rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
11238,ERR10782555,ERX10233132,ERS14439197,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 6,E MTAB 12503:Sample 6,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 6|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 6 p,Sample 6 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:bud|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-6_R1.fastq.gz 20170530.A-6_R2.fastq.gz,fastq fastq,14809693138.0,49038719.0,E MTAB 12503:20170530.A 6 R,0:151 1:151,A:4069749497;C:3367864217;G:3430269434;T:3928390721;N:13419269,151,151,,,4069749497,3367864217,3430269434,3928390721,13419269,ERX10233132,ERS14439197,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.83945,0.69977,0.27269,0.22488,0.74523,0.77654,0.4899,0.4358,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Multi-stage,Embryo,Whole Organism,All anatomical structures
11239,ERR10782554,ERX10233131,ERS14439196,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 5,E MTAB 12503:Sample 5,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 5|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 5 p,Sample 5 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:bud|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-5_R1.fastq.gz 20170530.A-5_R2.fastq.gz,fastq fastq,14954968728.0,49519764.0,E MTAB 12503:20170530.A 5 R,0:151 1:151,A:4063340262;C:3440933120;G:3455723079;T:3981396987;N:13575280,151,151,,,4063340262,3440933120,3455723079,3981396987,13575280,ERX10233131,ERS14439196,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.85891,0.86859,0.28842,0.28866,0.7349,0.75051,0.45532,0.49145,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Multi-stage,Embryo,Whole Organism,All anatomical structures
11240,ERR10782553,ERX10233130,ERS14439195,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 2,E MTAB 12503:Sample 2,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 2|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 2 p,Sample 2 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-2_R1.fastq.gz 20170530.A-2_R2.fastq.gz,fastq fastq,16267571562.0,53866131.0,E MTAB 12503:20170530.A 2 R,0:151 1:151,A:4395815325;C:3765428574;G:3780844712;T:4310729283;N:14753668,151,151,,,4395815325,3765428574,3780844712,4310729283,14753668,ERX10233130,ERS14439195,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.86977,0.8727,0.28497,0.28427,0.70763,0.72301,0.47478,0.47986,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
11241,ERR10782552,ERX10233129,ERS14439194,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 1,E MTAB 12503:Sample 1,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 1|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 1 p,Sample 1 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-1_R1.fastq.gz 20170530.A-1_R2.fastq.gz,fastq fastq,15446599662.0,51147681.0,E MTAB 12503:20170530.A 1 R,0:151 1:151,A:4289931639;C:3451135010;G:3474244788;T:4217248893;N:14039332,151,151,,,4289931639,3451135010,3474244788,4217248893,14039332,ERX10233129,ERS14439194,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.90114,0.90507,0.32128,0.32127,0.70232,0.71956,0.47336,0.47528,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
11242,ERR10782551,ERX10233128,ERS14439193,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 7,E MTAB 12503:Sample 7,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 7|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 7 p,Sample 7 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:bud|Experimental Factor: genotype:rbm8a d5/d5,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-7_R1.fastq.gz 20170530.A-7_R2.fastq.gz,fastq fastq,12726557236.0,42140918.0,E MTAB 12503:20170530.A 7 R,0:151 1:151,A:3510176970;C:2879679978;G:2932244172;T:3392911734;N:11544382,151,151,,,3510176970,2879679978,2932244172,3392911734,11544382,ERX10233128,ERS14439193,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.88531,0.88678,0.33279,0.3329,0.73545,0.74992,0.52548,0.52864,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Multi-stage,Embryo,Whole Organism,All anatomical structures
11243,ERR10782550,ERX10233127,ERS14439192,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 4,E MTAB 12503:Sample 4,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 4|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 4 p,Sample 4 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:rbm8a d5/d5,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-4_R1.fastq.gz 20170530.A-4_R2.fastq.gz,fastq fastq,15697575554.0,51978727.0,E MTAB 12503:20170530.A 4 R,0:151 1:151,A:4256444510;C:3622485921;G:3650190489;T:4154211501;N:14243133,151,151,,,4256444510,3622485921,3650190489,4154211501,14243133,ERX10233127,ERS14439192,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.87714,0.88071,0.29319,0.29235,0.69844,0.7164,0.47594,0.47385,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
11244,ERR10782549,ERX10233126,ERS14439191,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 3,E MTAB 12503:Sample 3,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 3|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 3 p,Sample 3 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:rbm8a d5/d5,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-3_R1.fastq.gz 20170530.A-3_R2.fastq.gz,fastq fastq,13839085674.0,45824787.0,E MTAB 12503:20170530.A 3 R,0:151 1:151,A:3812423011;C:3120168590;G:3163957945;T:3729983766;N:12552362,151,151,,,3812423011,3120168590,3163957945,3729983766,12552362,ERX10233126,ERS14439191,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.88987,0.74432,0.33651,0.27875,0.69229,0.72934,0.46981,0.46116,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
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,,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,,,,,,,,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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_L002_I1_001.fastq.gz WT_young_S16_L002_R1_001.fastq.gz WT_young_S16_L002_R2_001.fastq.gz,fastq fastq fastq,11547230144.0,90923072.0,E MTAB 14075:WT young S16 L002,0:8 1:28 2:91,A:2298760158;C:1887715706;G:1977278606;T:2109839457;N:405625,8,28,91,,2298760158,1887715706,1977278606,2109839457,405625,ERX12481366,ERS19896183,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United Kingdom,2024-11-05,Adult,Adult,Multi-tissue,Multi-system
15615,ERR13109737,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,,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,,,,,,,,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,1243074350,1030040216,1079454879,1133663108,7802,ERX12481366,ERS19896183,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,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,,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,,,,,,,,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,1248024810,1032976792,1082805513,1138855823,11178,ERX12481366,ERS19896183,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,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,,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,,,,,,,,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,1870197969,1535772308,1609450193,1716224344,300497,ERX12481366,ERS19896183,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,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,,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,,,,,,,,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,632762441,548488749,552881879,575917355,99600,ERX12481365,ERS19896182,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,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,,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,,,,,,,,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,820476445,710661272,715891121,746611018,142663,ERX12481365,ERS19896182,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,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,,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,,,,,,,,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,2205965370,1918372621,1938090305,1994285205,18975,ERX12481365,ERS19896182,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,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,,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,,,,,,,,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,2201626807,1916371507,1936001373,1989457619,13636,ERX12481365,ERS19896182,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,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,,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,,,,,,,,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,924628155,804435427,826904786,829920091,8584,ERX12481363,ERS19896180,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,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,,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,,,,,,,,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,924804478,805146986,827570549,829511132,5946,ERX12481363,ERS19896180,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,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,,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,,,,,,,,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,398278357,344264985,353424298,359473296,59383,ERX12481363,ERS19896180,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,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,,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,,,,,,,,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,476457271,411953563,422659830,430445714,77658,ERX12481363,ERS19896180,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,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,,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,,,,,,,,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,1452033851,1164601809,1229900451,1313862644,230628,ERX12481364,ERS19896181,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,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,,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,,,,,,,,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,601664996,487380557,514748426,541261211,3408,ERX12481364,ERS19896181,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,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,,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,,,,,,,,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,602793366,487819335,515271935,542618728,5141,ERX12481364,ERS19896181,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,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,,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,,,,,,,,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,1755361511,1408255848,1486295783,1588996810,309489,ERX12481364,ERS19896181,ERA30396266,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United Kingdom,2024-11-05,Adult,Adult,Multi-tissue,Multi-system
34262,SRR31595085,SRX26959911,SRS23429841,SRP549196,PRJNA1193812,Single cell transcriptome sequencing of zebrafish olfactory epithelium,PRJNA1193812,Other,We performed single cell sequencing in the olfactory epithelium of wild type zebrafish and zebrafish treated with alarm substances and compared them.,,,Alarm substances treatment Group,,CAS,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 year old|dev stage:adult CAS group|collection date:2020 10 10|geo loc name:China: Wuhan|sex:male|tissue:Olfactory epithelium CAS group|BioSampleModel:Model organism or animal,,,,,,,,,Single cell transcriptome of the AB zebrafish olfactory epithelium post treatment with alarm substances,CAS OE,CAS OE,sequencing libraries were loaded on an Illumina NextSeq 550AR with paired end kits. Read 1 was used to distinguish different transcripts of different cells. Read 2 was used to determine the genetic information.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,NextSeq 550,,SRP549196,,,CAS_S1_L001_R1_001.fastq.gz CAS_S1_L001_R2_001.fastq.gz,fastq fastq,54518124857.0,458135503.0,CAS S1 L001 R1 001.fastq.gz,0:28 1:91,A:15384916510;C:12274547586;G:14008767028;T:12837270924;N:12622809,28,91,,,15384916510,12274547586,14008767028,12837270924,12622809,SRX26959911,SRS23429841,SRA2027027,"Institute of Hydrobiology, Chinese Academy of Sciences|Chinese Academy of Sciences","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_generic,generic-scrnaseq-only,,China,2024-12-04,Adult,Adult,Brain,Nervous System
34263,SRR31595086,SRX26959910,SRS23429840,SRP549196,PRJNA1193812,Single cell transcriptome sequencing of zebrafish olfactory epithelium,PRJNA1193812,Other,We performed single cell sequencing in the olfactory epithelium of wild type zebrafish and zebrafish treated with alarm substances and compared them.,,,Blank control group,,CTR,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 year old|dev stage:adult CTR group|collection date:2020 10 10|geo loc name:China: Wuhan|sex:male|tissue:Olfactory epithelium CTR group|BioSampleModel:Model organism or animal,,,,,,,,,Single cell transcriptome of the AB strain zebrafish olfactory epithelium,CTR OE,CTR OE,sequencing libraries were loaded on an Illumina NextSeq 550AR with paired end kits. Read 1 was used to distinguish different transcripts of different cells. Read 2 was used to determine the genetic information.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,NextSeq 550,,SRP549196,,,CTR_S1_L001_R1_001.fastq.gz CTR_S1_L001_R2_001.fastq.gz,fastq fastq,50773421790.0,426667410.0,CTR S1 L001 R1 001.fastq.gz,0:28 1:91,A:14105926130;C:11510784907;G:13135577448;T:12011516484;N:9616821,28,91,,,14105926130,11510784907,13135577448,12011516484,9616821,SRX26959910,SRS23429840,SRA2027027,"Institute of Hydrobiology, Chinese Academy of Sciences|Chinese Academy of Sciences","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_generic,generic-scrnaseq-only,,China,2024-12-04,Adult,Adult,Brain,Nervous System
53593,SRR11886700,SRX8434172,SRS6745285,SRP265421,PRJNA559885,A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration,PRJNA559885,Other,The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities  while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic  developmental  cellular and molecular studies  the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio  we uncovered species specific and evolutionarily conserved genomic responses to amputation.,,,,zebrafish fin regeneration,zebrafish fin 1dpa,,strain:AB|isolate:12|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish blastema single cell,L41598,L41598,The African killifish and zebrafish single cell RNA seq were done with the 10x Chromium platform. About 20 fish were used for cell dissociation in each experiment. Hoechst stained cells 100 000 cells from the dissected blastema tissues at 1dpa were collected on ice using a BD Influx sorter. The viability of cells 94.5% was determined before loading cells into 10x Chromium platform.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP265421,,loader:fastq load.py,L41598_S1_L001_I1_001.fastq.gz L41598_S1_L001_R1_001.fastq.gz L41598_S1_L001_R2_001.fastq.gz L41598_S1_L002_I1_001.fastq.gz L41598_S1_L002_R1_001.fastq.gz L41598_S1_L002_R2_001.fastq.gz L41598_S1_L003_I1_001.fastq.gz L41598_S1_L003_R1_001.fastq.gz L41598_S1_L003_R2_001.fastq.gz L41598_S1_L004_I1_001.fastq.gz L41598_S1_L004_R1_001.fastq.gz L41598_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,52222012142.0,411196946.0,L41598 S1 L001 I1 001.fastq.gz,0:8 1:28 2:91,A:10978857897;C:7760934381;G:8557391299;T:10029401940;N:92336569,8,28,91,,10978857897,7760934381,8557391299,10029401940,92336569,SRX8434172,SRS6745285,SRA1081627,Stowers Institute for Medical Research|Sanchez lab,Stowers Institute for Medical Research,1,0.92629,,0.12539,,0.78589,,0.5225,,91,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2020-08-11,Adult,Adult,Fin,Surface Structure
68777,SRR18188990,SRX14335888,SRS12150682,SRP362100,PRJNA811725,Single cell sequencing of zebra fish primordial germ cell,PRJNA811725,Other,Based on the transcriptome  we constructed long non coding RNA lncRNA profile of zebrafish primordial germ cells PGCs to further discern functional lncRNA that might play role in PGCs development.,,,,,GC9,,strain:kop:EGFP 3 primeUTR nanos primordial germ cell transgenic line|isolate:Based on green fluorescence  single PGC was distinctively identified and picked out using a capillary tube|age:5hpf|dev stage:30% 50% epiboly|sex:not applicable|tissue:primordial germ cell|cell type:primordial germ cell|replicate:replicate3|BioSampleModel:Model organism or animal,,,,,,,,,3pgc,3 3pgc,3 3pgc,primordial germ cell from 5 hpf zebrafish embryos,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP362100,,,GC9_R1.fq.gz GC9_R2.fq.gz,fastq fastq,16392678600.0,54642262.0,GC9 R1.fq.gz,0:150 1:150,A:4548403510;C:3786937912;G:3801036342;T:4255236177;N:1064659,150,150,,,4548403510,3786937912,3801036342,4255236177,1064659,SRX14335888,SRS12150682,SRA1379556,Sun-Yat sen University|School of Marine Science,Sun-Yat sen University,2,0.92711,0.93044,0.08622,0.08652,0.79693,0.80306,0.58096,0.58168,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_generic,generic-scrnaseq-only,,China,2022-03-02,Multi-stage,Embryo,Gonad,Reproductive System
68778,SRR18188991,SRX14335887,SRS12150683,SRP362100,PRJNA811725,Single cell sequencing of zebra fish primordial germ cell,PRJNA811725,Other,Based on the transcriptome  we constructed long non coding RNA lncRNA profile of zebrafish primordial germ cells PGCs to further discern functional lncRNA that might play role in PGCs development.,,,,,GC4,,strain:kop:EGFP 3 primeUTR nanos primordial germ cell transgenic line|isolate:Based on green fluorescence  single PGC was distinctively identified and picked out using a capillary tube|age:5hpf|dev stage:30% 50% epiboly|sex:not applicable|tissue:primordial germ cell|cell type:primordial germ cell|replicate:replicate2|BioSampleModel:Model organism or animal,,,,,,,,,2pgc,2 2pgc,2 2pgc,primordial germ cell from 5 hpf zebrafish embryos,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP362100,,,GC4_R1.fq.gz GC4_R2.fq.gz,fastq fastq,14471348700.0,48237829.0,GC4 R1.fq.gz,0:150 1:150,A:4127039158;C:3211803959;G:3224340004;T:3907215356;N:950223,150,150,,,4127039158,3211803959,3224340004,3907215356,950223,SRX14335887,SRS12150683,SRA1379556,Sun-Yat sen University|School of Marine Science,Sun-Yat sen University,2,0.91951,0.91886,0.14001,0.14043,0.75777,0.76605,0.55643,0.55313,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_generic,generic-scrnaseq-only,,China,2022-03-02,Multi-stage,Embryo,Gonad,Reproductive System
68779,SRR18188992,SRX14335886,SRS12150681,SRP362100,PRJNA811725,Single cell sequencing of zebra fish primordial germ cell,PRJNA811725,Other,Based on the transcriptome  we constructed long non coding RNA lncRNA profile of zebrafish primordial germ cells PGCs to further discern functional lncRNA that might play role in PGCs development.,,,,,GC1,,strain:kop:EGFP 3 primeUTR nanos primordial germ cell transgenic line|isolate:Based on green fluorescence  single PGC was distinctively identified and picked out using a capillary tube|age:5hpf|dev stage:30% 50% epiboly|sex:not applicable|tissue:primordial germ cell|cell type:primordial germ cell|replicate:replicate1|BioSampleModel:Model organism or animal,,,,,,,,,1pgc,1 1pgc,1 1pgc,primordial germ cell from 5 hpf zebrafish embryos,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP362100,,,GC1_R1.fq.gz GC1_R2.fq.gz,fastq fastq,18801698100.0,62672327.0,GC1 R1.fq.gz,0:150 1:150,A:5242992703;C:4310290517;G:4334163362;T:4913025193;N:1226325,150,150,,,5242992703,4310290517,4334163362,4913025193,1226325,SRX14335886,SRS12150681,SRA1379556,Sun-Yat sen University|School of Marine Science,Sun-Yat sen University,2,0.93192,0.93277,0.09532,0.09559,0.78358,0.7906,0.5661,0.56344,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_generic,generic-scrnaseq-only,,China,2022-03-02,Multi-stage,Embryo,Gonad,Reproductive System
71597,SRR21780858,SRX17775679,SRS15301946,SRP400655,PRJNA885906,Cell Type Specific Responses to the Microbiota Across All Tissues of the Larval Zebrafish,PRJNA885906,Other,The transcriptional responses of the host zebrafish to the presence of the microbiota was assessed across all cell types throughout the larval body at single cell resolution. The goal of this work is to generate a resource for generating new hypotheses about the intricate interactions between animal hosts and their microbiota.,,,,BefA diss,BefA 1532,,strain:Tgins; eGFP|dev stage:6dpf|sex:not applicable|tissue:dissected digestive systems|BioSampleModel:Model organism or animal,,,,,,,,,germ free 6dpf dissected digestive systems  treated with protein,1532,1532,the cells are from dissected guts from germ free larvae but were treated with exogenous protein,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP400655,,,BefAdiss_S2_L008_R1_001.fastq.gz BefAdiss_S2_L008_R2_001.fastq.gz,fastq fastq,62618506720.0,355786970.0,BefAdiss S2 L008 R1 001.fastq.gz,0:26 1:150,A:18434729847;C:13374700052;G:13922149278;T:16789619859;N:97307684,26,150,,,18434729847,13374700052,13922149278,16789619859,97307684,SRX17775679,SRS15301946,SRA1511285,University of Oregon|Institute of Molecular Biology,University of Oregon,2,0.00182,0.89692,0.00064,0.07716,0.9962,0.82798,0.42608,0.6075,26,150,T,B,sc-like readlen,illumina,hiseq_era,unknown,random_priming,unknown,sc,unknown,unknown,,United States,2022-10-02,Larval,Larval,Gut,Digestive System
71598,SRR21780859,SRX17775678,SRS15301945,SRP400655,PRJNA885906,Cell Type Specific Responses to the Microbiota Across All Tissues of the Larval Zebrafish,PRJNA885906,Other,The transcriptional responses of the host zebrafish to the presence of the microbiota was assessed across all cell types throughout the larval body at single cell resolution. The goal of this work is to generate a resource for generating new hypotheses about the intricate interactions between animal hosts and their microbiota.,,,,GF diss2,GF 1531,,strain:Tgins; eGFP|dev stage:6dpf|sex:not applicable|tissue:dissected digestive systems|BioSampleModel:Model organism or animal,,,,,,,,,germ free 6dpf dissected digestive systems lane 2,1531,1531,the cells dissected guts from germ free larvae were split across two lanes library 1530/1531 come from same sample,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP400655,,,GFdiss2_S1_L004_R1_001.fastq.gz GFdiss2_S1_L004_R2_001.fastq.gz,fastq fastq,66862372720.0,379899845.0,GFdiss2 S1 L004 R1 001.fastq.gz,0:26 1:150,A:10814720171;C:8609009803;G:8785194946;T:9942289999;N:28711157801,26,150,,,10814720171,8609009803,8785194946,9942289999,28711157801,SRX17775678,SRS15301945,SRA1511285,University of Oregon|Institute of Molecular Biology,University of Oregon,2,0.00191,0.92014,0.00074,0.08575,0.99616,0.87793,0.35964,0.58459,26,150,T,B,sc-like readlen,illumina,hiseq_era,unknown,random_priming,unknown,sc,unknown,unknown,,United States,2022-10-02,Larval,Larval,Gut,Digestive System
71599,SRR21780860,SRX17775677,SRS15301944,SRP400655,PRJNA885906,Cell Type Specific Responses to the Microbiota Across All Tissues of the Larval Zebrafish,PRJNA885906,Other,The transcriptional responses of the host zebrafish to the presence of the microbiota was assessed across all cell types throughout the larval body at single cell resolution. The goal of this work is to generate a resource for generating new hypotheses about the intricate interactions between animal hosts and their microbiota.,,,,GF diss1,GF 1530,,strain:Tgins; eGFP|dev stage:6dpf|sex:not applicable|tissue:dissected digestive systems|BioSampleModel:Model organism or animal,,,,,,,,,germ free 6dpf dissected digestive systems lane 1,1530,1530,the cells dissected guts from germ free larvae were split across two lanes library 1530/1531 come from same sample,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP400655,,,GFdiss1_S1_L007_R1_001.fastq.gz GFdiss1_S1_L007_R2_001.fastq.gz,fastq fastq,63769716736.0,362327936.0,GFdiss1 S1 L007 R1 001.fastq.gz,0:26 1:150,A:18291156920;C:14095548431;G:14421791117;T:16786925671;N:174294597,26,150,,,18291156920,14095548431,14421791117,16786925671,174294597,SRX17775677,SRS15301944,SRA1511285,University of Oregon|Institute of Molecular Biology,University of Oregon,2,0.00172,0.91725,0.00064,0.08763,0.99648,0.82804,0.39234,0.5982,26,150,T,B,sc-like readlen,illumina,hiseq_era,unknown,random_priming,unknown,sc,unknown,unknown,,United States,2022-10-02,Larval,Larval,Gut,Digestive System
71600,SRR21780861,SRX17775676,SRS15301943,SRP400655,PRJNA885906,Cell Type Specific Responses to the Microbiota Across All Tissues of the Larval Zebrafish,PRJNA885906,Other,The transcriptional responses of the host zebrafish to the presence of the microbiota was assessed across all cell types throughout the larval body at single cell resolution. The goal of this work is to generate a resource for generating new hypotheses about the intricate interactions between animal hosts and their microbiota.,,,,GF1,GF1 HWLY5BBXX,,strain:Tgnkx2.2a; eGFP|dev stage:6dpf|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,germ free no microbiota 6dpf whole larvae,HWLY5BBXX GF1,HWLY5BBXX GF1,data is culmination of two HiSeq4000 runs. One run  CV/GF samples were both run on the same line and in the second run  CV/GF samples were run on individual lanes. Data was demultiplexed and treatment groups combined for total number of reads per group to be above spec.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP400655,,,GF1_S2_L006_R2_001.fastq.gz GF1_S2_L006_R1_001.fastq.gz,fastq fastq,43844549700.0,146148499.0,GF1 S2 L006 R1 001.fastq.gz,0:150 1:150,A:10577324109;C:7388773641;G:8146030296;T:17727050506;N:5371148,150,150,,,10577324109,7388773641,8146030296,17727050506,5371148,SRX17775676,SRS15301943,SRA1511285,University of Oregon|Institute of Molecular Biology,University of Oregon,2,0.02507,0.90549,0.00575,0.09697,0.99348,0.79091,0.53513,0.47471,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,unknown,unknown,,United States,2022-10-02,Larval,Larval,Whole Organism,All anatomical structures
71601,SRR21780862,SRX17775675,SRS15301942,SRP400655,PRJNA885906,Cell Type Specific Responses to the Microbiota Across All Tissues of the Larval Zebrafish,PRJNA885906,Other,The transcriptional responses of the host zebrafish to the presence of the microbiota was assessed across all cell types throughout the larval body at single cell resolution. The goal of this work is to generate a resource for generating new hypotheses about the intricate interactions between animal hosts and their microbiota.,,,,CV2,CV2 HWLY5BBXX,,strain:Tgnkx2.2a; eGFP|dev stage:6dpf|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,conventional 6dpf whole larvae,HWLY5BBXX CV2,HWLY5BBXX CV2,data is culmination of two HiSeq4000 runs. One run  CV/GF samples were both run on the same line and in the second run  CV/GF samples were run on individual lanes. Data was demultiplexed and treatment groups combined for total number of reads per group to be above spec.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP400655,,,CV2_S1_L006_R1_001.fastq.gz CV2_S1_L006_R2_001.fastq.gz,fastq fastq,42260060400.0,140866868.0,CV2 S1 L006 R1 001.fastq.gz,0:150 1:150,A:10306378433;C:7083604228;G:7794391616;T:17070639212;N:5046911,150,150,,,10306378433,7083604228,7794391616,17070639212,5046911,SRX17775675,SRS15301942,SRA1511285,University of Oregon|Institute of Molecular Biology,University of Oregon,2,0.0311,0.89818,0.0069,0.11191,0.99257,0.78642,0.52164,0.50459,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,unknown,unknown,,United States,2022-10-02,Larval,Larval,Whole Organism,All anatomical structures