{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"RANDOM\", experiment.library_strategy = \"RNA-Seq\" and tissue_curation_coarse = \"Multi-system\"", "rows": [[15614, "ERR13109732", "ERX12481366", "ERS19896183", "ERP160330", "PRJEB75769", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E-MTAB-14075", "Transcriptome Analysis", "The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans  heterozygous germline mutations in GATA2 often lead to a loss of function of one allele  causing GATA2 haploinsufficiency. In mice  Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However  whereas Gata2 null mice are lethal at embryonic day E 10.53  Gata2 heterozygous Gata2+/  mice survive to maturity with normal blood values. However  mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness  they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b /  redirects HSPCs differentiation bias  thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations  we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia  a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome  we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", "WT young", "SAMEA115618603", "Department of Hematology cancer institute ErasmusMC", "ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT", null, null, null, null, null, null, null, null, "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E MTAB 14075:WT young p", "WT young p", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. 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In humans  heterozygous germline mutations in GATA2 often lead to a loss of function of one allele  causing GATA2 haploinsufficiency. In mice  Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However  whereas Gata2 null mice are lethal at embryonic day E 10.53  Gata2 heterozygous Gata2+/  mice survive to maturity with normal blood values. However  mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness  they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b /  redirects HSPCs differentiation bias  thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations  we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia  a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome  we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", "WT young", "SAMEA115618603", "Department of Hematology cancer institute ErasmusMC", "ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT", null, null, null, null, null, null, null, null, "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E MTAB 14075:WT young p", "WT young p", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP160330", "Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", "WT_young_run2_S10_L001_I1_001.fastq.gz WT_young_run2_S10_L001_R1_001.fastq.gz WT_young_run2_S10_L001_R2_001.fastq.gz", "fastq fastq fastq", 6300899375.0, 50407195.0, "E MTAB 14075:WT young run2 S10 L001", "0:8 1:28 2:89", "A:1243074350;C:1030040216;G:1079454879;T:1133663108;N:7802", 8, 28, 89, null, 1243074350, 1030040216, 1079454879, 1133663108, 7802, "ERX12481366", "ERS19896183", "ERA30396266", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2024-11-05", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15616, "ERR13109733", "ERX12481366", "ERS19896183", "ERP160330", "PRJEB75769", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E-MTAB-14075", "Transcriptome Analysis", "The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans  heterozygous germline mutations in GATA2 often lead to a loss of function of one allele  causing GATA2 haploinsufficiency. In mice  Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However  whereas Gata2 null mice are lethal at embryonic day E 10.53  Gata2 heterozygous Gata2+/  mice survive to maturity with normal blood values. However  mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness  they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b /  redirects HSPCs differentiation bias  thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations  we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia  a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome  we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", "WT young", "SAMEA115618603", "Department of Hematology cancer institute ErasmusMC", "ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT", null, null, null, null, null, null, null, null, "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E MTAB 14075:WT young p", "WT young p", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP160330", "Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", "WT_young_run2_S10_L002_I1_001.fastq.gz WT_young_run2_S10_L002_R1_001.fastq.gz WT_young_run2_S10_L002_R2_001.fastq.gz", "fastq fastq fastq", 6323980500.0, 50591844.0, "E MTAB 14075:WT young run2 S10 L002", "0:8 1:28 2:89", "A:1248024810;C:1032976792;G:1082805513;T:1138855823;N:11178", 8, 28, 89, null, 1248024810, 1032976792, 1082805513, 1138855823, 11178, "ERX12481366", "ERS19896183", "ERA30396266", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2024-11-05", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15617, "ERR13109728", "ERX12481366", "ERS19896183", "ERP160330", "PRJEB75769", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E-MTAB-14075", "Transcriptome Analysis", "The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans  heterozygous germline mutations in GATA2 often lead to a loss of function of one allele  causing GATA2 haploinsufficiency. In mice  Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However  whereas Gata2 null mice are lethal at embryonic day E 10.53  Gata2 heterozygous Gata2+/  mice survive to maturity with normal blood values. However  mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness  they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b /  redirects HSPCs differentiation bias  thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations  we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia  a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome  we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", "WT young", "SAMEA115618603", "Department of Hematology cancer institute ErasmusMC", "ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT", null, null, null, null, null, null, null, null, "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E MTAB 14075:WT young p", "WT young p", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP160330", "Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", "WT_young_S16_L001_I1_001.fastq.gz WT_young_S16_L001_R1_001.fastq.gz WT_young_S16_L001_R2_001.fastq.gz", "fastq fastq fastq", 9395132467.0, 73977421.0, "E MTAB 14075:WT young S16 L001", "0:8 1:28 2:91", "A:1870197969;C:1535772308;G:1609450193;T:1716224344;N:300497", 8, 28, 91, null, 1870197969, 1535772308, 1609450193, 1716224344, 300497, "ERX12481366", "ERS19896183", "ERA30396266", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2024-11-05", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15618, "ERR13109727", "ERX12481365", "ERS19896182", "ERP160330", "PRJEB75769", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E-MTAB-14075", "Transcriptome Analysis", "The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans  heterozygous germline mutations in GATA2 often lead to a loss of function of one allele  causing GATA2 haploinsufficiency. In mice  Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However  whereas Gata2 null mice are lethal at embryonic day E 10.53  Gata2 heterozygous Gata2+/  mice survive to maturity with normal blood values. However  mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness  they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b /  redirects HSPCs differentiation bias  thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations  we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia  a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome  we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", "WT aged", "SAMEA115618602", "Department of Hematology cancer institute ErasmusMC", "ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT", null, null, null, null, null, null, null, null, "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E MTAB 14075:WT aged p", "WT aged p", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP160330", "Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", "WT_aged_S15_L001_I1_001.fastq.gz WT_aged_S15_L001_R1_001.fastq.gz WT_aged_S15_L001_R2_001.fastq.gz", "fastq fastq fastq", 3224055528.0, 25386264.0, "E MTAB 14075:WT aged S15 L001", "0:8 1:28 2:91", "A:632762441;C:548488749;G:552881879;T:575917355;N:99600", 8, 28, 91, null, 632762441, 548488749, 552881879, 575917355, 99600, "ERX12481365", "ERS19896182", "ERA30396266", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2024-11-05", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15619, "ERR13109729", "ERX12481365", "ERS19896182", "ERP160330", "PRJEB75769", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E-MTAB-14075", "Transcriptome Analysis", "The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans  heterozygous germline mutations in GATA2 often lead to a loss of function of one allele  causing GATA2 haploinsufficiency. In mice  Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However  whereas Gata2 null mice are lethal at embryonic day E 10.53  Gata2 heterozygous Gata2+/  mice survive to maturity with normal blood values. However  mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness  they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b /  redirects HSPCs differentiation bias  thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations  we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia  a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome  we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", "WT aged", "SAMEA115618602", "Department of Hematology cancer institute ErasmusMC", "ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT", null, null, null, null, null, null, null, null, "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E MTAB 14075:WT aged p", "WT aged p", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP160330", "Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", "WT_aged_S15_L002_I1_001.fastq.gz WT_aged_S15_L002_R1_001.fastq.gz WT_aged_S15_L002_R2_001.fastq.gz", "fastq fastq fastq", 4178136043.0, 32898709.0, "E MTAB 14075:WT aged S15 L002", "0:8 1:28 2:91", "A:820476445;C:710661272;G:715891121;T:746611018;N:142663", 8, 28, 91, null, 820476445, 710661272, 715891121, 746611018, 142663, "ERX12481365", "ERS19896182", "ERA30396266", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2024-11-05", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15620, "ERR13109731", "ERX12481365", "ERS19896182", "ERP160330", "PRJEB75769", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E-MTAB-14075", "Transcriptome Analysis", "The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans  heterozygous germline mutations in GATA2 often lead to a loss of function of one allele  causing GATA2 haploinsufficiency. In mice  Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However  whereas Gata2 null mice are lethal at embryonic day E 10.53  Gata2 heterozygous Gata2+/  mice survive to maturity with normal blood values. However  mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness  they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b /  redirects HSPCs differentiation bias  thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations  we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia  a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome  we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", "WT aged", "SAMEA115618602", "Department of Hematology cancer institute ErasmusMC", "ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT", null, null, null, null, null, null, null, null, "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E MTAB 14075:WT aged p", "WT aged p", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP160330", "Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", "WT_aged_run2_S13_L002_I1_001.fastq.gz WT_aged_run2_S13_L002_R1_001.fastq.gz WT_aged_run2_S13_L002_R2_001.fastq.gz", "fastq fastq fastq", 11315635500.0, 90525084.0, "E MTAB 14075:WT aged run2 S13 L002", "0:8 1:28 2:89", "A:2205965370;C:1918372621;G:1938090305;T:1994285205;N:18975", 8, 28, 89, null, 2205965370, 1918372621, 1938090305, 1994285205, 18975, "ERX12481365", "ERS19896182", "ERA30396266", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2024-11-05", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15621, "ERR13109734", "ERX12481365", "ERS19896182", "ERP160330", "PRJEB75769", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E-MTAB-14075", "Transcriptome Analysis", "The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans  heterozygous germline mutations in GATA2 often lead to a loss of function of one allele  causing GATA2 haploinsufficiency. In mice  Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However  whereas Gata2 null mice are lethal at embryonic day E 10.53  Gata2 heterozygous Gata2+/  mice survive to maturity with normal blood values. However  mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness  they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b /  redirects HSPCs differentiation bias  thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations  we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia  a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome  we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", "WT aged", "SAMEA115618602", "Department of Hematology cancer institute ErasmusMC", "ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT", null, null, null, null, null, null, null, null, "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E MTAB 14075:WT aged p", "WT aged p", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP160330", "Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", "WT_aged_run2_S13_L001_I1_001.fastq.gz WT_aged_run2_S13_L001_R1_001.fastq.gz WT_aged_run2_S13_L001_R2_001.fastq.gz", "fastq fastq fastq", 11297009750.0, 90376078.0, "E MTAB 14075:WT aged run2 S13 L001", "0:8 1:28 2:89", "A:2201626807;C:1916371507;G:1936001373;T:1989457619;N:13636", 8, 28, 89, null, 2201626807, 1916371507, 1936001373, 1989457619, 13636, "ERX12481365", "ERS19896182", "ERA30396266", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2024-11-05", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15622, "ERR13109730", "ERX12481363", "ERS19896180", "ERP160330", "PRJEB75769", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E-MTAB-14075", "Transcriptome Analysis", "The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans  heterozygous germline mutations in GATA2 often lead to a loss of function of one allele  causing GATA2 haploinsufficiency. In mice  Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However  whereas Gata2 null mice are lethal at embryonic day E 10.53  Gata2 heterozygous Gata2+/  mice survive to maturity with normal blood values. However  mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness  they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b /  redirects HSPCs differentiation bias  thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations  we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia  a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome  we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", "Het aged", "SAMEA115618600", "Department of Hematology cancer institute ErasmusMC", "ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO", null, null, null, null, null, null, null, null, "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E MTAB 14075:Het aged p", "Het aged p", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP160330", "Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", "Het_aged_run2_S14_L002_I1_001.fastq.gz Het_aged_run2_S14_L002_R1_001.fastq.gz Het_aged_run2_S14_L002_R2_001.fastq.gz", "fastq fastq fastq", 4755473375.0, 38043787.0, "E MTAB 14075:Het aged run2 S14 L002", "0:8 1:28 2:89", "A:924628155;C:804435427;G:826904786;T:829920091;N:8584", 8, 28, 89, null, 924628155, 804435427, 826904786, 829920091, 8584, "ERX12481363", "ERS19896180", "ERA30396266", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2024-11-05", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15623, "ERR13109738", "ERX12481363", "ERS19896180", "ERP160330", "PRJEB75769", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E-MTAB-14075", "Transcriptome Analysis", "The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans  heterozygous germline mutations in GATA2 often lead to a loss of function of one allele  causing GATA2 haploinsufficiency. In mice  Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However  whereas Gata2 null mice are lethal at embryonic day E 10.53  Gata2 heterozygous Gata2+/  mice survive to maturity with normal blood values. However  mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness  they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b /  redirects HSPCs differentiation bias  thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations  we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia  a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome  we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", "Het aged", "SAMEA115618600", "Department of Hematology cancer institute ErasmusMC", "ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO", null, null, null, null, null, null, null, null, "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E MTAB 14075:Het aged p", "Het aged p", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP160330", "Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", "Het_aged_run2_S14_L001_I1_001.fastq.gz Het_aged_run2_S14_L001_R1_001.fastq.gz Het_aged_run2_S14_L001_R2_001.fastq.gz", "fastq fastq fastq", 4757077375.0, 38056619.0, "E MTAB 14075:Het aged run2 S14 L001", "0:8 1:28 2:89", "A:924804478;C:805146986;G:827570549;T:829511132;N:5946", 8, 28, 89, null, 924804478, 805146986, 827570549, 829511132, 5946, "ERX12481363", "ERS19896180", "ERA30396266", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2024-11-05", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15624, "ERR13109725", "ERX12481363", "ERS19896180", "ERP160330", "PRJEB75769", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E-MTAB-14075", "Transcriptome Analysis", "The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans  heterozygous germline mutations in GATA2 often lead to a loss of function of one allele  causing GATA2 haploinsufficiency. In mice  Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However  whereas Gata2 null mice are lethal at embryonic day E 10.53  Gata2 heterozygous Gata2+/  mice survive to maturity with normal blood values. However  mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness  they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b /  redirects HSPCs differentiation bias  thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations  we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia  a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome  we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", "Het aged", "SAMEA115618600", "Department of Hematology cancer institute ErasmusMC", "ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO", null, null, null, null, null, null, null, null, "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E MTAB 14075:Het aged p", "Het aged p", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP160330", "Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", "Het_aged_S13_L001_I1_001.fastq.gz Het_aged_S13_L001_R1_001.fastq.gz Het_aged_S13_L001_R2_001.fastq.gz", "fastq fastq fastq", 2031302643.0, 15994509.0, "E MTAB 14075:Het aged S13 L001", "0:8 1:28 2:91", "A:398278357;C:344264985;G:353424298;T:359473296;N:59383", 8, 28, 91, null, 398278357, 344264985, 353424298, 359473296, 59383, "ERX12481363", "ERS19896180", "ERA30396266", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2024-11-05", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15625, "ERR13109739", "ERX12481363", "ERS19896180", "ERP160330", "PRJEB75769", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E-MTAB-14075", "Transcriptome Analysis", "The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans  heterozygous germline mutations in GATA2 often lead to a loss of function of one allele  causing GATA2 haploinsufficiency. In mice  Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However  whereas Gata2 null mice are lethal at embryonic day E 10.53  Gata2 heterozygous Gata2+/  mice survive to maturity with normal blood values. However  mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness  they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b /  redirects HSPCs differentiation bias  thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations  we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia  a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome  we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", "Het aged", "SAMEA115618600", "Department of Hematology cancer institute ErasmusMC", "ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO", null, null, null, null, null, null, null, null, "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E MTAB 14075:Het aged p", "Het aged p", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP160330", "Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", "Het_aged_S13_L002_I1_001.fastq.gz Het_aged_S13_L002_R1_001.fastq.gz Het_aged_S13_L002_R2_001.fastq.gz", "fastq fastq fastq", 2430576292.0, 19138396.0, "E MTAB 14075:Het aged S13 L002", "0:8 1:28 2:91", "A:476457271;C:411953563;G:422659830;T:430445714;N:77658", 8, 28, 91, null, 476457271, 411953563, 422659830, 430445714, 77658, "ERX12481363", "ERS19896180", "ERA30396266", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2024-11-05", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15626, "ERR13109736", "ERX12481364", "ERS19896181", "ERP160330", "PRJEB75769", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E-MTAB-14075", "Transcriptome Analysis", "The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans  heterozygous germline mutations in GATA2 often lead to a loss of function of one allele  causing GATA2 haploinsufficiency. In mice  Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However  whereas Gata2 null mice are lethal at embryonic day E 10.53  Gata2 heterozygous Gata2+/  mice survive to maturity with normal blood values. However  mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness  they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b /  redirects HSPCs differentiation bias  thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations  we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia  a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome  we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", "Het young", "SAMEA115618601", "Department of Hematology cancer institute ErasmusMC", "ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO", null, null, null, null, null, null, null, null, "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E MTAB 14075:Het young p", "Het young p", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP160330", "Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", "Het_young_S14_L001_I1_001.fastq.gz Het_young_S14_L001_R1_001.fastq.gz Het_young_S14_L001_R2_001.fastq.gz", "fastq fastq fastq", 7202197051.0, 56710213.0, "E MTAB 14075:Het young S14 L001", "0:8 1:28 2:91", "A:1452033851;C:1164601809;G:1229900451;T:1313862644;N:230628", 8, 28, 91, null, 1452033851, 1164601809, 1229900451, 1313862644, 230628, "ERX12481364", "ERS19896181", "ERA30396266", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2024-11-05", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15627, "ERR13109740", "ERX12481364", "ERS19896181", "ERP160330", "PRJEB75769", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E-MTAB-14075", "Transcriptome Analysis", "The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans  heterozygous germline mutations in GATA2 often lead to a loss of function of one allele  causing GATA2 haploinsufficiency. In mice  Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However  whereas Gata2 null mice are lethal at embryonic day E 10.53  Gata2 heterozygous Gata2+/  mice survive to maturity with normal blood values. However  mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness  they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b /  redirects HSPCs differentiation bias  thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations  we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia  a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome  we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", "Het young", "SAMEA115618601", "Department of Hematology cancer institute ErasmusMC", "ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO", null, null, null, null, null, null, null, null, "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E MTAB 14075:Het young p", "Het young p", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP160330", "Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", "Het_young_run2_S11_L001_I1_001.fastq.gz Het_young_run2_S11_L001_R1_001.fastq.gz Het_young_run2_S11_L001_R2_001.fastq.gz", "fastq fastq fastq", 3012722750.0, 24101782.0, "E MTAB 14075:Het young run2 S11 L001", "0:8 1:28 2:89", "A:601664996;C:487380557;G:514748426;T:541261211;N:3408", 8, 28, 89, null, 601664996, 487380557, 514748426, 541261211, 3408, "ERX12481364", "ERS19896181", "ERA30396266", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2024-11-05", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15628, "ERR13109735", "ERX12481364", "ERS19896181", "ERP160330", "PRJEB75769", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E-MTAB-14075", "Transcriptome Analysis", "The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans  heterozygous germline mutations in GATA2 often lead to a loss of function of one allele  causing GATA2 haploinsufficiency. In mice  Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However  whereas Gata2 null mice are lethal at embryonic day E 10.53  Gata2 heterozygous Gata2+/  mice survive to maturity with normal blood values. However  mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness  they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b /  redirects HSPCs differentiation bias  thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations  we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia  a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome  we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", "Het young", "SAMEA115618601", "Department of Hematology cancer institute ErasmusMC", "ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO", null, null, null, null, null, null, null, null, "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E MTAB 14075:Het young p", "Het young p", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP160330", "Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", "Het_young_run2_S11_L002_I1_001.fastq.gz Het_young_run2_S11_L002_R1_001.fastq.gz Het_young_run2_S11_L002_R2_001.fastq.gz", "fastq fastq fastq", 3017568125.0, 24140545.0, "E MTAB 14075:Het young run2 S11 L002", "0:8 1:28 2:89", "A:602793366;C:487819335;G:515271935;T:542618728;N:5141", 8, 28, 89, null, 602793366, 487819335, 515271935, 542618728, 5141, "ERX12481364", "ERS19896181", "ERA30396266", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2024-11-05", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15629, "ERR13109726", "ERX12481364", "ERS19896181", "ERP160330", "PRJEB75769", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E-MTAB-14075", "Transcriptome Analysis", "The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans  heterozygous germline mutations in GATA2 often lead to a loss of function of one allele  causing GATA2 haploinsufficiency. In mice  Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However  whereas Gata2 null mice are lethal at embryonic day E 10.53  Gata2 heterozygous Gata2+/  mice survive to maturity with normal blood values. However  mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness  they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b /  redirects HSPCs differentiation bias  thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations  we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia  a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome  we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing.", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", "Het young", "SAMEA115618601", "Department of Hematology cancer institute ErasmusMC", "ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO", null, null, null, null, null, null, null, null, "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "E MTAB 14075:Het young p", "Het young p", "Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP160330", "Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish", "ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05", "Het_young_S14_L002_I1_001.fastq.gz Het_young_S14_L002_R1_001.fastq.gz Het_young_S14_L002_R2_001.fastq.gz", "fastq fastq fastq", 8707482077.0, 68562851.0, "E MTAB 14075:Het young S14 L002", "0:8 1:28 2:91", "A:1755361511;C:1408255848;G:1486295783;T:1588996810;N:309489", 8, 28, 91, null, 1755361511, 1408255848, 1486295783, 1588996810, 309489, "ERX12481364", "ERS19896181", "ERA30396266", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2024-11-05", "Adult", "Adult", "Multi-tissue", "Multi-system"], [39635, "SRR1974165", "SRX994290", "SRS907736", "SRP057116", "PRJNA280983", "Danio rerio strain:CG2 Transcriptome or Gene expression", "PRJNA280983", "Other", "CG2 homozygous diploid zebrafish line.", null, null, null, "Model organism or animal sample from Danio rerio CG2", "CG2 immune related tissues", null, "strain:CG2|dev stage:adult|sex:not determined|tissue:kidney  intestine  gills and spleen|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "CG2 normalized RNA seq pooled kidney  intestine  gills and spleen", "CG2 Normalized", "CG2", "A single adult CG2 zebrafish was euthanized and the kidney  intestine  gills and spleen were dissected and combined for RNA extraction Trizol  Life Technologies. RNA was prepared for sequencing with the TruSeq RNA kit Illumina and sequenced 2 x 100 bp paired end reads on a single lane of a HiSeq2000 Illumina.In an effort to detect rare transcripts  a normalization procedure also was employed. Normalized cDNA was achieved with the MINT Universal cDNA synthesis and TRIMMER DIRECT cDNA normalization kits Evrogen which was then prepared for sequencing with the TruSeq DNA kit Illumina. Average insert size of 200 bps.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP057116", null, null, "130508_I1089_FCC1VKUACXX_L1_NCSU-GSL-0099_2.fq.gz 130508_I1089_FCC1VKUACXX_L1_NCSU-GSL-0099_1.fq.gz", "fastq fastq", 32265477800.0, 161327389.0, "CG2 Normalized", "0:100 1:100", "A:9100821450;C:6628233467;G:7212252211;T:9279872090;N:44298582", 100, 100, null, null, 9100821450, 6628233467, 7212252211, 9279872090, 44298582, "SRX994290", "SRS907736", "SRA258497", "North Carolina State University", "North Carolina State University", 2, 0.83842, 0.78503, 0.19412, 0.17922, 0.69704, 0.71959, 0.48624, 0.4789, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-04-18", "Adult", "Adult", "Multi-tissue", "Multi-system"], [41035, "SRR3581677", "SRX1797273", "SRS1465195", "SRP075626", "PRJNA322629", "Mycobacterial infection of adult zebrafish", "PRJNA322629", "Other", "RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.", null, null, null, "Fluorescence activated cell sorted macrophages4", "iRed4", null, "breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Fluorescence activated cell sorted macrophages from kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "iRed4", "iRed4", "iRed4", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP075626", null, null, "iRed4.fastq.gz", "fastq", 2577391029.0, 50537079.0, "iRed4.fastq.gz", "0:51", "A:740368299;C:555561208;G:558570747;T:722870515;N:20260", 51, null, null, null, 740368299, 555561208, 558570747, 722870515, 20260, "SRX1797273", "SRS1465195", "SRA429040", "Duke University|Molecular Genetics &amp; Microbiology", "Duke University", 1, 0.87886, null, 0.09748, null, 0.75676, null, 0.49364, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-05-25", "Adult", "Adult", "Multi-tissue", "Multi-system"], [41036, "SRR3581675", "SRX1797272", "SRS1465194", "SRP075626", "PRJNA322629", "Mycobacterial infection of adult zebrafish", "PRJNA322629", "Other", "RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.", null, null, null, "Fluorescence activated cell sorted macrophages3", "iRed3", null, "breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Fluorescence activated cell sorted macrophages from kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "iRed3", "iRed3", "iRed3", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP075626", null, null, "iRed3.fastq.gz", "fastq", 2300094339.0, 45099889.0, "iRed3.fastq.gz", "0:51", "A:664396273;C:491535578;G:495836023;T:648307877;N:18588", 51, null, null, null, 664396273, 491535578, 495836023, 648307877, 18588, "SRX1797272", "SRS1465194", "SRA429039", "Duke University|Molecular Genetics &amp; Microbiology", "Duke University", 1, 0.88281, null, 0.15449, null, 0.75507, null, 0.47198, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-06-24", "Adult", "Adult", "Multi-tissue", "Multi-system"], [41037, "SRR3581674", "SRX1797271", "SRS1465193", "SRP075626", "PRJNA322629", "Mycobacterial infection of adult zebrafish", "PRJNA322629", "Other", "RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.", null, null, null, "Fluorescence activated cell sorted macrophages2", "iRed2", null, "breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Fluorescence activated cell sorted macrophages from kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "iRed2", "iRed2", "iRed2", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP075626", null, null, "iRed2.fastq.gz", "fastq", 1652550807.0, 32402957.0, "iRed2.fastq.gz", "0:51", "A:528348867;C:306088006;G:305625547;T:512475625;N:12762", 51, null, null, null, 528348867, 306088006, 305625547, 512475625, 12762, "SRX1797271", "SRS1465193", "SRA429038", "Duke University|Molecular Genetics &amp; Microbiology", "Duke University", 1, 0.83699, null, 0.16858, null, 0.76688, null, 0.49036, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-05-25", "Adult", "Adult", "Multi-tissue", "Multi-system"], [44993, "SRR6450489", "SRX3541479", "SRS2819522", "SRP128591", "PRJNA427078", "zebrafish Genome sequencing", "PRJNA427078", "Whole Genome Sequencing", "Genome re sequencing and transcriptome sequencing", null, null, null, "Zebrafish transcriptome", "Zebrafish trans", null, "ecotype:lab|age:6 month|sex:missing|tissue:skin muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish:adult", "WHZEBqrvEAAFRABPEI", "WHZEBqrvEAAFRABPEI", "skin  muscle", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP128591", null, null, "161208_I188_FCCA319ANXX_L8_WHZEBqrvEAAFRABPEI-113_2.fq.gz 161208_I188_FCCA319ANXX_L8_WHZEBqrvEAAFRABPEI-113_1.fq.gz", "fastq fastq", 3600021250.0, 14400085.0, "161208 I188 FCCA319ANXX L8 WHZEBqrvEAAFRABPEI 113 2.fq.gz", "0:125 1:125", "A:934930854;C:868403521;G:876791881;T:918413816;N:1481178", 125, 125, null, null, 934930854, 868403521, 876791881, 918413816, 1481178, "SRX3541479", "SRS2819522", "SRA645021", "BGI", "BGI", 2, 0.9521, 0.95139, 0.03254, 0.03384, 0.78072, 0.782, 0.51124, 0.50752, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-01-08", "Adult", "Adult", "Multi-tissue", "Multi-system"], [44994, "SRR6450490", "SRX3541478", "SRS2819522", "SRP128591", "PRJNA427078", "zebrafish Genome sequencing", "PRJNA427078", "Whole Genome Sequencing", "Genome re sequencing and transcriptome sequencing", null, null, null, "Zebrafish transcriptome", "Zebrafish trans", null, "ecotype:lab|age:6 month|sex:missing|tissue:skin muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish:adult", "WHZEBqrvEAAERAAPEI", "WHZEBqrvEAAERAAPEI", "skin  muscle", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP128591", null, null, "161208_I188_FCCA319ANXX_L8_WHZEBqrvEAAERAAPEI-112_1.fq.gz 161208_I188_FCCA319ANXX_L8_WHZEBqrvEAAERAAPEI-112_2.fq.gz", "fastq fastq", 3746428750.0, 14985715.0, "161208 I188 FCCA319ANXX L8 WHZEBqrvEAAERAAPEI 112 2.fq.gz", "0:125 1:125", "A:943900815;C:931886385;G:943833449;T:925283757;N:1524344", 125, 125, null, null, 943900815, 931886385, 943833449, 925283757, 1524344, "SRX3541478", "SRS2819522", "SRA645021", "BGI", "BGI", 2, 0.95425, 0.95353, 0.06014, 0.06092, 0.77871, 0.78092, 0.55488, 0.55289, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-11-26", "Adult", "Adult", "Multi-tissue", "Multi-system"], [44995, "SRR6450499", "SRX3541469", "SRS2819522", "SRP128591", "PRJNA427078", "zebrafish Genome sequencing", "PRJNA427078", "Whole Genome Sequencing", "Genome re sequencing and transcriptome sequencing", null, null, null, "Zebrafish transcriptome", "Zebrafish trans", null, "ecotype:lab|age:6 month|sex:missing|tissue:skin muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish:adult", "WHZEBqrvEAAGRABPEI", "WHZEBqrvEAAGRABPEI", "skin  muscle", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP128591", null, null, "161208_I188_FCCA319ANXX_L8_WHZEBqrvEAAGRABPEI-127_1.fq.gz 161208_I188_FCCA319ANXX_L8_WHZEBqrvEAAGRABPEI-127_2.fq.gz", "fastq fastq", 3692839750.0, 14771359.0, "161208 I188 FCCA319ANXX L8 WHZEBqrvEAAGRABPEI 127 2.fq.gz", "0:125 1:125", "A:954324405;C:894321874;G:903805870;T:938852024;N:1535577", 125, 125, null, null, 954324405, 894321874, 903805870, 938852024, 1535577, "SRX3541469", "SRS2819522", "SRA645021", "BGI", "BGI", 2, 0.95186, 0.9505, 0.03508, 0.03577, 0.77321, 0.77607, 0.51196, 0.50758, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-11-26", "Adult", "Adult", "Multi-tissue", "Multi-system"], [44996, "SRR6450500", "SRX3541468", "SRS2819522", "SRP128591", "PRJNA427078", "zebrafish Genome sequencing", "PRJNA427078", "Whole Genome Sequencing", "Genome re sequencing and transcriptome sequencing", null, null, null, "Zebrafish transcriptome", "Zebrafish trans", null, "ecotype:lab|age:6 month|sex:missing|tissue:skin muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish:adult", "WHZEBqrvEAADRABPEI", "WHZEBqrvEAADRABPEI", "skin  muscle", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP128591", null, null, "161208_I188_FCCA319ANXX_L8_WHZEBqrvEAADRABPEI-110_1.fq.gz 161208_I188_FCCA319ANXX_L8_WHZEBqrvEAADRABPEI-110_2.fq.gz", "fastq fastq", 3765918500.0, 15063674.0, "161208 I188 FCCA319ANXX L8 WHZEBqrvEAADRABPEI 110 1.fq.gz", "0:125 1:125", "A:978737405;C:906962900;G:914851569;T:963799416;N:1567210", 125, 125, null, null, 978737405, 906962900, 914851569, 963799416, 1567210, "SRX3541468", "SRS2819522", "SRA645021", "BGI", "BGI", 2, 0.94834, 0.9475, 0.03675, 0.03738, 0.76211, 0.76506, 0.5095, 0.50295, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-11-26", "Adult", "Adult", "Multi-tissue", "Multi-system"], [44997, "SRR6450501", "SRX3541467", "SRS2819522", "SRP128591", "PRJNA427078", "zebrafish Genome sequencing", "PRJNA427078", "Whole Genome Sequencing", "Genome re sequencing and transcriptome sequencing", null, null, null, "Zebrafish transcriptome", "Zebrafish trans", null, "ecotype:lab|age:6 month|sex:missing|tissue:skin muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish:adult", "WHZEBqrvEAACRAAPEI", "WHZEBqrvEAACRAAPEI", "skin muscle", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP128591", null, null, "161208_I188_FCCA319ANXX_L8_WHZEBqrvEAACRAAPEI-109_1.fq.gz 161208_I188_FCCA319ANXX_L8_WHZEBqrvEAACRAAPEI-109_2.fq.gz", "fastq fastq", 3262728000.0, 13050912.0, "161208 I188 FCCA319ANXX L8 WHZEBqrvEAACRAAPEI 109 2.fq.gz", "0:125 1:125", "A:841105717;C:792680416;G:803830714;T:823771562;N:1339591", 125, 125, null, null, 841105717, 792680416, 803830714, 823771562, 1339591, "SRX3541467", "SRS2819522", "SRA645021", "BGI", "BGI", 2, 0.95367, 0.95244, 0.02953, 0.0301, 0.7839, 0.78516, 0.47404, 0.52072, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-11-26", "Adult", "Adult", "Multi-tissue", "Multi-system"], [44998, "SRR6450502", "SRX3541466", "SRS2819522", "SRP128591", "PRJNA427078", "zebrafish Genome sequencing", "PRJNA427078", "Whole Genome Sequencing", "Genome re sequencing and transcriptome sequencing", null, null, null, "Zebrafish transcriptome", "Zebrafish trans", null, "ecotype:lab|age:6 month|sex:missing|tissue:skin muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish:adult", "WHZEBqrvEAAHRABPEI", "WHZEBqrvEAAHRABPEI", "skin  muscle", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP128591", null, null, "161208_I188_FCCA319ANXX_L8_WHZEBqrvEAAHRABPEI-128_1.fq.gz 161208_I188_FCCA319ANXX_L8_WHZEBqrvEAAHRABPEI-128_2.fq.gz", "fastq fastq", 3710501500.0, 14842006.0, "161208 I188 FCCA319ANXX L8 WHZEBqrvEAAHRABPEI 128 1.fq.gz", "0:125 1:125", "A:955350214;C:902731408;G:912565284;T:938345980;N:1508614", 125, 125, null, null, 955350214, 902731408, 912565284, 938345980, 1508614, "SRX3541466", "SRS2819522", "SRA645021", "BGI", "BGI", 2, 0.95634, 0.9563, 0.03159, 0.03301, 0.77293, 0.77579, 0.50883, 0.50743, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-11-26", "Adult", "Adult", "Multi-tissue", "Multi-system"], [61657, "SRR12926111", "SRX9390273", "SRS7609571", "SRP289515", "PRJNA672972", "Transcriptome sequencing of CG1 zebrafish immune related tissues", "PRJNA672972", "Other", "CG1 is a homozygous diploid line of zebrafish. Due to the clonal nature of this line  minimal genetic variation among individuals is expected. In anticipation of a draft genome for the CG1 line of zebrafish  the research community may find value in transcriptome data from the same genetic background. Kidney  intestine  gills and spleen from six adult CG1 zebrafish were dissected and RNA from each tissue type was extracted Trizol  Life Technologies. Equal amounts of RNA were pooled together prior to NGS library prep.", null, null, null, null, "Danio rerio CG1", null, "strain:CG1|dev stage:adult|sex:not collected|tissue:kidney  spleen  liver  intestine and gills|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of CG1 Danio rerio: immune related tissues", "NO059", "NO059", "Equal amounts of RNA extracted from kidney  spleen  intestine  liver and gills of six zebrafish were pooled prior to library prep and paired read sequencing via a NovaSeq 6000.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP289515", null, null, "NS059_1.fq.gz NS059_2.fq.gz", "fastq fastq", 6206095500.0, 20686985.0, "NS059 1.fq.gz", "0:150 1:150", "A:1672977157;C:1431352025;G:1440567087;T:1661082893;N:116338", 150, 150, null, null, 1672977157, 1431352025, 1440567087, 1661082893, 116338, "SRX9390273", "SRS7609571", "SRA1149693", "NCSU - CVM|Molecular 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[study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_selection\" = :p0 and \"experiment.library_strategy\" 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"http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system", "selected": true}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=RANDOM&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 36, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=RANDOM&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system&experiment.library_layout=PAIRED", "selected": false}, {"value": "SINGLE", "label": "SINGLE", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=RANDOM&experiment.library_strategy=RNA-Seq&tissue_curation_coarse=Multi-system&experiment.library_layout=SINGLE", 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