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
11813,ERR11788863,ERX11187331,ERS16221143,ERP149944,PRJEB64780,A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain,E-MTAB-13223,Transcriptome Analysis,To understand the cellular basis of the immune compartment of the zebrafish brain we have established reliable protocols for dissociation and prospective isolation of brain leukocytes  using fluorescent transgenic lines. By combining this approach with single cell RNA sequencing  we have generated a gene expression atlas composed of the distinct immune cells present in the homeostatic brain. These analyses revealed the presence of subpopulations of mononuclear phagocytes and other leukocytes  including cell types that have not been  or have been poorly  characterized so far. Here  we present the characterization of a new mononuclear phagocyte population that represents an important fraction among all brain leukocytes.  Adult brain single cell suspensions were prepared from adult Tgp2ry12:GFP; cd45:DsRed fish n=3 and a total of 14 000 cd45:DsRed+ cells were processed for single cell profiling using the 10x Genomics platform.,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,,Protocols: FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3  were dissected in 0.9X Dulbecco′s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33°C for 30 45 minutes  fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4ºC 10 min and filtered through a 40µm nylon mesh. Just before flow cytometry analysis  using calcein violet to exclude dead cells 1µM  Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson. RNA Illumina,Sample 1,SAMEA114235870,Universite Libre de Bruxelles,ENA FIRST PUBLIC:2023 12 25T01:15:29Z|ENA LAST UPDATE:2023 12 25T01:15:29Z|External Id:SAMEA114235870|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:29Z|INSDC last update:2023 12 25T01:15:29Z|INSDC status:public|Submitter Id:E MTAB 13223:Sample 1|age:5|broker name:ArrayExpress|cell type:leukocyte|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:pool of 3 fish|isolate:not applicable|organism part:brain|sample name:E MTAB 13223:Sample 1|scientific name:Danio rerio|sex:male and female|strain:AB,,,,,,,,,A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain,E MTAB 13223:Sample 1 p,Sample 1 p,A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain,FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3  were dissected in 0.9X Dulbecco′s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33°C for 30 45 minutes  fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4ºC 10 min and filtered through a 40µm nylon mesh. Just before flow cytometry analysis  using calcein violet to exclude dead cells 1µM  Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson.  RNA Illumina,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP149944,NextSeq 550 paired end sequencing; A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,L41805_Track-81843_R1.fastq.gz L41805_Track-81843_R2.fastq.gz,fastq fastq,5545444464.0,66017196.0,E MTAB 13223:L41805 Track 81843,0:28 1:56,A:1576174024;C:1193175858;G:1221776615;T:1551009004;N:3308963,28,56,,,1576174024,1193175858,1221776615,1551009004,3308963,ERX11187331,ERS16221143,ERA26318932,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.00738,0.90151,0.00285,0.20553,0.99072,0.82402,0.4645,0.53817,28,56,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-12-25,Adult,Adult,Brain,Nervous System
11814,ERR11788864,ERX11187331,ERS16221143,ERP149944,PRJEB64780,A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain,E-MTAB-13223,Transcriptome Analysis,To understand the cellular basis of the immune compartment of the zebrafish brain we have established reliable protocols for dissociation and prospective isolation of brain leukocytes  using fluorescent transgenic lines. By combining this approach with single cell RNA sequencing  we have generated a gene expression atlas composed of the distinct immune cells present in the homeostatic brain. These analyses revealed the presence of subpopulations of mononuclear phagocytes and other leukocytes  including cell types that have not been  or have been poorly  characterized so far. Here  we present the characterization of a new mononuclear phagocyte population that represents an important fraction among all brain leukocytes.  Adult brain single cell suspensions were prepared from adult Tgp2ry12:GFP; cd45:DsRed fish n=3 and a total of 14 000 cd45:DsRed+ cells were processed for single cell profiling using the 10x Genomics platform.,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,,Protocols: FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3  were dissected in 0.9X Dulbecco′s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33°C for 30 45 minutes  fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4ºC 10 min and filtered through a 40µm nylon mesh. Just before flow cytometry analysis  using calcein violet to exclude dead cells 1µM  Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson. RNA Illumina,Sample 1,SAMEA114235870,Universite Libre de Bruxelles,ENA FIRST PUBLIC:2023 12 25T01:15:29Z|ENA LAST UPDATE:2023 12 25T01:15:29Z|External Id:SAMEA114235870|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:29Z|INSDC last update:2023 12 25T01:15:29Z|INSDC status:public|Submitter Id:E MTAB 13223:Sample 1|age:5|broker name:ArrayExpress|cell type:leukocyte|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:pool of 3 fish|isolate:not applicable|organism part:brain|sample name:E MTAB 13223:Sample 1|scientific name:Danio rerio|sex:male and female|strain:AB,,,,,,,,,A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain,E MTAB 13223:Sample 1 p,Sample 1 p,A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain,FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3  were dissected in 0.9X Dulbecco′s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33°C for 30 45 minutes  fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4ºC 10 min and filtered through a 40µm nylon mesh. Just before flow cytometry analysis  using calcein violet to exclude dead cells 1µM  Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson.  RNA Illumina,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP149944,NextSeq 550 paired end sequencing; A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,L41805_Track-81377_R1.fastq.gz L41805_Track-81377_R2.fastq.gz,fastq fastq,3184137096.0,37906394.0,E MTAB 13223:L41805 Track 81377,0:28 1:56,A:899943184;C:685571078;G:703849582;T:889228559;N:5544693,28,56,,,899943184,685571078,703849582,889228559,5544693,ERX11187331,ERS16221143,ERA26318932,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.00734,0.90077,0.00293,0.20318,0.99064,0.82765,0.47994,0.53473,28,56,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-12-25,Adult,Adult,Brain,Nervous System