.marinum granuloma cells", "GSM4913139", null, "source name:WT Zebrafish granuloma cels|tissue:Granulomas|cell type:Granuloma cells|zebrafish strain:*AB", "*AB wildtype zebrafish M.marinum granuloma cells", "10X Cell Ranger was used to demultiplex raw base call BCL files generated by an Illumina sequencer into FASTQ before aligning them to the Ensembl zebrafish genome assembly GRCz11.96  performed filtering  barcode and UMI counting. Genome build: GRCz11.96 Supplementary files format and content: WTGran.matrix.mtx:  Gene barcode matrix in Market Exchange Format MEX for Mus musculus Uninjured Control & Injured1d  tibialis anterior muscle cells. Columns correspond to individual cellsbarcodes  while rows correspond to genes. Supplementary files format and content: WTGran.features.tsv: Genes corresponding to row indices in matrix.mtx. Gene ID and gene name are stored in the first and second column. Supplementary files format and content: WTGran.barcodes.tsv: Barcode sequences that correspond to column indices in matrix.mtx.", "WT Zebrafish granuloma cels", null, "Granulomas were microdissected from of tissues 14 days post infection and cells dissociated using 30 minute incubation with 0.05% trypsin/EDTA Library preparation was done using Chromium Single Cell 3\u2019 GEM  Library and Gel Bead Kit v3.", "Adult  wildtype *AB zebrafish were infected with 350 fluorescent bacteria of M. marinum.", "tissue:Granulomas|cell type:Granuloma cells|zebrafish strain:*AB", "GSM4913139", "GSM4913139: *AB wildtype zebrafish M.marinum granuloma cells; Danio rerio; RNA Seq", "GSM4913139", null, "1", "Granulomas were microdissected from of tissues 14 days post infection and cells dissociated using 30 minute incubation with 0.05% trypsin/EDTA Library preparation was done using Chromium Single Cell three prime GEM  Library and Gel Bead Kit v3.", "GEO Accession:GSM4913139", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP293088", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=5761 S1 L001 I1 001.fastq.gz   read2PairFiles=5761 S1 L001 R1 001.fastq.gz   read3PairFiles=5761 S1 L001 R2 001.fastq.gz", "5761_S1_L001_I1_001.fastq.gz 5761_S1_L001_R1_001.fastq.gz 5761_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 13295345266.0, 104687758.0, "GSM4913139 r1", "0:8 1:28 2:91", "A:3755348831;C:2900888340;G:2979576059;T:3656820253;N:2711783", 8, 28, 91, null, 3755348831, 2900888340, 2979576059, 3656820253, 2711783, "SRX9527457", "SRS7734428", "SRA1160946", "GEO", "Tobin, Molecular Genetics and Microbiology, Duke University", 1, 0.92709, null, 0.13791, null, 0.81929, null, 0.57724, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-18", "Adult", "Adult", "Blood", "Hematopoietic System"], [61984, "SRR13080693", "SRX9527457", "SRS7734428", "SRP293088", "PRJNA679243", "A Non Canonical Type 2 Immune Response Coordinates Tuberculous Granuloma Formation and Epithelialization", "GSE161712", "Other", "Using the zebrafish M. marinum model  we identify the basis of granuloma macrophage transformation. Single cell RNA seq analysis of zebrafish granulomas as well as analysis of M. tuberculosis infected macaques reveal that  even in the presence of robust type 1 immune responses  countervailing type 2 signals associate with macrophage epithelialization. We find that type 2 immune signaling  mediated via stat6  is absolutely required for epithelialization and granuloma formation. Overall design: Wildtype zebrafish M. marinum granuloma single cell RNAseq profile.", null, "pubmed:33761328", null, "*AB wildtype zebrafish M.marinum granuloma cells", "GSM4913139", null, "source name:WT Zebrafish granuloma cels|tissue:Granulomas|cell type:Granuloma cells|zebrafish strain:*AB", "*AB wildtype zebrafish M.marinum granuloma cells", "10X Cell Ranger was used to demultiplex raw base call BCL files generated by an Illumina sequencer into FASTQ before aligning them to the Ensembl zebrafish genome assembly GRCz11.96  performed filtering  barcode and UMI counting. Genome build: GRCz11.96 Supplementary files format and content: WTGran.matrix.mtx:  Gene barcode matrix in Market Exchange Format MEX for Mus musculus Uninjured Control & Injured1d  tibialis anterior muscle cells. Columns correspond to individual cellsbarcodes  while rows correspond to genes. Supplementary files format and content: WTGran.features.tsv: Genes corresponding to row indices in matrix.mtx. Gene ID and gene name are stored in the first and second column. Supplementary files format and content: WTGran.barcodes.tsv: Barcode sequences that correspond to column indices in matrix.mtx.", "WT Zebrafish granuloma cels", null, "Granulomas were microdissected from of tissues 14 days post infection and cells dissociated using 30 minute incubation with 0.05% trypsin/EDTA Library preparation was done using Chromium Single Cell 3\u2019 GEM  Library and Gel Bead Kit v3.", "Adult  wildtype *AB zebrafish were infected with 350 fluorescent bacteria of M. marinum.", "tissue:Granulomas|cell type:Granuloma cells|zebrafish strain:*AB", "GSM4913139", "GSM4913139: *AB wildtype zebrafish M.marinum granuloma cells; Danio rerio; RNA Seq", "GSM4913139", null, "1", "Granulomas were microdissected from of tissues 14 days post infection and cells dissociated using 30 minute incubation with 0.05% trypsin/EDTA Library preparation was done using Chromium Single Cell three prime GEM  Library and Gel Bead Kit v3.", "GEO Accession:GSM4913139", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP293088", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=5895 S1 L001 I1 001.fastq.gz   read2PairFiles=5895 S1 L001 R1 001.fastq.gz   read3PairFiles=5895 S1 L001 R2 001.fastq.gz", "5895_S1_L001_I1_001.fastq.gz 5895_S1_L001_R1_001.fastq.gz 5895_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 17723636384.0, 139556192.0, "GSM4913139 r2", "0:8 1:28 2:91", "A:4955483447;C:3902218538;G:4036183306;T:4807856940;N:21894153", 8, 28, 91, null, 4955483447, 3902218538, 4036183306, 4807856940, 21894153, "SRX9527457", "SRS7734428", "SRA1160946", "GEO", "Tobin, Molecular Genetics and Microbiology, Duke University", 1, 0.9176, null, 0.13304, null, 0.81462, null, 0.57616, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-18", "Adult", "Adult", "Blood", "Hematopoietic System"], [65651, "SRR15483596", "SRX11783413", "SRS9786611", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "runx1:mCherry+ at 52 hpf #2 replicate", "GSM5525118", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:runx1+23:nls mCherry", "runx1:mCherry+ at 52 hpf #2 replicate", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:runx1+23:nls mCherry", "GSM5525118", "GSM5525118: runx1:mCherry+ at 52 hpf #2 replicate; Danio rerio; RNA Seq", "GSM5525118", null, "1", "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525118", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=R2 2 S1 L001 R1 001.fastq.gz   read2PairFiles=R2 2 S1 L001 R2 001.fastq.gz   read3PairFiles=R2 2 S1 L001 I1 001.fastq.gz", "R2-2_S1_L001_I1_001.fastq.gz R2-2_S1_L001_R1_001.fastq.gz R2-2_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 59162946612.0, 192087489.0, "GSM5525118 r1", "0:150 1:150 2:8", "A:6826510360;C:7720741166;G:7033747534;T:7231279942;N:844348", 150, 150, 8, null, 6826510360, 7720741166, 7033747534, 7231279942, 844348, "SRX11783413", "SRS9786611", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.95266, null, 0.01784, null, 0.93022, null, 0.46235, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65652, "SRR15483597", "SRX11783413", "SRS9786611", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "runx1:mCherry+ at 52 hpf #2 replicate", "GSM5525118", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:runx1+23:nls mCherry", "runx1:mCherry+ at 52 hpf #2 replicate", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:runx1+23:nls mCherry", "GSM5525118", "GSM5525118: runx1:mCherry+ at 52 hpf #2 replicate; Danio rerio; RNA Seq", "GSM5525118", null, "1", "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525118", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=R2 2 S1 L002 R1 001.fastq.gz   read2PairFiles=R2 2 S1 L002 R2 001.fastq.gz   read3PairFiles=R2 2 S1 L002 I1 001.fastq.gz", "R2-2_S1_L002_I1_001.fastq.gz R2-2_S1_L002_R1_001.fastq.gz R2-2_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 67940768588.0, 220586911.0, "GSM5525118 r2", "0:150 1:150 2:8", "A:7901205395;C:8819719149;G:8118311347;T:8243562587;N:5238172", 150, 150, 8, null, 7901205395, 8819719149, 8118311347, 8243562587, 5238172, "SRX11783413", "SRS9786611", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.94536, null, 0.018, null, 0.92839, null, 0.45489, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65653, "SRR15483594", "SRX11783412", "SRS9786609", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "runx1:mCherry+ at 52 hpf #1", "GSM5525117", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:runx1+23:nls mCherry", "runx1:mCherry+ at 52 hpf #1", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:runx1+23:nls mCherry", "GSM5525117", "GSM5525117: runx1:mCherry+ at 52 hpf #1; Danio rerio; RNA Seq", "GSM5525117", null, "1", "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525117", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=R2 1 S1 L001 R1 001.fastq.gz   read2PairFiles=R2 1 S1 L001 R2 001.fastq.gz   read3PairFiles=R2 1 S1 L001 I1 001.fastq.gz", "R2-1_S1_L001_I1_001.fastq.gz R2-1_S1_L001_R1_001.fastq.gz R2-1_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 64542996056.0, 209555182.0, "GSM5525117 r1", "0:150 1:150 2:8", "A:7500200023;C:8401456631;G:7492567345;T:8038123819;N:929482", 150, 150, 8, null, 7500200023, 8401456631, 7492567345, 8038123819, 929482, "SRX11783412", "SRS9786609", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.94027, null, 0.01204, null, 0.94107, null, 0.46801, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65654, "SRR15483595", "SRX11783412", "SRS9786609", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "runx1:mCherry+ at 52 hpf #1", "GSM5525117", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:runx1+23:nls mCherry", "runx1:mCherry+ at 52 hpf #1", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:runx1+23:nls mCherry", "GSM5525117", "GSM5525117: runx1:mCherry+ at 52 hpf #1; Danio rerio; RNA Seq", "GSM5525117", null, "1", "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525117", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=R2 1 S1 L002 R1 001.fastq.gz   read2PairFiles=R2 1 S1 L002 R2 001.fastq.gz   read3PairFiles=R2 1 S1 L002 I1 001.fastq.gz", "R2-1_S1_L002_I1_001.fastq.gz R2-1_S1_L002_R1_001.fastq.gz R2-1_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 61129147772.0, 198471259.0, "GSM5525117 r2", "0:150 1:150 2:8", "A:7164346674;C:7911114850;G:7135136885;T:7555336618;N:4753823", 150, 150, 8, null, 7164346674, 7911114850, 7135136885, 7555336618, 4753823, "SRX11783412", "SRS9786609", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.93152, null, 0.01164, null, 0.94152, null, 0.46255, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65655, "SRR15483588", "SRX11783411", "SRS9786608", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate", "GSM5525116", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525116", "GSM5525116: draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate; Danio rerio; RNA Seq", "GSM5525116", null, "1", "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=DG2 2 S1 L001 R1 001.fastq.gz   read2PairFiles=DG2 2 S1 L001 R2 001.fastq.gz   read3PairFiles=DG2 2 S1 L001 I1 001.fastq.gz", "DG2-2_S1_L001_I1_001.fastq.gz DG2-2_S1_L001_R1_001.fastq.gz DG2-2_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 58062154920.0, 188513490.0, "GSM5525116 r1", "0:150 1:150 2:8", "A:6786904201;C:7461082970;G:6741279762;T:7286929534;N:827033", 150, 150, 8, null, 6786904201, 7461082970, 6741279762, 7286929534, 827033, "SRX11783411", "SRS9786608", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.9442, null, 0.02532, null, 0.92577, null, 0.45185, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65656, "SRR15483589", "SRX11783411", "SRS9786608", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate", "GSM5525116", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525116", "GSM5525116: draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate; Danio rerio; RNA Seq", "GSM5525116", null, "1", "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=DG2 2 S1 L002 R1 001.fastq.gz   read2PairFiles=DG2 2 S1 L002 R2 001.fastq.gz   read3PairFiles=DG2 2 S1 L002 I1 001.fastq.gz", "DG2-2_S1_L002_I1_001.fastq.gz DG2-2_S1_L002_R1_001.fastq.gz DG2-2_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 71629010068.0, 232561721.0, "GSM5525116 r2", "0:150 1:150 2:8", "A:8422157482;C:9164931651;G:8346143692;T:8946552575;N:4472750", 150, 150, 8, null, 8422157482, 9164931651, 8346143692, 8946552575, 4472750, "SRX11783411", "SRS9786608", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.93666, null, 0.02678, null, 0.92232, null, 0.44942, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65657, "SRR15483590", "SRX11783411", "SRS9786608", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate", "GSM5525116", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525116", "GSM5525116: draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate; Danio rerio; RNA Seq", "GSM5525116", null, "1", "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, null, "DG2-2_S1_L003_R1_001.fastq.gz DG2-2_S1_L003_R2_001.fastq.gz", "fastq fastq", 32047702200.0, 106825674.0, "GSM5525116 r3", "0:150 1:150", "A:7309683350;C:6236246000;G:6254785333;T:12244316725;N:2670792", 150, 150, null, null, 7309683350, 6236246000, 6254785333, 12244316725, 2670792, "SRX11783411", "SRS9786608", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 2, 0.01831, 0.94417, 0.00206, 0.02463, 0.99691, 0.92423, 0.53203, 0.45728, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65658, "SRR15483591", "SRX11783411", "SRS9786608", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate", "GSM5525116", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525116", "GSM5525116: draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate; Danio rerio; RNA Seq", "GSM5525116", null, "1", "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, null, "DG2-2_S1_L004_R1_001.fastq.gz DG2-2_S1_L004_R2_001.fastq.gz", "fastq fastq", 37463959500.0, 124879865.0, "GSM5525116 r4", "0:150 1:150", "A:8552446843;C:7287672885;G:7301637904;T:14319175980;N:3025888", 150, 150, null, null, 8552446843, 7287672885, 7301637904, 14319175980, 3025888, "SRX11783411", "SRS9786608", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 2, 0.0179, 0.94533, 0.00191, 0.0243, 0.99691, 0.92261, 0.49722, 0.45421, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65659, "SRR15483592", "SRX11783411", "SRS9786608", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate", "GSM5525116", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525116", "GSM5525116: draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate; Danio rerio; RNA Seq", "GSM5525116", null, "1", "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, null, "DG2-2_S1_L005_R1_001.fastq.gz DG2-2_S1_L005_R2_001.fastq.gz", "fastq fastq", 30981057900.0, 103270193.0, "GSM5525116 r5", "0:150 1:150", "A:7076201480;C:6026934261;G:6065200560;T:11810111130;N:2610469", 150, 150, null, null, 7076201480, 6026934261, 6065200560, 11810111130, 2610469, "SRX11783411", "SRS9786608", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 2, 0.01658, 0.93855, 0.00198, 0.02394, 0.99734, 0.92476, 0.53823, 0.45548, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65660, "SRR15483593", "SRX11783411", "SRS9786608", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate", "GSM5525116", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525116", "GSM5525116: draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate; Danio rerio; RNA Seq", "GSM5525116", null, "1", "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, null, "DG2-2_S1_L006_R1_001.fastq.gz DG2-2_S1_L006_R2_001.fastq.gz", "fastq fastq", 33497811000.0, 111659370.0, "GSM5525116 r6", "0:150 1:150", "A:7673047524;C:6494998239;G:6520425795;T:12806463581;N:2875861", 150, 150, null, null, 7673047524, 6494998239, 6520425795, 12806463581, 2875861, "SRX11783411", "SRS9786608", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 2, 0.01712, 0.94074, 0.00206, 0.02516, 0.99701, 0.92318, 0.56268, 0.45333, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65661, "SRR15483582", "SRX11783410", "SRS9786606", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP  at 52 hpf #1", "GSM5525115", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP  at 52 hpf #1", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525115", "GSM5525115: draculin:mCherry+;gata1:GFP  at 52 hpf #1; Danio rerio; RNA Seq", "GSM5525115", null, "1", "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=DG2 1 S1 L001 R1 001.fastq.gz   read2PairFiles=DG2 1 S1 L001 R2 001.fastq.gz   read3PairFiles=DG2 1 S1 L001 I1 001.fastq.gz", "DG2-1_S1_L001_I1_001.fastq.gz DG2-1_S1_L001_R1_001.fastq.gz DG2-1_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 53816019796.0, 174727337.0, "GSM5525115 r1", "0:150 1:150 2:8", "A:6268319263;C:6935405810;G:6236287882;T:6768309909;N:777686", 150, 150, 8, null, 6268319263, 6935405810, 6236287882, 6768309909, 777686, "SRX11783410", "SRS9786606", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.94373, null, 0.02418, null, 0.93206, null, 0.4538, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65662, "SRR15483583", "SRX11783410", "SRS9786606", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP  at 52 hpf #1", "GSM5525115", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP  at 52 hpf #1", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525115", "GSM5525115: draculin:mCherry+;gata1:GFP  at 52 hpf #1; Danio rerio; RNA Seq", "GSM5525115", null, "1", "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=DG2 1 S1 L002 R1 001.fastq.gz   read2PairFiles=DG2 1 S1 L002 R2 001.fastq.gz   read3PairFiles=DG2 1 S1 L002 I1 001.fastq.gz", "DG2-1_S1_L002_I1_001.fastq.gz DG2-1_S1_L002_R1_001.fastq.gz DG2-1_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 56656687472.0, 183950284.0, "GSM5525115 r2", "0:150 1:150 2:8", "A:6636746214;C:7271043747;G:6588518102;T:7092648593;N:3585944", 150, 150, 8, null, 6636746214, 7271043747, 6588518102, 7092648593, 3585944, "SRX11783410", "SRS9786606", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.9348, null, 0.02385, null, 0.93156, null, 0.45273, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65663, "SRR15483584", "SRX11783410", "SRS9786606", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP  at 52 hpf #1", "GSM5525115", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP  at 52 hpf #1", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525115", "GSM5525115: draculin:mCherry+;gata1:GFP  at 52 hpf #1; Danio rerio; RNA Seq", "GSM5525115", null, "1", "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, null, "DG2-1_S1_L003_R1_001.fastq.gz DG2-1_S1_L003_R2_001.fastq.gz", "fastq fastq", 33218500800.0, 110728336.0, "GSM5525115 r3", "0:150 1:150", "A:7550847416;C:6408594085;G:6405597564;T:12826295610;N:27166125", 150, 150, null, null, 7550847416, 6408594085, 6405597564, 12826295610, 27166125, "SRX11783410", "SRS9786606", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 2, 0.02176, 0.94163, 0.00286, 0.02347, 0.99703, 0.92991, 0.46265, 0.45574, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65664, "SRR15483585", "SRX11783410", "SRS9786606", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP  at 52 hpf #1", "GSM5525115", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP  at 52 hpf #1", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525115", "GSM5525115: draculin:mCherry+;gata1:GFP  at 52 hpf #1; Danio rerio; RNA Seq", "GSM5525115", null, "1", "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, null, "DG2-1_S1_L004_R1_001.fastq.gz DG2-1_S1_L004_R2_001.fastq.gz", "fastq fastq", 33634915800.0, 112116386.0, "GSM5525115 r4", "0:150 1:150", "A:7645827173;C:6494042604;G:6493405590;T:12974094595;N:27545838", 150, 150, null, null, 7645827173, 6494042604, 6493405590, 12974094595, 27545838, "SRX11783410", "SRS9786606", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 2, 0.02104, 0.9407, 0.00263, 0.02247, 0.99701, 0.93257, 0.49246, 0.4561, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65665, "SRR15483586", "SRX11783410", "SRS9786606", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP  at 52 hpf #1", "GSM5525115", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP  at 52 hpf #1", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525115", "GSM5525115: draculin:mCherry+;gata1:GFP  at 52 hpf #1; Danio rerio; RNA Seq", "GSM5525115", null, "1", "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, null, "DG2-1_S1_L005_R1_001.fastq.gz DG2-1_S1_L005_R2_001.fastq.gz", "fastq fastq", 34113860700.0, 113712869.0, "GSM5525115 r5", "0:150 1:150", "A:7749471214;C:6598363925;G:6596788535;T:13141319294;N:27917732", 150, 150, null, null, 7749471214, 6598363925, 6596788535, 13141319294, 27917732, "SRX11783410", "SRS9786606", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 2, 0.02131, 0.94056, 0.0023, 0.02334, 0.99719, 0.93164, 0.50985, 0.45474, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65666, "SRR15483587", "SRX11783410", "SRS9786606", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP  at 52 hpf #1", "GSM5525115", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP  at 52 hpf #1", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525115", "GSM5525115: draculin:mCherry+;gata1:GFP  at 52 hpf #1; Danio rerio; RNA Seq", "GSM5525115", null, "1", "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, null, "DG2-1_S1_L006_R1_001.fastq.gz DG2-1_S1_L006_R2_001.fastq.gz", "fastq fastq", 34597356600.0, 115324522.0, "GSM5525115 r6", "0:150 1:150", "A:7866654210;C:6690644103;G:6695640643;T:13316020558;N:28397086", 150, 150, null, null, 7866654210, 6690644103, 6695640643, 13316020558, 28397086, "SRX11783410", "SRS9786606", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 2, 0.02131, 0.94082, 0.00235, 0.02244, 0.99665, 0.93089, 0.53827, 0.45518, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65667, "SRR15483581", "SRX11783409", "SRS9786607", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP  at 30 hpf #2 replicate", "GSM5525114", null, "tissue:hematopoietic cells|developmental stage:30 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP  at 30 hpf #2 replicate", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:30 hpf line:draculin:mCherry;gata1:GFP", "GSM5525114", "GSM5525114: draculin:mCherry+;gata1:GFP  at 30 hpf #2 replicate; Danio rerio; RNA Seq", "GSM5525114", null, "1", "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525114", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=DG1 3 S1 L001 R1 001.fastq.gz   read2PairFiles=DG1 3 S1 L001 R2 001.fastq.gz   read3PairFiles=DG1 3 S1 L001 I1 001.fastq.gz", "DG1-3_S1_L001_I1_001.fastq.gz DG1-3_S1_L001_R1_001.fastq.gz DG1-3_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 53654080172.0, 174201559.0, "GSM5525114 r1", "0:150 1:150 2:8", "A:6842604916;C:6327854414;G:6203934909;T:6755061460;N:778151", 150, 150, 8, null, 6842604916, 6327854414, 6203934909, 6755061460, 778151, "SRX11783409", "SRS9786607", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.92988, null, 0.06632, null, 0.84691, null, 0.45741, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [65668, "SRR15483580", "SRX11783408", "SRS9786605", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP  at 30 hpf #1", "GSM5525113", null, "tissue:hematopoietic cells|developmental stage:30 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP  at 30 hpf #1", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:30 hpf line:draculin:mCherry;gata1:GFP", "GSM5525113", "GSM5525113: draculin:mCherry+;gata1:GFP  at 30 hpf #1; Danio rerio; RNA Seq", "GSM5525113", null, "1", "draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525113", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=DG1 2 S1 L001 R1 001.fastq.gz   read2PairFiles=DG1 2 S1 L001 R2 001.fastq.gz   read3PairFiles=DG1 2 S1 L001 I1 001.fastq.gz", "DG1-2_S1_L001_I1_001.fastq.gz DG1-2_S1_L001_R1_001.fastq.gz DG1-2_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 65514487192.0, 212709374.0, "GSM5525113 r1", "0:150 1:150 2:8", "A:8050271487;C:8057897221;G:7684156435;T:8113136954;N:944003", 150, 150, 8, null, 8050271487, 8057897221, 7684156435, 8113136954, 944003, "SRX11783408", "SRS9786605", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.94401, null, 0.03521, null, 0.88339, null, 0.35428, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [67584, "SRR17218121", "SRX13397710", "SRS11300870", "SRP350544", "PRJNA788489", "Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish", "GSE190794", "Transcriptome Analysis", "The zebrafish has proven to be a valuable model organism for studying hematopoiesis  but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus  elucidated B and T cell developmental trajectories  and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations  a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically  kidney marrows only were dissected from 3 adult GESTALT zebrafish  paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish  and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample  whereas 4 lanes were used for the juvenile thymi to obtain 4 technical replicates.", null, "pubmed:35938989", null, "Juvenile  Thymus  4", "GSM5732082", null, "tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "Juvenile  Thymus  4", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms", "sorted live thymus cells", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "GSM5732082", "GSM5732082: Juvenile  Thymus  4; Danio rerio; RNA Seq", "GSM5732082", null, "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "GEO Accession:GSM5732082", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350544", null, "loader:fastq load.py", "4wpfThymus_6_S4_L001_I1_001.fastq.gz 4wpfThymus_6_S4_L001_R1_001.fastq.gz 4wpfThymus_6_S4_L001_R2_001.fastq.gz", "fastq fastq fastq", 14767492309.0, 116279467.0, "GSM5732082 r1", "0:8 1:28 2:91", "A:3176407665;C:2147673056;G:2551453338;T:2705740495;N:156943", 8, 28, 91, null, 3176407665, 2147673056, 2551453338, 2705740495, 156943, "SRX13397710", "SRS11300870", "SRA1342645", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.87149, null, 0.22037, null, 0.84049, null, 0.53423, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-13", "Multi-stage", "Multi-stage", "Thymus", "Hematopoietic System"], [67585, "SRR17218122", "SRX13397710", "SRS11300870", "SRP350544", "PRJNA788489", "Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish", "GSE190794", "Transcriptome Analysis", "The zebrafish has proven to be a valuable model organism for studying hematopoiesis  but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus  elucidated B and T cell developmental trajectories  and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations  a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically  kidney marrows only were dissected from 3 adult GESTALT zebrafish  paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish  and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample  whereas 4 lanes were used for the juvenile thymi to obtain 4 technical replicates.", null, "pubmed:35938989", null, "Juvenile  Thymus  4", "GSM5732082", null, "tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "Juvenile  Thymus  4", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms", "sorted live thymus cells", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "GSM5732082", "GSM5732082: Juvenile  Thymus  4; Danio rerio; RNA Seq", "GSM5732082", null, "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "GEO Accession:GSM5732082", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350544", null, "loader:fastq load.py", "4wpfThymus_6_S4_L002_I1_001.fastq.gz 4wpfThymus_6_S4_L002_R1_001.fastq.gz 4wpfThymus_6_S4_L002_R2_001.fastq.gz", "fastq fastq fastq", 14660763541.0, 115439083.0, "GSM5732082 r2", "0:8 1:28 2:91", "A:3154820274;C:2128697452;G:2532561232;T:2688755742;N:121853", 8, 28, 91, null, 3154820274, 2128697452, 2532561232, 2688755742, 121853, "SRX13397710", "SRS11300870", "SRA1342645", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.87166, null, 0.22046, null, 0.8407, null, 0.5334, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-13", "Multi-stage", "Multi-stage", "Thymus", "Hematopoietic System"], [67586, "SRR17218119", "SRX13397709", "SRS11300871", "SRP350544", "PRJNA788489", "Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish", "GSE190794", "Transcriptome Analysis", "The zebrafish has proven to be a valuable model organism for studying hematopoiesis  but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus  elucidated B and T cell developmental trajectories  and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations  a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically  kidney marrows only were dissected from 3 adult GESTALT zebrafish  paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish  and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample  whereas 4 lanes were used for the juvenile thymi to obtain 4 technical replicates.", null, "pubmed:35938989", null, "Juvenile  Thymus  3", "GSM5732081", null, "tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "Juvenile  Thymus  3", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms", "sorted live thymus cells", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "GSM5732081", "GSM5732081: Juvenile  Thymus  3; Danio rerio; RNA Seq", "GSM5732081", null, "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "GEO Accession:GSM5732081", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350544", null, "loader:fastq load.py", "4wpfThymus_5_S3_L001_I1_001.fastq.gz 4wpfThymus_5_S3_L001_R1_001.fastq.gz 4wpfThymus_5_S3_L001_R2_001.fastq.gz", "fastq fastq fastq", 14488701909.0, 114084267.0, "GSM5732081 r1", "0:8 1:28 2:91", "A:3107408243;C:2119850736;G:2503503910;T:2650750983;N:154425", 8, 28, 91, null, 3107408243, 2119850736, 2503503910, 2650750983, 154425, "SRX13397709", "SRS11300871", "SRA1342645", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.85944, null, 0.20997, null, 0.84064, null, 0.53634, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-13", "Multi-stage", "Multi-stage", "Thymus", "Hematopoietic System"], [67587, "SRR17218120", "SRX13397709", "SRS11300871", "SRP350544", "PRJNA788489", "Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish", "GSE190794", "Transcriptome Analysis", "The zebrafish has proven to be a valuable model organism for studying hematopoiesis  but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus  elucidated B and T cell developmental trajectories  and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations  a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically  kidney marrows only were dissected from 3 adult GESTALT zebrafish  paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish  and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample  whereas 4 lanes were used for the juvenile thymi to obtain 4 technical replicates.", null, "pubmed:35938989", null, "Juvenile  Thymus  3", "GSM5732081", null, "tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "Juvenile  Thymus  3", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms", "sorted live thymus cells", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "GSM5732081", "GSM5732081: Juvenile  Thymus  3; Danio rerio; RNA Seq", "GSM5732081", null, "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "GEO Accession:GSM5732081", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350544", null, "loader:fastq load.py", "4wpfThymus_5_S3_L002_I1_001.fastq.gz 4wpfThymus_5_S3_L002_R1_001.fastq.gz 4wpfThymus_5_S3_L002_R2_001.fastq.gz", "fastq fastq fastq", 14352524508.0, 113012004.0, "GSM5732081 r2", "0:8 1:28 2:91", "A:3079316058;C:2096769810;G:2479668921;T:2628218918;N:118657", 8, 28, 91, null, 3079316058, 2096769810, 2479668921, 2628218918, 118657, "SRX13397709", "SRS11300871", "SRA1342645", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.85981, null, 0.21085, null, 0.8393, null, 0.52667, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-13", "Multi-stage", "Multi-stage", "Thymus", "Hematopoietic System"], [67588, "SRR17218117", "SRX13397708", "SRS11300869", "SRP350544", "PRJNA788489", "Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish", "GSE190794", "Transcriptome Analysis", "The zebrafish has proven to be a valuable model organism for studying hematopoiesis  but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus  elucidated B and T cell developmental trajectories  and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations  a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically  kidney marrows only were dissected from 3 adult GESTALT zebrafish  paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish  and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample  whereas 4 lanes were used for the juvenile thymi to obtain 4 technical replicates.", null, "pubmed:35938989", null, "Juvenile  Thymus  2", "GSM5732080", null, "tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "Juvenile  Thymus  2", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms", "sorted live thymus cells", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "GSM5732080", "GSM5732080: Juvenile  Thymus  2; Danio rerio; RNA Seq", "GSM5732080", null, "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "GEO Accession:GSM5732080", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350544", null, "loader:fastq load.py", "4wpfThymus_3_S2_L001_I1_001.fastq.gz 4wpfThymus_3_S2_L001_R1_001.fastq.gz 4wpfThymus_3_S2_L001_R2_001.fastq.gz", "fastq fastq fastq", 17459416821.0, 137475723.0, "GSM5732080 r1", "0:8 1:28 2:91", "A:3740652508;C:2562291967;G:3023715848;T:3183446304;N:184166", 8, 28, 91, null, 3740652508, 2562291967, 3023715848, 3183446304, 184166, "SRX13397708", "SRS11300869", "SRA1342645", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.84416, null, 0.21191, null, 0.83897, null, 0.53108, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-13", "Multi-stage", "Multi-stage", "Thymus", "Hematopoietic System"], [67589, "SRR17218118", "SRX13397708", "SRS11300869", "SRP350544", "PRJNA788489", "Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish", "GSE190794", "Transcriptome Analysis", "The zebrafish has proven to be a valuable model organism for studying hematopoiesis  but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus  elucidated B and T cell developmental trajectories  and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations  a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically  kidney marrows only were dissected from 3 adult GESTALT zebrafish  paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish  and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample  whereas 4 lanes were used for the juvenile thymi to obtain 4 technical replicates.", null, "pubmed:35938989", null, "Juvenile  Thymus  2", "GSM5732080", null, "tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "Juvenile  Thymus  2", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms", "sorted live thymus cells", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "GSM5732080", "GSM5732080: Juvenile  Thymus  2; Danio rerio; RNA Seq", "GSM5732080", null, "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "GEO Accession:GSM5732080", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350544", null, "loader:fastq load.py", "4wpfThymus_3_S2_L002_I1_001.fastq.gz 4wpfThymus_3_S2_L002_R1_001.fastq.gz 4wpfThymus_3_S2_L002_R2_001.fastq.gz", "fastq fastq fastq", 17241251014.0, 135757882.0, "GSM5732080 r2", "0:8 1:28 2:91", "A:3695117374;C:2526230853;G:2985988000;T:3146489343;N:141692", 8, 28, 91, null, 3695117374, 2526230853, 2985988000, 3146489343, 141692, "SRX13397708", "SRS11300869", "SRA1342645", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.84569, null, 0.21301, null, 0.83899, null, 0.53404, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-13", "Multi-stage", "Multi-stage", "Thymus", "Hematopoietic System"], [67590, "SRR17218115", "SRX13397707", "SRS11300868", "SRP350544", "PRJNA788489", "Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish", "GSE190794", "Transcriptome Analysis", "The zebrafish has proven to be a valuable model organism for studying hematopoiesis  but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus  elucidated B and T cell developmental trajectories  and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations  a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically  kidney marrows only were dissected from 3 adult GESTALT zebrafish  paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish  and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample  whereas 4 lanes were used for the juvenile thymi to obtain 4 technical replicates.", null, "pubmed:35938989", null, "Juvenile  Thymus  1", "GSM5732079", null, "tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "Juvenile  Thymus  1", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms", "sorted live thymus cells", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "GSM5732079", "GSM5732079: Juvenile  Thymus  1; Danio rerio; RNA Seq", "GSM5732079", null, "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "GEO Accession:GSM5732079", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350544", null, "loader:fastq load.py", "4wpfThymus_1_S1_L001_I1_001.fastq.gz 4wpfThymus_1_S1_L001_R1_001.fastq.gz 4wpfThymus_1_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 16221392627.0, 127727501.0, "GSM5732079 r1", "0:8 1:28 2:91", "A:3503038095;C:2359078159;G:2792714907;T:2968200161;N:171269", 8, 28, 91, null, 3503038095, 2359078159, 2792714907, 2968200161, 171269, "SRX13397707", "SRS11300868", "SRA1342645", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.84501, null, 0.21705, null, 0.8379, null, 0.53566, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-13", "Multi-stage", "Multi-stage", "Thymus", "Hematopoietic System"], [67591, "SRR17218116", "SRX13397707", "SRS11300868", "SRP350544", "PRJNA788489", "Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish", "GSE190794", "Transcriptome Analysis", "The zebrafish has proven to be a valuable model organism for studying hematopoiesis  but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus  elucidated B and T cell developmental trajectories  and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations  a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically  kidney marrows only were dissected from 3 adult GESTALT zebrafish  paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish  and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample  whereas 4 lanes were used for the juvenile thymi to obtain 4 technical replicates.", null, "pubmed:35938989", null, "Juvenile  Thymus  1", "GSM5732079", null, "tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "Juvenile  Thymus  1", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms", "sorted live thymus cells", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "GSM5732079", "GSM5732079: Juvenile  Thymus  1; Danio rerio; RNA Seq", "GSM5732079", null, "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "GEO Accession:GSM5732079", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350544", null, "loader:fastq load.py", "4wpfThymus_1_S1_L002_I1_001.fastq.gz 4wpfThymus_1_S1_L002_R1_001.fastq.gz 4wpfThymus_1_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 16074886951.0, 126573913.0, "GSM5732079 r2", "0:8 1:28 2:91", "A:3472769520;C:2334135014;G:2767323491;T:2943866297;N:131761", 8, 28, 91, null, 3472769520, 2334135014, 2767323491, 2943866297, 131761, "SRX13397707", "SRS11300868", "SRA1342645", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.84624, null, 0.21812, null, 0.83918, null, 0.52823, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-13", "Multi-stage", "Multi-stage", "Thymus", "Hematopoietic System"], [67592, "SRR17218113", "SRX13397706", "SRS11300867", "SRP350544", "PRJNA788489", "Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish", "GSE190794", "Transcriptome Analysis", "The zebrafish has proven to be a valuable model organism for studying hematopoiesis  but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus  elucidated B and T cell developmental trajectories  and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations  a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically  kidney marrows only were dissected from 3 adult GESTALT zebrafish  paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish  and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample  whereas 4 lanes were used for the juvenile thymi to obtain 4 technical replicates.", null, "pubmed:35938989", null, "Adult  Thymus  2", "GSM5732078", null, "tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Adult|age:3 mpf bleed:yes|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "Adult  Thymus  2", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms", "sorted live thymus cells", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Adult|age:3 mpf bleed:yes|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "GSM5732078", "GSM5732078: Adult  Thymus  2; Danio rerio; RNA Seq", "GSM5732078", null, "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "GEO Accession:GSM5732078", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350544", null, "loader:fastq load.py", "lck-eGFP_Thymus_2__S4_L001_I1_001.fastq.gz lck-eGFP_Thymus_2__S4_L001_R1_001.fastq.gz lck-eGFP_Thymus_2__S4_L001_R2_001.fastq.gz", "fastq fastq fastq", 13928486651.0, 110400658.0, "GSM5732078 r1", "0:8 1:27.57 2:90.59", "A:2982389810;C:2043569636;G:2322019641;T:2652821180;N:252711", 8, 27, 90, null, 2982389810, 2043569636, 2322019641, 2652821180, 252711, "SRX13397706", "SRS11300867", "SRA1342645", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.9102, null, 0.22477, null, 0.80227, null, 0.51027, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-13", "Adult", "Adult", "Thymus", "Hematopoietic System"], [67593, "SRR17218114", "SRX13397706", "SRS11300867", "SRP350544", "PRJNA788489", "Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish", "GSE190794", "Transcriptome Analysis", "The zebrafish has proven to be a valuable model organism for studying hematopoiesis  but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus  elucidated B and T cell developmental trajectories  and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations  a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically  kidney marrows only were dissected from 3 adult GESTALT zebrafish  paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish  and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample  whereas 4 lanes were used for the juvenile thymi to obtain 4 technical replicates.", null, "pubmed:35938989", null, "Adult  Thymus  2", "GSM5732078", null, "tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Adult|age:3 mpf bleed:yes|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "Adult  Thymus  2", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms", "sorted live thymus cells", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Adult|age:3 mpf bleed:yes|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "GSM5732078", "GSM5732078: Adult  Thymus  2; Danio rerio; RNA Seq", "GSM5732078", null, "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "GEO Accession:GSM5732078", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350544", null, "loader:fastq load.py", "lck-eGFP_Thymus_2__S4_L002_I1_001.fastq.gz lck-eGFP_Thymus_2__S4_L002_R1_001.fastq.gz lck-eGFP_Thymus_2__S4_L002_R2_001.fastq.gz", "fastq fastq fastq", 13882495233.0, 110035762.0, "GSM5732078 r2", "0:8 1:27.57 2:90.59", "A:2973325031;C:2035977607;G:2312724405;T:2645711786;N:286217", 8, 27, 90, null, 2973325031, 2035977607, 2312724405, 2645711786, 286217, "SRX13397706", "SRS11300867", "SRA1342645", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.9095, null, 0.22389, null, 0.80135, null, 0.52051, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-13", "Adult", "Adult", "Thymus", "Hematopoietic System"], [67594, "SRR17218111", "SRX13397705", "SRS11300865", "SRP350544", "PRJNA788489", "Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish", "GSE190794", "Transcriptome Analysis", "The zebrafish has proven to be a valuable model organism for studying hematopoiesis  but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus  elucidated B and T cell developmental trajectories  and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations  a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically  kidney marrows only were dissected from 3 adult GESTALT zebrafish  paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish  and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample  whereas 4 lanes were used for the juvenile thymi to obtain 4 technical replicates.", null, "pubmed:35938989", null, "Adult  Thymus  1", "GSM5732077", null, "tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Adult|age:3 mpf bleed:yes|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "Adult  Thymus  1", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms", "sorted live thymus cells", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Adult|age:3 mpf bleed:yes|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "GSM5732077", "GSM5732077: Adult  Thymus  1; Danio rerio; RNA Seq", "GSM5732077", null, "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "GEO Accession:GSM5732077", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350544", null, "loader:fastq load.py", "lck-eGFP_Thymus_1__S4_L001_I1_001.fastq.gz lck-eGFP_Thymus_1__S4_L001_R1_001.fastq.gz lck-eGFP_Thymus_1__S4_L001_R2_001.fastq.gz", "fastq fastq fastq", 13683556018.0, 108451992.0, "GSM5732077 r1", "0:8 1:27.57 2:90.60", "A:2970924288;C:1965313899;G:2264518373;T:2624238930;N:636831", 8, 27, 90, null, 2970924288, 1965313899, 2264518373, 2624238930, 636831, "SRX13397705", "SRS11300865", "SRA1342645", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.91685, null, 0.27522, null, 0.81105, null, 0.52662, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-13", "Adult", "Adult", "Thymus", "Hematopoietic System"], [67595, "SRR17218112", "SRX13397705", "SRS11300865", "SRP350544", "PRJNA788489", "Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish", "GSE190794", "Transcriptome Analysis", "The zebrafish has proven to be a valuable model organism for studying hematopoiesis  but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus  elucidated B and T cell developmental trajectories  and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations  a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically  kidney marrows only were dissected from 3 adult GESTALT zebrafish  paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish  and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample  whereas 4 lanes were used for the juvenile thymi to obtain 4 technical replicates.", null, "pubmed:35938989", null, "Adult  Thymus  1", "GSM5732077", null, "tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Adult|age:3 mpf bleed:yes|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "Adult  Thymus  1", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms", "sorted live thymus cells", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Adult|age:3 mpf bleed:yes|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "GSM5732077", "GSM5732077: Adult  Thymus  1; Danio rerio; RNA Seq", "GSM5732077", null, "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "GEO Accession:GSM5732077", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350544", null, "loader:fastq load.py", "lck-eGFP_Thymus_1__S4_L002_I1_001.fastq.gz lck-eGFP_Thymus_1__S4_L002_R1_001.fastq.gz lck-eGFP_Thymus_1__S4_L002_R2_001.fastq.gz", "fastq fastq fastq", 13739084909.0, 108892246.0, "GSM5732077 r2", "0:8 1:27.57 2:90.60", "A:2986926683;C:1971756062;G:2268315286;T:2638089379;N:417199", 8, 27, 90, null, 2986926683, 1971756062, 2268315286, 2638089379, 417199, "SRX13397705", "SRS11300865", "SRA1342645", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.91881, null, 0.27676, null, 0.81217, null, 0.5208, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-13", "Adult", "Adult", "Thymus", "Hematopoietic System"], [67608, "SRR17218097", "SRX13397698", "SRS11300859", "SRP350544", "PRJNA788489", "Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish", "GSE190794", "Transcriptome Analysis", "The zebrafish has proven to be a valuable model organism for studying hematopoiesis  but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus  elucidated B and T cell developmental trajectories  and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations  a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically  kidney marrows only were dissected from 3 adult GESTALT zebrafish  paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish  and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample  whereas 4 lanes were used for the juvenile thymi to obtain 4 technical replicates.", null, "pubmed:35938989", null, "Adult  Thymus  4", "GSM5732070", null, "tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:GESTALT|developmental stage:Adult|age:4 mpf bleed:yes|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "Adult  Thymus  4", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms", "sorted live thymus cells", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "cell type:sorted live thymus cells|strain:GESTALT|developmental stage:Adult|age:4 mpf bleed:yes|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "GSM5732070", "GSM5732070: Adult  Thymus  4; Danio rerio; RNA Seq", "GSM5732070", null, "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "GEO Accession:GSM5732070", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350544", null, "loader:fastq load.py", "Fish_24_Thymus__S3_L001_I1_001.fastq.gz Fish_24_Thymus__S3_L001_R1_001.fastq.gz Fish_24_Thymus__S3_L001_R2_001.fastq.gz", "fastq fastq fastq", 18278645709.0, 144870332.0, "GSM5732070 r1", "0:8 1:27.57 2:90.60", "A:3985081516;C:2643040166;G:3063178524;T:3433439412;N:330251", 8, 27, 90, null, 3985081516, 2643040166, 3063178524, 3433439412, 330251, "SRX13397698", "SRS11300859", "SRA1342645", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.92193, null, 0.26629, null, 0.81191, null, 0.5476, null, 87, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-13", "Adult", "Adult", "Thymus", "Hematopoietic System"], [67609, "SRR17218098", "SRX13397698", "SRS11300859", "SRP350544", "PRJNA788489", "Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish", "GSE190794", "Transcriptome Analysis", "The zebrafish has proven to be a valuable model organism for studying hematopoiesis  but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus  elucidated B and T cell developmental trajectories  and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations  a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically  kidney marrows only were dissected from 3 adult GESTALT zebrafish  paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish  and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample  whereas 4 lanes were used for the juvenile thymi to obtain 4 technical replicates.", null, "pubmed:35938989", null, "Adult  Thymus  4", "GSM5732070", null, "tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:GESTALT|developmental stage:Adult|age:4 mpf bleed:yes|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "Adult  Thymus  4", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms", "sorted live thymus cells", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "cell type:sorted live thymus cells|strain:GESTALT|developmental stage:Adult|age:4 mpf bleed:yes|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "GSM5732070", "GSM5732070: Adult  Thymus  4; Danio rerio; RNA Seq", "GSM5732070", null, "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "GEO Accession:GSM5732070", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350544", null, "loader:fastq load.py", "Fish_24_Thymus__S3_L002_I1_001.fastq.gz Fish_24_Thymus__S3_L002_R1_001.fastq.gz Fish_24_Thymus__S3_L002_R2_001.fastq.gz", "fastq fastq fastq", 18204716552.0, 144284032.0, "GSM5732070 r2", "0:8 1:27.57 2:90.60", "A:3970235370;C:2631055170;G:3048647071;T:3421683260;N:373327", 8, 27, 90, null, 3970235370, 2631055170, 3048647071, 3421683260, 373327, "SRX13397698", "SRS11300859", "SRA1342645", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.9219, null, 0.26619, null, 0.80971, null, 0.54097, null, 90, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-13", "Adult", "Adult", "Thymus", "Hematopoietic System"], [67614, "SRR17218091", "SRX13397695", "SRS11300857", "SRP350544", "PRJNA788489", "Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish", "GSE190794", "Transcriptome Analysis", "The zebrafish has proven to be a valuable model organism for studying hematopoiesis  but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus  elucidated B and T cell developmental trajectories  and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations  a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically  kidney marrows only were dissected from 3 adult GESTALT zebrafish  paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish  and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample  whereas 4 lanes were used for the juvenile thymi to obtain 4 technical replicates.", null, "pubmed:35938989", null, "Adult  Thymus  3", "GSM5732067", null, "tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:GESTALT|developmental stage:Adult|age:4 mpf bleed:yes|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "Adult  Thymus  3", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms", "sorted live thymus cells", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "cell type:sorted live thymus cells|strain:GESTALT|developmental stage:Adult|age:4 mpf bleed:yes|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "GSM5732067", "GSM5732067: Adult  Thymus  3; Danio rerio; RNA Seq", "GSM5732067", null, "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "GEO Accession:GSM5732067", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350544", null, "loader:fastq load.py", "Fish_22_Thymus__S3_L001_I1_001.fastq.gz Fish_22_Thymus__S3_L001_R1_001.fastq.gz Fish_22_Thymus__S3_L001_R2_001.fastq.gz", "fastq fastq fastq", 15755989697.0, 124869852.0, "GSM5732067 r1", "0:8 1:27.57 2:90.61", "A:3460847047;C:2243842372;G:2624369866;T:2984076004;N:733016", 8, 27, 90, null, 3460847047, 2243842372, 2624369866, 2984076004, 733016, "SRX13397695", "SRS11300857", "SRA1342645", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.91732, null, 0.27669, null, 0.81669, null, 0.55139, null, 90, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-13", "Adult", "Adult", "Thymus", "Hematopoietic System"], [67615, "SRR17218092", "SRX13397695", "SRS11300857", "SRP350544", "PRJNA788489", "Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish", "GSE190794", "Transcriptome Analysis", "The zebrafish has proven to be a valuable model organism for studying hematopoiesis  but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus  elucidated B and T cell developmental trajectories  and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations  a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically  kidney marrows only were dissected from 3 adult GESTALT zebrafish  paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish  and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample  whereas 4 lanes were used for the juvenile thymi to obtain 4 technical replicates.", null, "pubmed:35938989", null, "Adult  Thymus  3", "GSM5732067", null, "tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:GESTALT|developmental stage:Adult|age:4 mpf bleed:yes|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "Adult  Thymus  3", "The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms", "sorted live thymus cells", null, "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3\u2019 v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "Zebrafish were maintained in accordance with Boston Children\u2019s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children\u2019s Hospital ARCH guidelines.", "cell type:sorted live thymus cells|strain:GESTALT|developmental stage:Adult|age:4 mpf bleed:yes|dissection buffer:0.5% BSA in HBSS  no Ca2+ or Mg2+|dissection temperature:room temperature", "GSM5732067", "GSM5732067: Adult  Thymus  3; Danio rerio; RNA Seq", "GSM5732067", null, "1", "Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 \u03bcL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample  assessed by Trypan blue staining  and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles. scRNA Seq", "GEO Accession:GSM5732067", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350544", null, "loader:fastq load.py", "Fish_22_Thymus__S3_L002_I1_001.fastq.gz Fish_22_Thymus__S3_L002_R1_001.fastq.gz Fish_22_Thymus__S3_L002_R2_001.fastq.gz", "fastq fastq fastq", 15822948086.0, 125400460.0, "GSM5732067 r2", "0:8 1:27.57 2:90.61", "A:3480626521;C:2251532188;G:2629092513;T:3000199704;N:484646", 8, 27, 90, null, 3480626521, 2251532188, 2629092513, 3000199704, 484646, "SRX13397695", "SRS11300857", "SRA1342645", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.91806, null, 0.27586, null, 0.81588, null, 0.5457, null, 90, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-13", "Adult", "Adult", "Thymus", "Hematopoietic System"]], "truncated": false, "filtered_table_rows_count": 48, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", 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