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
10166,ERR5762357,ERX5471113,ERS6291553,ERP128548,PRJEB44492,scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,E-MTAB-10370,Transcriptome Analysis,GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice  its role during adult hematopoiesis is incompletely understood. In zebrafish  mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs  whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation  but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells  we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population  we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09,,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 V2. Library was prepared using the manufacturers protocol 10x Chromium V2.,wt2 gata2b,SAMEA8606934,Erasmus Medical Center,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606934|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:wt2 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:wt2 gata2b|sampling site:kidney marrow|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,E MTAB 10370:wt2 gata2b p,wt2 gata2b p,scRNA seq of kidney marrow cells from Gata2b deficient 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 V2. Library was prepared using the manufacturers  protocol 10x Chromium V2.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP128548,Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09,wt2_gata2b.bam,bam,25266437196.0,277653156.0,E MTAB 10370:wt2 gata2b,0:91,A:7555470312;C:5144518052;G:5682746714;T:6882396490;N:1305628,91,,,,7555470312,5144518052,5682746714,6882396490,1305628,ERX5471113,ERS6291553,ERA4089475,Erasmus Medical Center|European Nucleotide Archive,Erasmus Medical Center|European Nucleotide Archive,1,0.90876,,0.18424,,0.84017,,0.55508,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Netherlands,2022-04-09,Adult,Adult,Kidney,Renal System
10167,ERR5762356,ERX5471112,ERS6291552,ERP128548,PRJEB44492,scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,E-MTAB-10370,Transcriptome Analysis,GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice  its role during adult hematopoiesis is incompletely understood. In zebrafish  mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs  whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation  but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells  we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population  we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09,,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 V2. Library was prepared using the manufacturers protocol 10x Chromium V2.,wt1 gata2b,SAMEA8606933,Erasmus Medical Center,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606933|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:wt1 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:wt1 gata2b|sampling site:kidney marrow|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,E MTAB 10370:wt1 gata2b p,wt1 gata2b p,scRNA seq of kidney marrow cells from Gata2b deficient 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 V2. Library was prepared using the manufacturers  protocol 10x Chromium V2.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP128548,Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09,wt1_gata2b.bam,bam,36376708095.0,399744045.0,E MTAB 10370:wt1 gata2b,0:91,A:10397161431;C:8128518427;G:8799445454;T:9049686061;N:1896722,91,,,,10397161431,8128518427,8799445454,9049686061,1896722,ERX5471112,ERS6291552,ERA4089475,Erasmus Medical Center|European Nucleotide Archive,Erasmus Medical Center|European Nucleotide Archive,1,0.94708,,0.08938,,0.85449,,0.52917,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Netherlands,2022-04-09,Adult,Adult,Kidney,Renal System
10168,ERR5762355,ERX5471111,ERS6291551,ERP128548,PRJEB44492,scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,E-MTAB-10370,Transcriptome Analysis,GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice  its role during adult hematopoiesis is incompletely understood. In zebrafish  mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs  whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation  but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells  we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population  we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09,,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 V2. Library was prepared using the manufacturers protocol 10x Chromium V2.,hom2 gata2b,SAMEA8606932,Erasmus Medical Center,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606932|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:hom2 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:gata2b / |isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:hom2 gata2b|sampling site:kidney marrow|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,E MTAB 10370:hom2 gata2b p,hom2 gata2b p,scRNA seq of kidney marrow cells from Gata2b deficient 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 V2. Library was prepared using the manufacturers  protocol 10x Chromium V2.,Experimental Factor: genotype:gata2b / ,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP128548,Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09,hom2_gata2b.bam,bam,22416887402.0,246339422.0,E MTAB 10370:hom2 gata2b,0:91,A:6732382430;C:4540586585;G:4933684272;T:6209137814;N:1096301,91,,,,6732382430,4540586585,4933684272,6209137814,1096301,ERX5471111,ERS6291551,ERA4089475,Erasmus Medical Center|European Nucleotide Archive,Erasmus Medical Center|European Nucleotide Archive,1,0.91306,,0.21566,,0.83469,,0.53782,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Netherlands,2022-04-09,Adult,Adult,Kidney,Renal System
10169,ERR5762354,ERX5471110,ERS6291550,ERP128548,PRJEB44492,scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,E-MTAB-10370,Transcriptome Analysis,GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice  its role during adult hematopoiesis is incompletely understood. In zebrafish  mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs  whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation  but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells  we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population  we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09,,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 V2. Library was prepared using the manufacturers protocol 10x Chromium V2.,hom1 gata2b,SAMEA8606931,Erasmus Medical Center,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606931|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:hom1 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:gata2b / |isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:hom1 gata2b|sampling site:kidney marrow|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,E MTAB 10370:hom1 gata2b p,hom1 gata2b p,scRNA seq of kidney marrow cells from Gata2b deficient 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 V2. Library was prepared using the manufacturers  protocol 10x Chromium V2.,Experimental Factor: genotype:gata2b / ,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP128548,Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09,hom1_gata2b.bam,bam,18004290759.0,197849349.0,E MTAB 10370:hom1 gata2b,0:91,A:5232521408;C:3876317502;G:4287902596;T:4606191653;N:1357600,91,,,,5232521408,3876317502,4287902596,4606191653,1357600,ERX5471110,ERS6291550,ERA4089475,Erasmus Medical Center|European Nucleotide Archive,Erasmus Medical Center|European Nucleotide Archive,1,0.94131,,0.08871,,0.83465,,0.52792,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Netherlands,2022-04-09,Adult,Adult,Kidney,Renal System