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
19476,ERR14208827,ERX13611047,ERS22979745,ERP167299,PRJEB83709,YTHDF2 and ASD DM,3296f78e-e1c0-43ea-968c-53fe04e67615,Other,Among autistic individuals  a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However  many of the genes contributing to ASD DM have yet to be delineated. In this study  we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection  totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM  including CHD8 and PTEN. By performing functional network analysis  we expanded to additional candidate genes  including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish  we modeled a de novo tandem duplication impacting YTHDF2  encoding an N6 methyladenosine m6A mRNA reader  in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size  while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain  providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader  YTHDC1  in our ASD DM cohort. Though we highlight only two cases to date  our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,,Single cell RNA sequencing of zebrafish heads,Scrambled 1 sample,SAMEA117628607,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC status:public|Submitter Id:Sample 004|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 004|scientific name:Danio rerio,,,,,,,,,Raw reads: Scrambled 1 sample,webin reads Scrambled 1 sample,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP167299,Raw reads: Scrambled 1 sample,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,F04.bam,bam,8497741.0,104283.0,webin reads Scrambled 1 sample,0:81.49,A:2628864;C:1112827;G:2146146;T:2609768;N:136,81,,,,2628864,1112827,2146146,2609768,136,ERX13611047,ERS22979745,ERA31123309,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-02-01,Larval,Larval,Head,Nervous System
19477,ERR14208813,ERX13611033,ERS22979748,ERP167299,PRJEB83709,YTHDF2 and ASD DM,3296f78e-e1c0-43ea-968c-53fe04e67615,Other,Among autistic individuals  a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However  many of the genes contributing to ASD DM have yet to be delineated. In this study  we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection  totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM  including CHD8 and PTEN. By performing functional network analysis  we expanded to additional candidate genes  including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish  we modeled a de novo tandem duplication impacting YTHDF2  encoding an N6 methyladenosine m6A mRNA reader  in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size  while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain  providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader  YTHDC1  in our ASD DM cohort. Though we highlight only two cases to date  our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,,Single cell RNA sequencing of zebrafish heads,ythdf2KO 1 sample,SAMEA117628610,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC status:public|Submitter Id:Sample 007|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 007|scientific name:Danio rerio,,,,,,,,,Raw reads: ythdf2KO 1 sample,webin reads ythdf2KO 1 sample,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP167299,Raw reads: ythdf2KO 1 sample,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,D09.bam,bam,673213184.0,8122011.0,webin reads ythdf2KO 1 sample,0:82.89,A:180836688;C:107076381;G:193711319;T:191586188;N:2608,82,,,,180836688,107076381,193711319,191586188,2608,ERX13611033,ERS22979748,ERA31123295,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-02-01,Larval,Larval,Head,Nervous System
19478,ERR14208811,ERX13611031,ERS22979755,ERP167299,PRJEB83709,YTHDF2 and ASD DM,3296f78e-e1c0-43ea-968c-53fe04e67615,Other,Among autistic individuals  a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However  many of the genes contributing to ASD DM have yet to be delineated. In this study  we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection  totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM  including CHD8 and PTEN. By performing functional network analysis  we expanded to additional candidate genes  including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish  we modeled a de novo tandem duplication impacting YTHDF2  encoding an N6 methyladenosine m6A mRNA reader  in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size  while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain  providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader  YTHDC1  in our ASD DM cohort. Though we highlight only two cases to date  our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,,Single cell RNA sequencing of zebrafish heads,GFP 6 sample,SAMEA117628617,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC status:public|Submitter Id:Sample 014|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 014|scientific name:Danio rerio,,,,,,,,,Raw reads: GFP 6 sample,webin reads GFP 6 sample,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP167299,Raw reads: GFP 6 sample,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,H01.bam,bam,337553787.0,3153658.0,webin reads GFP 6 sample,0:107.04,A:81816649;C:55524538;G:113686171;T:86525390;N:1039,107,,,,81816649,55524538,113686171,86525390,1039,ERX13611031,ERS22979755,ERA31123293,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-02-01,Larval,Larval,Head,Nervous System
19479,ERR14208821,ERX13611041,ERS22979752,ERP167299,PRJEB83709,YTHDF2 and ASD DM,3296f78e-e1c0-43ea-968c-53fe04e67615,Other,Among autistic individuals  a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However  many of the genes contributing to ASD DM have yet to be delineated. In this study  we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection  totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM  including CHD8 and PTEN. By performing functional network analysis  we expanded to additional candidate genes  including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish  we modeled a de novo tandem duplication impacting YTHDF2  encoding an N6 methyladenosine m6A mRNA reader  in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size  while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain  providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader  YTHDC1  in our ASD DM cohort. Though we highlight only two cases to date  our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,,Single cell RNA sequencing of zebrafish heads,ythdf2KO 5 sample,SAMEA117628614,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC status:public|Submitter Id:Sample 011|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 011|scientific name:Danio rerio,,,,,,,,,Raw reads: ythdf2KO 5 sample,webin reads ythdf2KO 5 sample,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP167299,Raw reads: ythdf2KO 5 sample,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,G10.bam,bam,226771232.0,2050630.0,webin reads ythdf2KO 5 sample,0:110.59,A:56944731;C:30766256;G:83820146;T:55239221;N:878,110,,,,56944731,30766256,83820146,55239221,878,ERX13611041,ERS22979752,ERA31123303,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-02-01,Larval,Larval,Head,Nervous System
19480,ERR14208818,ERX13611038,ERS22979750,ERP167299,PRJEB83709,YTHDF2 and ASD DM,3296f78e-e1c0-43ea-968c-53fe04e67615,Other,Among autistic individuals  a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However  many of the genes contributing to ASD DM have yet to be delineated. In this study  we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection  totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM  including CHD8 and PTEN. By performing functional network analysis  we expanded to additional candidate genes  including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish  we modeled a de novo tandem duplication impacting YTHDF2  encoding an N6 methyladenosine m6A mRNA reader  in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size  while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain  providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader  YTHDC1  in our ASD DM cohort. Though we highlight only two cases to date  our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,,Single cell RNA sequencing of zebrafish heads,ythdf2KO 3 sample,SAMEA117628612,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC status:public|Submitter Id:Sample 009|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 009|scientific name:Danio rerio,,,,,,,,,Raw reads: ythdf2KO 3 sample,webin reads ythdf2KO 3 sample,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP167299,Raw reads: ythdf2KO 3 sample,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,G08.bam,bam,351425328.0,3771763.0,webin reads ythdf2KO 3 sample,0:93.17,A:83933175;C:50138103;G:128300798;T:89051913;N:1339,93,,,,83933175,50138103,128300798,89051913,1339,ERX13611038,ERS22979750,ERA31123300,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-02-01,Larval,Larval,Head,Nervous System
19481,ERR14208826,ERX13611046,ERS22979758,ERP167299,PRJEB83709,YTHDF2 and ASD DM,3296f78e-e1c0-43ea-968c-53fe04e67615,Other,Among autistic individuals  a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However  many of the genes contributing to ASD DM have yet to be delineated. In this study  we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection  totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM  including CHD8 and PTEN. By performing functional network analysis  we expanded to additional candidate genes  including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish  we modeled a de novo tandem duplication impacting YTHDF2  encoding an N6 methyladenosine m6A mRNA reader  in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size  while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain  providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader  YTHDC1  in our ASD DM cohort. Though we highlight only two cases to date  our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,,Single cell RNA sequencing of zebrafish heads,YTHDF2 3 sample,SAMEA117628620,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC status:public|Submitter Id:Sample 017|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 017|scientific name:Danio rerio,,,,,,,,,Raw reads: YTHDF2 3 sample,webin reads YTHDF2 3 sample,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP167299,Raw reads: YTHDF2 3 sample,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,E01.bam,bam,181017083.0,1670383.0,webin reads YTHDF2 3 sample,0:108.37,A:38910474;C:31607688;G:67095095;T:43403227;N:599,108,,,,38910474,31607688,67095095,43403227,599,ERX13611046,ERS22979758,ERA31123308,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-02-01,Larval,Larval,Head,Nervous System
19482,ERR14208815,ERX13611035,ERS22979749,ERP167299,PRJEB83709,YTHDF2 and ASD DM,3296f78e-e1c0-43ea-968c-53fe04e67615,Other,Among autistic individuals  a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However  many of the genes contributing to ASD DM have yet to be delineated. In this study  we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection  totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM  including CHD8 and PTEN. By performing functional network analysis  we expanded to additional candidate genes  including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish  we modeled a de novo tandem duplication impacting YTHDF2  encoding an N6 methyladenosine m6A mRNA reader  in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size  while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain  providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader  YTHDC1  in our ASD DM cohort. Though we highlight only two cases to date  our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,,Single cell RNA sequencing of zebrafish heads,ythdf2KO 2 sample,SAMEA117628611,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC status:public|Submitter Id:Sample 008|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 008|scientific name:Danio rerio,,,,,,,,,Raw reads: ythdf2KO 2 sample,webin reads ythdf2KO 2 sample,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP167299,Raw reads: ythdf2KO 2 sample,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,D10.bam,bam,282414832.0,2675188.0,webin reads ythdf2KO 2 sample,0:105.57,A:73651155;C:41694223;G:96485766;T:70582706;N:982,105,,,,73651155,41694223,96485766,70582706,982,ERX13611035,ERS22979749,ERA31123297,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-02-01,Larval,Larval,Head,Nervous System
19483,ERR14208804,ERX13611024,ERS22979742,ERP167299,PRJEB83709,YTHDF2 and ASD DM,3296f78e-e1c0-43ea-968c-53fe04e67615,Other,Among autistic individuals  a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However  many of the genes contributing to ASD DM have yet to be delineated. In this study  we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection  totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM  including CHD8 and PTEN. By performing functional network analysis  we expanded to additional candidate genes  including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish  we modeled a de novo tandem duplication impacting YTHDF2  encoding an N6 methyladenosine m6A mRNA reader  in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size  while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain  providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader  YTHDC1  in our ASD DM cohort. Though we highlight only two cases to date  our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,,Single cell RNA sequencing of zebrafish heads,GFP 1 sample,SAMEA117628604,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC status:public|Submitter Id:Sample 001|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 001|scientific name:Danio rerio,,,,,,,,,Raw reads: GFP 1 sample,webin reads GFP 1 sample,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP167299,Raw reads: GFP 1 sample,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,F01.bam,bam,8036009.0,97716.0,webin reads GFP 1 sample,0:82.24,A:2445867;C:1074319;G:2086526;T:2429153;N:144,82,,,,2445867,1074319,2086526,2429153,144,ERX13611024,ERS22979742,ERA31123286,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-02-01,Larval,Larval,Head,Nervous System
19484,ERR14208829,ERX13611049,ERS22979747,ERP167299,PRJEB83709,YTHDF2 and ASD DM,3296f78e-e1c0-43ea-968c-53fe04e67615,Other,Among autistic individuals  a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However  many of the genes contributing to ASD DM have yet to be delineated. In this study  we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection  totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM  including CHD8 and PTEN. By performing functional network analysis  we expanded to additional candidate genes  including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish  we modeled a de novo tandem duplication impacting YTHDF2  encoding an N6 methyladenosine m6A mRNA reader  in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size  while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain  providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader  YTHDC1  in our ASD DM cohort. Though we highlight only two cases to date  our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,,Single cell RNA sequencing of zebrafish heads,Scrambled 3 sample,SAMEA117628609,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC status:public|Submitter Id:Sample 006|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 006|scientific name:Danio rerio,,,,,,,,,Raw reads: Scrambled 3 sample,webin reads Scrambled 3 sample,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP167299,Raw reads: Scrambled 3 sample,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,F06.bam,bam,90051514.0,910768.0,webin reads Scrambled 3 sample,0:98.87,A:30132090;C:13700682;G:16323331;T:29894332;N:1079,98,,,,30132090,13700682,16323331,29894332,1079,ERX13611049,ERS22979747,ERA31123311,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-02-01,Larval,Larval,Head,Nervous System
19485,ERR14208809,ERX13611029,ERS22979753,ERP167299,PRJEB83709,YTHDF2 and ASD DM,3296f78e-e1c0-43ea-968c-53fe04e67615,Other,Among autistic individuals  a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However  many of the genes contributing to ASD DM have yet to be delineated. In this study  we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection  totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM  including CHD8 and PTEN. By performing functional network analysis  we expanded to additional candidate genes  including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish  we modeled a de novo tandem duplication impacting YTHDF2  encoding an N6 methyladenosine m6A mRNA reader  in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size  while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain  providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader  YTHDC1  in our ASD DM cohort. Though we highlight only two cases to date  our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,,Single cell RNA sequencing of zebrafish heads,GFP 4 sample,SAMEA117628615,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC status:public|Submitter Id:Sample 012|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 012|scientific name:Danio rerio,,,,,,,,,Raw reads: GFP 4 sample,webin reads GFP 4 sample,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP167299,Raw reads: GFP 4 sample,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,G11.bam,bam,72278736.0,751207.0,webin reads GFP 4 sample,0:96.22,A:17589630;C:11153310;G:25212154;T:18323416;N:226,96,,,,17589630,11153310,25212154,18323416,226,ERX13611029,ERS22979753,ERA31123291,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-02-01,Larval,Larval,Head,Nervous System
19486,ERR14208806,ERX13611026,ERS22979743,ERP167299,PRJEB83709,YTHDF2 and ASD DM,3296f78e-e1c0-43ea-968c-53fe04e67615,Other,Among autistic individuals  a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However  many of the genes contributing to ASD DM have yet to be delineated. In this study  we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection  totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM  including CHD8 and PTEN. By performing functional network analysis  we expanded to additional candidate genes  including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish  we modeled a de novo tandem duplication impacting YTHDF2  encoding an N6 methyladenosine m6A mRNA reader  in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size  while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain  providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader  YTHDC1  in our ASD DM cohort. Though we highlight only two cases to date  our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,,Single cell RNA sequencing of zebrafish heads,GFP 2 sample,SAMEA117628605,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC status:public|Submitter Id:Sample 002|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 002|scientific name:Danio rerio,,,,,,,,,Raw reads: GFP 2 sample,webin reads GFP 2 sample,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP167299,Raw reads: GFP 2 sample,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,F02.bam,bam,19196592.0,230075.0,webin reads GFP 2 sample,0:83.44,A:5957309;C:2709511;G:4434875;T:6094552;N:345,83,,,,5957309,2709511,4434875,6094552,345,ERX13611026,ERS22979743,ERA31123288,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-02-01,Larval,Larval,Head,Nervous System
19487,ERR14208810,ERX13611030,ERS22979754,ERP167299,PRJEB83709,YTHDF2 and ASD DM,3296f78e-e1c0-43ea-968c-53fe04e67615,Other,Among autistic individuals  a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However  many of the genes contributing to ASD DM have yet to be delineated. In this study  we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection  totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM  including CHD8 and PTEN. By performing functional network analysis  we expanded to additional candidate genes  including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish  we modeled a de novo tandem duplication impacting YTHDF2  encoding an N6 methyladenosine m6A mRNA reader  in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size  while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain  providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader  YTHDC1  in our ASD DM cohort. Though we highlight only two cases to date  our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,,Single cell RNA sequencing of zebrafish heads,GFP 5 sample,SAMEA117628616,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC status:public|Submitter Id:Sample 013|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 013|scientific name:Danio rerio,,,,,,,,,Raw reads: GFP 5 sample,webin reads GFP 5 sample,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP167299,Raw reads: GFP 5 sample,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,G12.bam,bam,431708790.0,5173015.0,webin reads GFP 5 sample,0:83.45,A:119077902;C:68329173;G:126879243;T:117420803;N:1669,83,,,,119077902,68329173,126879243,117420803,1669,ERX13611030,ERS22979754,ERA31123292,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-02-01,Larval,Larval,Head,Nervous System
19488,ERR14208828,ERX13611048,ERS22979746,ERP167299,PRJEB83709,YTHDF2 and ASD DM,3296f78e-e1c0-43ea-968c-53fe04e67615,Other,Among autistic individuals  a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However  many of the genes contributing to ASD DM have yet to be delineated. In this study  we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection  totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM  including CHD8 and PTEN. By performing functional network analysis  we expanded to additional candidate genes  including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish  we modeled a de novo tandem duplication impacting YTHDF2  encoding an N6 methyladenosine m6A mRNA reader  in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size  while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain  providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader  YTHDC1  in our ASD DM cohort. Though we highlight only two cases to date  our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,,Single cell RNA sequencing of zebrafish heads,Scrambled 2 sample,SAMEA117628608,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC status:public|Submitter Id:Sample 005|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 005|scientific name:Danio rerio,,,,,,,,,Raw reads: Scrambled 2 sample,webin reads Scrambled 2 sample,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP167299,Raw reads: Scrambled 2 sample,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,F05.bam,bam,32695808.0,357320.0,webin reads Scrambled 2 sample,0:91.50,A:10989624;C:4719485;G:5954777;T:11031603;N:319,91,,,,10989624,4719485,5954777,11031603,319,ERX13611048,ERS22979746,ERA31123310,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-02-01,Larval,Larval,Head,Nervous System
19489,ERR14208819,ERX13611039,ERS22979751,ERP167299,PRJEB83709,YTHDF2 and ASD DM,3296f78e-e1c0-43ea-968c-53fe04e67615,Other,Among autistic individuals  a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However  many of the genes contributing to ASD DM have yet to be delineated. In this study  we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection  totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM  including CHD8 and PTEN. By performing functional network analysis  we expanded to additional candidate genes  including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish  we modeled a de novo tandem duplication impacting YTHDF2  encoding an N6 methyladenosine m6A mRNA reader  in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size  while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain  providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader  YTHDC1  in our ASD DM cohort. Though we highlight only two cases to date  our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,,Single cell RNA sequencing of zebrafish heads,ythdf2KO 4 sample,SAMEA117628613,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC status:public|Submitter Id:Sample 010|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 010|scientific name:Danio rerio,,,,,,,,,Raw reads: ythdf2KO 4 sample,webin reads ythdf2KO 4 sample,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP167299,Raw reads: ythdf2KO 4 sample,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,G09.bam,bam,254231539.0,2766205.0,webin reads ythdf2KO 4 sample,0:91.91,A:63984512;C:40328422;G:86431821;T:63485754;N:1030,91,,,,63984512,40328422,86431821,63485754,1030,ERX13611039,ERS22979751,ERA31123301,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-02-01,Larval,Larval,Head,Nervous System
19490,ERR14208808,ERX13611028,ERS22979744,ERP167299,PRJEB83709,YTHDF2 and ASD DM,3296f78e-e1c0-43ea-968c-53fe04e67615,Other,Among autistic individuals  a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However  many of the genes contributing to ASD DM have yet to be delineated. In this study  we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection  totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM  including CHD8 and PTEN. By performing functional network analysis  we expanded to additional candidate genes  including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish  we modeled a de novo tandem duplication impacting YTHDF2  encoding an N6 methyladenosine m6A mRNA reader  in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size  while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain  providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader  YTHDC1  in our ASD DM cohort. Though we highlight only two cases to date  our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,,Single cell RNA sequencing of zebrafish heads,GFP 3 sample,SAMEA117628606,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC status:public|Submitter Id:Sample 003|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 003|scientific name:Danio rerio,,,,,,,,,Raw reads: GFP 3 sample,webin reads GFP 3 sample,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP167299,Raw reads: GFP 3 sample,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,F03.bam,bam,35932988.0,419944.0,webin reads GFP 3 sample,0:85.57,A:11252929;C:5321445;G:8032297;T:11325814;N:503,85,,,,11252929,5321445,8032297,11325814,503,ERX13611028,ERS22979744,ERA31123290,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-02-01,Larval,Larval,Head,Nervous System
19491,ERR14208825,ERX13611045,ERS22979757,ERP167299,PRJEB83709,YTHDF2 and ASD DM,3296f78e-e1c0-43ea-968c-53fe04e67615,Other,Among autistic individuals  a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However  many of the genes contributing to ASD DM have yet to be delineated. In this study  we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection  totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM  including CHD8 and PTEN. By performing functional network analysis  we expanded to additional candidate genes  including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish  we modeled a de novo tandem duplication impacting YTHDF2  encoding an N6 methyladenosine m6A mRNA reader  in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size  while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain  providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader  YTHDC1  in our ASD DM cohort. Though we highlight only two cases to date  our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,,Single cell RNA sequencing of zebrafish heads,YTHDF2 2 sample,SAMEA117628619,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC status:public|Submitter Id:Sample 016|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 016|scientific name:Danio rerio,,,,,,,,,Raw reads: YTHDF2 2 sample,webin reads YTHDF2 2 sample,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP167299,Raw reads: YTHDF2 2 sample,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,D12.bam,bam,626993184.0,7599502.0,webin reads YTHDF2 2 sample,0:82.50,A:182701108;C:91008174;G:172822143;T:180459253;N:2506,82,,,,182701108,91008174,172822143,180459253,2506,ERX13611045,ERS22979757,ERA31123307,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-02-01,Larval,Larval,Head,Nervous System
19492,ERR14208822,ERX13611042,ERS22979756,ERP167299,PRJEB83709,YTHDF2 and ASD DM,3296f78e-e1c0-43ea-968c-53fe04e67615,Other,Among autistic individuals  a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However  many of the genes contributing to ASD DM have yet to be delineated. In this study  we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection  totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM  including CHD8 and PTEN. By performing functional network analysis  we expanded to additional candidate genes  including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish  we modeled a de novo tandem duplication impacting YTHDF2  encoding an N6 methyladenosine m6A mRNA reader  in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size  while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain  providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader  YTHDC1  in our ASD DM cohort. Though we highlight only two cases to date  our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,,Single cell RNA sequencing of zebrafish heads,YTHDF2 1 sample,SAMEA117628618,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC status:public|Submitter Id:Sample 015|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 015|scientific name:Danio rerio,,,,,,,,,Raw reads: YTHDF2 1 sample,webin reads YTHDF2 1 sample,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP167299,Raw reads: YTHDF2 1 sample,ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01,D11.bam,bam,120748751.0,1368887.0,webin reads YTHDF2 1 sample,0:88.21,A:34957526;C:19985010;G:32927086;T:32878659;N:470,88,,,,34957526,19985010,32927086,32878659,470,ERX13611042,ERS22979756,ERA31123304,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-02-01,Larval,Larval,Head,Nervous System
30691,SRR28270998,SRX23880961,SRS20704477,SRP494117,PRJNA1085662,Roxithromycin exposure induces motoneuron malformation and behavioral deficits of zebrafish by interfering with the differentiation of motor neuron progenitor cells,PRJNA1085662,Other,Roxithromycin ROX  a commonly used macrolide antibiotic  is extensively employed in human medicine and livestock industries. Due to its structural stability and resistance to biological degradation  ROX persists as a resilient environmental contaminant  detectable in aquatic ecosystems and food products. However  our understanding of the potential health risks to humans from continuous ROX exposure remains limited. In this study  we used the zebrafish as a vertebrate model to explore the potential developmental toxicity of early ROX exposure  particularly focusing on its effects on locomotor functionality and motoneuron development. Early exposure to ROX induces marked developmental toxicity in zebrafish embryos  significantly reducing hatch rates  body lengths  and increased malformation rates. Moreover  ROX exposure adversely affected the locomotive capacity of zebrafish embryos  and observations in transgenic zebrafish Tghb9:eGFP revealed axonal loss in motor neurons  evident through reduced or irregular axonal lengths. Concurrently  abnormal apoptosis in ROX exposed zebrafish embryos intensified alongside the upregulation of apoptosis related genes bax  bcl2  caspase 3a. Single cell sequencing further disclosed substantial effects of ROX on genes involved in the differentiation of motor neuron progenitor cells ngn1  olig2  axon development cd82a  mbpa  plp1b  sema5a  and neuroimmunity aplnrb  aplnra in zebrafish larvae. Furthermore  the motor neuron defects induced by ROX can be rescued by administering ngn1 agonist. In summary  ROX exposure leads to early life abnormalities in zebrafish motor neurons and locomotor behavior by hindering the differentiation of motor neuron progenitor cells and inducing abnormal apoptosis.,,,,,WT,,strain:not provided|isolate:not provided|breed:not provided|cultivar:not provided|ecotype:not provided|age:not provided|dev stage:not provided|collection date:not provided|geo loc name:not provided|sex:not provided|tissue:Cerebrum|BioSampleModel:Model organism or animal,,,,,,,,,Roxithromycin exposure induces mot1uron malformation and behavioral deficits of zebrafish by interfering with the differentiation of motor neuron progenitor cells,DANIO,DANIO,Illumina Second Generation Sequencing,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,SINGLE,BGISEQ,BGISEQ-500,,SRP494117,,,WT_S1_L001_I1_001.fastq.gz,fastq,7991376264.0,998922033.0,WT S1 L001 I1 001.fastq.gz,0:8,A:2573734851;C:1426474966;G:1492966198;T:2498173074;N:27175,8,,,,2573734851,1426474966,1492966198,2498173074,27175,SRX23880961,SRS20704477,SRA1820072,shantou university|Neurobiology Center,shantou university,1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,bgi,bgi,unknown,poly_a,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-03-11,Undetermined,Multi-stage,Brain,Nervous System
54345,SRR10126111,SRX6854760,SRS5392962,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 1 01 E02,GSM4080997,,tissue:Brain|sorting:RG|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.0813302707773932,RG 1 01 E02,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.0813302707773932,GSM4080997,GSM4080997: RG 1 01 E02; Danio rerio; RNA Seq,GSM4080997,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080997,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23839_RG_1_01_E02.bam,bam,16444652.0,216377.0,GSM4080997 r1,0:76,A:4583352;C:3984328;G:3906383;T:3970500;N:89,76,,,,4583352,3984328,3906383,3970500,89,SRX6854760,SRS5392962,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.26908,,0.09242,,0.99825,,0.67661,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54346,SRR10126110,SRX6854759,SRS5392961,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 1 01 B02,GSM4080996,,tissue:Brain|sorting:RG|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.137111856361026,RG 1 01 B02,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.137111856361026,GSM4080996,GSM4080996: RG 1 01 B02; Danio rerio; RNA Seq,GSM4080996,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080996,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23836_RG_1_01_B02.bam,bam,14345076.0,188751.0,GSM4080996 r1,0:76,A:4237579;C:3235570;G:3240300;T:3631525;N:102,76,,,,4237579,3235570,3240300,3631525,102,SRX6854759,SRS5392961,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.37026,,0.12862,,0.99805,,0.83484,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54347,SRR10126109,SRX6854758,SRS5392960,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 1 01 C01,GSM4080995,,tissue:Brain|sorting:RG|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.596981146320204,RG 1 01 C01,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.596981146320204,GSM4080995,GSM4080995: RG 1 01 C01; Danio rerio; RNA Seq,GSM4080995,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080995,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23829_RG_1_01_C01_mod.bam,bam,44287252.0,582727.0,GSM4080995 r1,0:76,A:12057290;C:10158222;G:10161190;T:11910345;N:205,76,,,,12057290,10158222,10161190,11910345,205,SRX6854758,SRS5392960,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.83606,,0.11078,,0.97364,,0.51554,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54348,SRR10126108,SRX6854757,SRS5392959,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 1 01 G02,GSM4080994,,tissue:Brain|sorting:RG|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.336437957921624,RG 1 01 G02,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.336437957921624,GSM4080994,GSM4080994: RG 1 01 G02; Danio rerio; RNA Seq,GSM4080994,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080994,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23841_RG_1_01_G02_mod.bam,bam,18090356.0,238031.0,GSM4080994 r1,0:76,A:5124071;C:4154073;G:4123933;T:4688206;N:73,76,,,,5124071,4154073,4123933,4688206,73,SRX6854757,SRS5392959,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.63512,,0.05239,,0.99257,,0.67835,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54349,SRR10126107,SRX6854756,SRS5392958,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 1 01 F02,GSM4080993,,tissue:Brain|sorting:RG|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.169583947726024,RG 1 01 F02,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.169583947726024,GSM4080993,GSM4080993: RG 1 01 F02; Danio rerio; RNA Seq,GSM4080993,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080993,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23840_RG_1_01_F02.bam,bam,13143060.0,172935.0,GSM4080993 r1,0:76,A:3676240;C:3051166;G:3081467;T:3334128;N:59,76,,,,3676240,3051166,3081467,3334128,59,SRX6854756,SRS5392958,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.4252,,0.0971,,0.99697,,0.81536,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54350,SRR10126106,SRX6854755,SRS5392957,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,ON30 01 F12,GSM4080992,,tissue:Brain|sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.307951918399687,ON30 01 F12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.307951918399687,GSM4080992,GSM4080992: ON30 01 F12; Danio rerio; RNA Seq,GSM4080992,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080992,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L22296_ON30_01_F12_mod.bam,bam,45464644.0,598219.0,GSM4080992 r1,0:76,A:13070969;C:9463048;G:9617299;T:13313099;N:229,76,,,,13070969,9463048,9617299,13313099,229,SRX6854755,SRS5392957,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.85125,,0.28428,,0.94795,,0.49176,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54351,SRR10126105,SRX6854754,SRS5392956,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG31 01 H12,GSM4080991,,tissue:Brain|sorting:RG|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.349622553699452,RG31 01 H12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.349622553699452,GSM4080991,GSM4080991: RG31 01 H12; Danio rerio; RNA Seq,GSM4080991,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080991,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L22298_RG31_01_H12_mod.bam,bam,54043448.0,711098.0,GSM4080991 r1,0:76,A:14990424;C:11836357;G:12008841;T:15207589;N:237,76,,,,14990424,11836357,12008841,15207589,237,SRX6854754,SRS5392956,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.85818,,0.139,,0.95706,,0.49646,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54352,SRR10126104,SRX6854753,SRS5392955,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,ON29 01 E12,GSM4080990,,tissue:Brain|sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.270605518893939,ON29 01 E12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.270605518893939,GSM4080990,GSM4080990: ON29 01 E12; Danio rerio; RNA Seq,GSM4080990,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080990,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L22295_ON29_01_E12_mod.bam,bam,31968716.0,420641.0,GSM4080990 r1,0:76,A:9066610;C:6733147;G:6934070;T:9234786;N:103,76,,,,9066610,6733147,6934070,9234786,103,SRX6854753,SRS5392955,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.76341,,0.34992,,0.97583,,0.47889,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54353,SRR10126103,SRX6854752,SRS5392954,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,ON27 01 C12,GSM4080989,,tissue:Brain|sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.207435774030802,ON27 01 C12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.207435774030802,GSM4080989,GSM4080989: ON27 01 C12; Danio rerio; RNA Seq,GSM4080989,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080989,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L22293_ON27_01_C12_mod.bam,bam,36635572.0,482047.0,GSM4080989 r1,0:76,A:10775220;C:6902317;G:7294618;T:11663244;N:173,76,,,,10775220,6902317,7294618,11663244,173,SRX6854752,SRS5392954,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.6712,,0.38208,,0.98563,,0.6672,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54354,SRR10126102,SRX6854751,SRS5392953,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,ON28 01 D12,GSM4080988,,tissue:Brain|sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.361448206817182,ON28 01 D12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.361448206817182,GSM4080988,GSM4080988: ON28 01 D12; Danio rerio; RNA Seq,GSM4080988,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080988,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L22294_ON28_01_D12_mod.bam,bam,48734088.0,641238.0,GSM4080988 r1,0:76,A:13468719;C:10758080;G:10910748;T:13596298;N:243,76,,,,13468719,10758080,10910748,13596298,243,SRX6854751,SRS5392953,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.88752,,0.18774,,0.94911,,0.46357,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54355,SRR10126101,SRX6854750,SRS5392952,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,ON26 01 B12,GSM4080987,,tissue:Brain|sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.400282577622292,ON26 01 B12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.400282577622292,GSM4080987,GSM4080987: ON26 01 B12; Danio rerio; RNA Seq,GSM4080987,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080987,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L22292_ON26_01_B12_mod.bam,bam,46093468.0,606493.0,GSM4080987 r1,0:76,A:12497312;C:10446137;G:10539301;T:12610508;N:210,76,,,,12497312,10446137,10539301,12610508,210,SRX6854750,SRS5392952,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.89062,,0.07593,,0.95146,,0.50127,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54356,SRR10126100,SRX6854749,SRS5392951,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,ON25 01 A12,GSM4080986,,tissue:Brain|sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.36034551688211,ON25 01 A12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.36034551688211,GSM4080986,GSM4080986: ON25 01 A12; Danio rerio; RNA Seq,GSM4080986,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080986,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L22291_ON25_01_A12_mod.bam,bam,56456068.0,742843.0,GSM4080986 r1,0:76,A:16017845;C:12025190;G:12186747;T:16226025;N:261,76,,,,16017845,12025190,12186747,16226025,261,SRX6854749,SRS5392951,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.87174,,0.20317,,0.94446,,0.48709,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54357,SRR10126099,SRX6854748,SRS5392950,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,ON24 01 H11,GSM4080985,,tissue:Brain|sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.324713155088674,ON24 01 H11,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.324713155088674,GSM4080985,GSM4080985: ON24 01 H11; Danio rerio; RNA Seq,GSM4080985,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080985,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L22290_ON24_01_H11_mod.bam,bam,49961108.0,657383.0,GSM4080985 r1,0:76,A:14127615;C:10704711;G:10835971;T:14292589;N:222,76,,,,14127615,10704711,10835971,14292589,222,SRX6854748,SRS5392950,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.87519,,0.24291,,0.91543,,0.48833,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54358,SRR10126098,SRX6854747,SRS5392949,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,ON20 01 D11,GSM4080984,,tissue:Brain|sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.345805160446015,ON20 01 D11,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.345805160446015,GSM4080984,GSM4080984: ON20 01 D11; Danio rerio; RNA Seq,GSM4080984,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080984,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L22286_ON20_01_D11_mod.bam,bam,45645220.0,600595.0,GSM4080984 r1,0:76,A:12652866;C:10016610;G:10144796;T:12830749;N:199,76,,,,12652866,10016610,10144796,12830749,199,SRX6854747,SRS5392949,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.8612,,0.21429,,0.94649,,0.51433,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54359,SRR10126097,SRX6854746,SRS5392948,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,ON19 01 C11,GSM4080983,,tissue:Brain|sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.342848231466316,ON19 01 C11,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.342848231466316,GSM4080983,GSM4080983: ON19 01 C11; Danio rerio; RNA Seq,GSM4080983,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080983,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L22285_ON19_01_C11_mod.bam,bam,44588516.0,586691.0,GSM4080983 r1,0:76,A:12252079;C:9823426;G:9954660;T:12558164;N:187,76,,,,12252079,9823426,9954660,12558164,187,SRX6854746,SRS5392948,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.8663,,0.1874,,0.95057,,0.48221,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54360,SRR10126096,SRX6854745,SRS5392947,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,ON18 01 B11,GSM4080982,,tissue:Brain|sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.356681923777462,ON18 01 B11,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.356681923777462,GSM4080982,GSM4080982: ON18 01 B11; Danio rerio; RNA Seq,GSM4080982,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080982,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L22284_ON18_01_B11_mod.bam,bam,41805776.0,550076.0,GSM4080982 r1,0:76,A:11557097;C:9225654;G:9383396;T:11639451;N:178,76,,,,11557097,9225654,9383396,11639451,178,SRX6854745,SRS5392947,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.88353,,0.19606,,0.93237,,0.49124,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54361,SRR10126095,SRX6854744,SRS5392946,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,ON23 01 G11,GSM4080981,,tissue:Brain|sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.337622302046746,ON23 01 G11,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.337622302046746,GSM4080981,GSM4080981: ON23 01 G11; Danio rerio; RNA Seq,GSM4080981,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080981,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L22289_ON23_01_G11_mod.bam,bam,34314608.0,451508.0,GSM4080981 r1,0:76,A:9639586;C:7428852;G:7549525;T:9696492;N:153,76,,,,9639586,7428852,7549525,9696492,153,SRX6854744,SRS5392946,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.87321,,0.25858,,0.95168,,0.504,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54362,SRR10126094,SRX6854743,SRS5392945,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,ON22 01 F11,GSM4080980,,tissue:Brain|sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.351704193217474,ON22 01 F11,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.351704193217474,GSM4080980,GSM4080980: ON22 01 F11; Danio rerio; RNA Seq,GSM4080980,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080980,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L22288_ON22_01_F11_mod.bam,bam,47930388.0,630663.0,GSM4080980 r1,0:76,A:13368035;C:10449666;G:10572110;T:13540361;N:216,76,,,,13368035,10449666,10572110,13540361,216,SRX6854743,SRS5392945,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.87895,,0.21319,,0.92736,,0.49859,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54363,SRR10126093,SRX6854742,SRS5392944,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,ON21 01 E11,GSM4080979,,tissue:Brain|sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.330638956789342,ON21 01 E11,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.330638956789342,GSM4080979,GSM4080979: ON21 01 E11; Danio rerio; RNA Seq,GSM4080979,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080979,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L22287_ON21_01_E11_mod.bam,bam,46820788.0,616063.0,GSM4080979 r1,0:76,A:13360602;C:9787624;G:10022727;T:13649641;N:194,76,,,,13360602,9787624,10022727,13649641,194,SRX6854742,SRS5392944,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.85652,,0.23734,,0.95629,,0.49147,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54364,SRR10126092,SRX6854741,SRS5392943,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,ON17 01 A11,GSM4080978,,tissue:Brain|sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.346374017705124,ON17 01 A11,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.346374017705124,GSM4080978,GSM4080978: ON17 01 A11; Danio rerio; RNA Seq,GSM4080978,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080978,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L22283_ON17_01_A11_mod.bam,bam,43871912.0,577262.0,GSM4080978 r1,0:76,A:12596782;C:9147890;G:9360119;T:12766904;N:217,76,,,,12596782,9147890,9360119,12766904,217,SRX6854741,SRS5392943,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.86532,,0.23115,,0.95369,,0.48216,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54365,SRR10126091,SRX6854740,SRS5392942,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,ON11 01 C10,GSM4080977,,tissue:Brain|sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.352909893939849,ON11 01 C10,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.352909893939849,GSM4080977,GSM4080977: ON11 01 C10; Danio rerio; RNA Seq,GSM4080977,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080977,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L22277_ON11_01_C10_mod.bam,bam,50586132.0,665607.0,GSM4080977 r1,0:76,A:14660026;C:10294910;G:10546028;T:15084936;N:232,76,,,,14660026,10294910,10546028,15084936,232,SRX6854740,SRS5392942,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.85185,,0.2673,,0.95134,,0.49125,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54366,SRR10126090,SRX6854739,SRS5392941,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,ON15 01 G10,GSM4080976,,tissue:Brain|sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.253181242078581,ON15 01 G10,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.253181242078581,GSM4080976,GSM4080976: ON15 01 G10; Danio rerio; RNA Seq,GSM4080976,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080976,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L22281_ON15_01_G10_mod.bam,bam,34478312.0,453662.0,GSM4080976 r1,0:76,A:10233215;C:6828213;G:6979097;T:10437637;N:150,76,,,,10233215,6828213,6979097,10437637,150,SRX6854739,SRS5392941,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.79781,,0.43575,,0.96185,,0.61011,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54367,SRR10126089,SRX6854738,SRS5392940,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,ON16 01 H10,GSM4080975,,tissue:Brain|sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.310093893429947,ON16 01 H10,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.310093893429947,GSM4080975,GSM4080975: ON16 01 H10; Danio rerio; RNA Seq,GSM4080975,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080975,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L22282_ON16_01_H10_mod.bam,bam,48896424.0,643374.0,GSM4080975 r1,0:76,A:14455624;C:9692935;G:9968124;T:14779517;N:224,76,,,,14455624,9692935,9968124,14779517,224,SRX6854738,SRS5392940,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.81285,,0.3318,,0.95836,,0.53689,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54368,SRR10126088,SRX6854737,SRS5392939,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,ON12 01 D10,GSM4080974,,tissue:Brain|sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.276868947734128,ON12 01 D10,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:MN|FISH id:bfx811 01|batch:bfx811|fraction mapped:0.276868947734128,GSM4080974,GSM4080974: ON12 01 D10; Danio rerio; RNA Seq,GSM4080974,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4080974,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L22278_ON12_01_D10_mod.bam,bam,37841616.0,497916.0,GSM4080974 r1,0:76,A:10647168;C:8108969;G:8204459;T:10880848;N:172,76,,,,10647168,8108969,8204459,10880848,172,SRX6854737,SRS5392939,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.83203,,0.31484,,0.953,,0.51363,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54369,SRR10126159,SRX6854736,SRS5392938,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 G04,GSM4081045,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.598622388793024,NBN 1 01 G04,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.598622388793024,GSM4081045,GSM4081045: NBN 1 01 G04; Danio rerio; RNA Seq,GSM4081045,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081045,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23857_NBN_1_01_G04_mod.bam,bam,32006260.0,421135.0,GSM4081045 r1,0:76,A:8610883;C:7464632;G:7494909;T:8435692;N:144,76,,,,8610883,7464632,7494909,8435692,144,SRX6854736,SRS5392938,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.84284,,0.06821,,0.97331,,0.50003,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54370,SRR10126158,SRX6854735,SRS5392937,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 D06,GSM4081044,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.472262681006012,NBN 1 01 D06,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.472262681006012,GSM4081044,GSM4081044: NBN 1 01 D06; Danio rerio; RNA Seq,GSM4081044,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081044,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23870_NBN_1_01_D06_mod.bam,bam,17948388.0,236163.0,GSM4081044 r1,0:76,A:5102234;C:3980009;G:4032598;T:4833465;N:82,76,,,,5102234,3980009,4032598,4833465,82,SRX6854735,SRS5392937,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.78433,,0.1433,,0.96895,,0.48146,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54371,SRR10126157,SRX6854734,SRS5392936,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 C06,GSM4081043,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.599218631820245,NBN 1 01 C06,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.599218631820245,GSM4081043,GSM4081043: NBN 1 01 C06; Danio rerio; RNA Seq,GSM4081043,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081043,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23869_NBN_1_01_C06_mod.bam,bam,26120972.0,343697.0,GSM4081043 r1,0:76,A:7285303;C:5839989;G:5890965;T:7104599;N:116,76,,,,7285303,5839989,5890965,7104599,116,SRX6854734,SRS5392936,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.82402,,0.12575,,0.96197,,0.52537,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54372,SRR10126156,SRX6854733,SRS5392935,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 B06,GSM4081042,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.532356598173024,NBN 1 01 B06,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.532356598173024,GSM4081042,GSM4081042: NBN 1 01 B06; Danio rerio; RNA Seq,GSM4081042,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081042,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23868_NBN_1_01_B06_mod.bam,bam,21147912.0,278262.0,GSM4081042 r1,0:76,A:6114562;C:4550647;G:4607053;T:5875555;N:95,76,,,,6114562,4550647,4607053,5875555,95,SRX6854733,SRS5392935,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.80519,,0.21215,,0.95189,,0.49894,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54373,SRR10126155,SRX6854732,SRS5392934,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 C07,GSM4081041,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.60565107325563,NBN 1 01 C07,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.60565107325563,GSM4081041,GSM4081041: NBN 1 01 C07; Danio rerio; RNA Seq,GSM4081041,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081041,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23877_NBN_1_01_C07_mod.bam,bam,17287644.0,227469.0,GSM4081041 r1,0:76,A:4734834;C:3930876;G:3976071;T:4645789;N:74,76,,,,4734834,3930876,3976071,4645789,74,SRX6854732,SRS5392934,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.86762,,0.10597,,0.96613,,0.50147,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54374,SRR10126154,SRX6854731,SRS5392933,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 H04,GSM4081040,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.652633269764681,NBN 1 01 H04,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.652633269764681,GSM4081040,GSM4081040: NBN 1 01 H04; Danio rerio; RNA Seq,GSM4081040,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081040,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23858_NBN_1_01_H04_mod.bam,bam,48253160.0,634910.0,GSM4081040 r1,0:76,A:13424063;C:10616166;G:10721823;T:13490887;N:221,76,,,,13424063,10616166,10721823,13490887,221,SRX6854731,SRS5392933,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.8954,,0.17409,,0.92884,,0.49388,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54375,SRR10126153,SRX6854730,SRS5392932,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 E06,GSM4081039,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.511207049654726,NBN 1 01 E06,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.511207049654726,GSM4081039,GSM4081039: NBN 1 01 E06; Danio rerio; RNA Seq,GSM4081039,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081039,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23871_NBN_1_01_E06_mod.bam,bam,29097056.0,382856.0,GSM4081039 r1,0:76,A:8234827;C:6362925;G:6406573;T:8092579;N:152,76,,,,8234827,6362925,6406573,8092579,152,SRX6854730,SRS5392932,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.86249,,0.26512,,0.94608,,0.48992,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54376,SRR10126152,SRX6854729,SRS5392931,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 H06,GSM4081038,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.568841409012561,NBN 1 01 H06,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.568841409012561,GSM4081038,GSM4081038: NBN 1 01 H06; Danio rerio; RNA Seq,GSM4081038,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081038,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23874_NBN_1_01_H06_mod.bam,bam,32537044.0,428119.0,GSM4081038 r1,0:76,A:8987726;C:7310607;G:7366703;T:8871862;N:146,76,,,,8987726,7310607,7366703,8871862,146,SRX6854729,SRS5392931,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.84497,,0.16471,,0.94351,,0.50267,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54377,SRR10126151,SRX6854728,SRS5392930,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 G06,GSM4081037,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.624181209060453,NBN 1 01 G06,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.624181209060453,GSM4081037,GSM4081037: NBN 1 01 G06; Danio rerio; RNA Seq,GSM4081037,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081037,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23873_NBN_1_01_G06_mod.bam,bam,12155364.0,159939.0,GSM4081037 r1,0:76,A:3344683;C:2708218;G:2783378;T:3319046;N:39,76,,,,3344683,2708218,2783378,3319046,39,SRX6854728,SRS5392930,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.89597,,0.11595,,0.95306,,0.46511,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54378,SRR10126150,SRX6854727,SRS5392929,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 A07,GSM4081036,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.51658557940085,NBN 1 01 A07,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.51658557940085,GSM4081036,GSM4081036: NBN 1 01 A07; Danio rerio; RNA Seq,GSM4081036,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081036,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23875_NBN_1_01_A07_mod.bam,bam,30545692.0,401917.0,GSM4081036 r1,0:76,A:8429583;C:6966930;G:7076371;T:8072681;N:127,76,,,,8429583,6966930,7076371,8072681,127,SRX6854727,SRS5392929,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.79087,,0.10941,,0.9656,,0.51011,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54379,SRR10126149,SRX6854726,SRS5392928,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 F06,GSM4081035,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.441816595438718,NBN 1 01 F06,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.441816595438718,GSM4081035,GSM4081035: NBN 1 01 F06; Danio rerio; RNA Seq,GSM4081035,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081035,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23872_NBN_1_01_F06_mod.bam,bam,18806276.0,247451.0,GSM4081035 r1,0:76,A:5151100;C:4382351;G:4395758;T:4876959;N:108,76,,,,5151100,4382351,4395758,4876959,108,SRX6854726,SRS5392928,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.79771,,0.10914,,0.97417,,0.46337,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54380,SRR10126148,SRX6854725,SRS5392927,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 A05,GSM4081034,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.623421981847154,NBN 1 01 A05,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.623421981847154,GSM4081034,GSM4081034: NBN 1 01 A05; Danio rerio; RNA Seq,GSM4081034,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081034,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23859_NBN_1_01_A05_mod.bam,bam,45494588.0,598613.0,GSM4081034 r1,0:76,A:12663962;C:10058009;G:10243997;T:12528371;N:249,76,,,,12663962,10058009,10243997,12528371,249,SRX6854725,SRS5392927,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.87452,,0.12669,,0.96439,,0.51002,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54381,SRR10126147,SRX6854724,SRS5392926,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 D07,GSM4081033,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.67121387283237,NBN 1 01 D07,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.67121387283237,GSM4081033,GSM4081033: NBN 1 01 D07; Danio rerio; RNA Seq,GSM4081033,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081033,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23878_NBN_1_01_D07_mod.bam,bam,31553604.0,415179.0,GSM4081033 r1,0:76,A:8714681;C:7062201;G:7131427;T:8645143;N:152,76,,,,8714681,7062201,7131427,8645143,152,SRX6854724,SRS5392926,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.8803,,0.14617,,0.94854,,0.50368,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54382,SRR10126146,SRX6854723,SRS5392925,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 E07,GSM4081032,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.594353386522259,NBN 1 01 E07,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.594353386522259,GSM4081032,GSM4081032: NBN 1 01 E07; Danio rerio; RNA Seq,GSM4081032,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081032,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23879_NBN_1_01_E07_mod.bam,bam,23124824.0,304274.0,GSM4081032 r1,0:76,A:6264129;C:5330640;G:5386597;T:6143334;N:124,76,,,,6264129,5330640,5386597,6143334,124,SRX6854723,SRS5392925,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.8456,,0.10134,,0.97072,,0.50122,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54383,SRR10126145,SRX6854722,SRS5392924,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 B07,GSM4081031,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.621934520586096,NBN 1 01 B07,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.621934520586096,GSM4081031,GSM4081031: NBN 1 01 B07; Danio rerio; RNA Seq,GSM4081031,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081031,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23876_NBN_1_01_B07_mod.bam,bam,19638324.0,258399.0,GSM4081031 r1,0:76,A:5518210;C:4339448;G:4434264;T:5346306;N:96,76,,,,5518210,4339448,4434264,5346306,96,SRX6854722,SRS5392924,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.89204,,0.1016,,0.96865,,0.48751,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54384,SRR10126144,SRX6854721,SRS5392923,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 A06,GSM4081030,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.555614689940042,NBN 1 01 A06,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.555614689940042,GSM4081030,GSM4081030: NBN 1 01 A06; Danio rerio; RNA Seq,GSM4081030,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081030,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23867_NBN_1_01_A06_mod.bam,bam,31688656.0,416956.0,GSM4081030 r1,0:76,A:8992439;C:6908404;G:7064869;T:8722777;N:167,76,,,,8992439,6908404,7064869,8722777,167,SRX6854721,SRS5392923,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.84889,,0.13507,,0.9781,,0.47411,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54385,SRR10126143,SRX6854720,SRS5392922,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 1 01 D04,GSM4081029,,tissue:Brain|sorting:RG|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.283621073701812,RG 1 01 D04,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.283621073701812,GSM4081029,GSM4081029: RG 1 01 D04; Danio rerio; RNA Seq,GSM4081029,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081029,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23854_RG_1_01_D04.bam,bam,12453588.0,163863.0,GSM4081029 r1,0:76,A:3624666;C:2746733;G:2769149;T:3312993;N:47,76,,,,3624666,2746733,2769149,3312993,47,SRX6854720,SRS5392922,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.55387,,0.08776,,0.99531,,0.77642,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54386,SRR10126142,SRX6854719,SRS5392921,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 F04,GSM4081028,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.605363358887721,NBN 1 01 F04,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.605363358887721,GSM4081028,GSM4081028: NBN 1 01 F04; Danio rerio; RNA Seq,GSM4081028,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081028,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23856_NBN_1_01_F04_mod.bam,bam,29777712.0,391812.0,GSM4081028 r1,0:76,A:8287380;C:6634583;G:6702315;T:8153300;N:134,76,,,,8287380,6634583,6702315,8153300,134,SRX6854719,SRS5392921,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.84681,,0.14822,,0.95899,,0.48218,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54387,SRR10126141,SRX6854718,SRS5392920,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 E04,GSM4081027,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.609232186919727,NBN 1 01 E04,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.609232186919727,GSM4081027,GSM4081027: NBN 1 01 E04; Danio rerio; RNA Seq,GSM4081027,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081027,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23855_NBN_1_01_E04_mod.bam,bam,27378468.0,360243.0,GSM4081027 r1,0:76,A:7514685;C:6210573;G:6248622;T:7404451;N:137,76,,,,7514685,6210573,6248622,7404451,137,SRX6854718,SRS5392920,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.87187,,0.14148,,0.95976,,0.50299,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54388,SRR10126140,SRX6854717,SRS5392919,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 1 01 C04,GSM4081026,,tissue:Brain|sorting:RG|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.00268022023117434,RG 1 01 C04,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.00268022023117434,GSM4081026,GSM4081026: RG 1 01 C04; Danio rerio; RNA Seq,GSM4081026,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081026,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23853_RG_1_01_C04.bam,bam,17779136.0,233936.0,GSM4081026 r1,0:76,A:4924836;C:3601615;G:4002066;T:5250537;N:82,76,,,,4924836,3601615,4002066,5250537,82,SRX6854717,SRS5392919,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.0068,,0.00479,,0.99924,,0.7546,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54389,SRR10126139,SRX6854716,SRS5392918,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 B05,GSM4081025,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.621158949173434,NBN 1 01 B05,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.621158949173434,GSM4081025,GSM4081025: NBN 1 01 B05; Danio rerio; RNA Seq,GSM4081025,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081025,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23860_NBN_1_01_B05_mod.bam,bam,23794460.0,313085.0,GSM4081025 r1,0:76,A:6486952;C:5421381;G:5559483;T:6326529;N:115,76,,,,6486952,5421381,5559483,6326529,115,SRX6854716,SRS5392918,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.88749,,0.09927,,0.97167,,0.51464,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54390,SRR10126138,SRX6854715,SRS5392917,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 F05,GSM4081024,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.64362181199638,NBN 1 01 F05,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.64362181199638,GSM4081024,GSM4081024: NBN 1 01 F05; Danio rerio; RNA Seq,GSM4081024,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081024,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23864_NBN_1_01_F05_mod.bam,bam,34841136.0,458436.0,GSM4081024 r1,0:76,A:9468415;C:7931856;G:8068046;T:9372618;N:201,76,,,,9468415,7931856,8068046,9372618,201,SRX6854715,SRS5392917,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.89991,,0.09645,,0.9612,,0.50107,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54391,SRR10126137,SRX6854714,SRS5392916,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 1 01 B04,GSM4081023,,tissue:Brain|sorting:RG|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.0618454523025616,RG 1 01 B04,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.0618454523025616,GSM4081023,GSM4081023: RG 1 01 B04; Danio rerio; RNA Seq,GSM4081023,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081023,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23852_RG_1_01_B04.bam,bam,17866536.0,235086.0,GSM4081023 r1,0:76,A:5812722;C:3360958;G:3602639;T:5090127;N:90,76,,,,5812722,3360958,3602639,5090127,90,SRX6854714,SRS5392916,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.17133,,0.06449,,0.99898,,0.84014,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54392,SRR10126136,SRX6854713,SRS5392915,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 1 01 E05,GSM4081022,,tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.613943437547748,NBN 1 01 E05,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.613943437547748,GSM4081022,GSM4081022: NBN 1 01 E05; Danio rerio; RNA Seq,GSM4081022,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081022,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L23863_NBN_1_01_E05_mod.bam,bam,20887840.0,274840.0,GSM4081022 r1,0:76,A:5698091;C:4760347;G:4878634;T:5550655;N:113,76,,,,5698091,4760347,4878634,5550655,113,SRX6854713,SRS5392915,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.86848,,0.10705,,0.96698,,0.51406,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54393,SRR10126303,SRX6854712,SRS5392914,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 4 03 G02,GSM4081189,,tissue:Brain|sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.396319736087877,NBN 4 03 G02,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.396319736087877,GSM4081189,GSM4081189: NBN 4 03 G02; Danio rerio; RNA Seq,GSM4081189,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081189,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24033_NBN_4_03_G02_mod.bam,bam,32481184.0,427384.0,GSM4081189 r1,0:76,A:8891977;C:7560196;G:7559085;T:8469795;N:131,76,,,,8891977,7560196,7559085,8469795,131,SRX6854712,SRS5392914,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.78442,,0.1628,,0.97847,,0.47401,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54394,SRR10126302,SRX6854711,SRS5392913,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 4 03 F02,GSM4081188,,tissue:Brain|sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.419934962554198,NBN 4 03 F02,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.419934962554198,GSM4081188,GSM4081188: NBN 4 03 F02; Danio rerio; RNA Seq,GSM4081188,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081188,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24032_NBN_4_03_F02_mod.bam,bam,40102160.0,527660.0,GSM4081188 r1,0:76,A:10964163;C:9350144;G:9306636;T:10480993;N:224,76,,,,10964163,9350144,9306636,10480993,224,SRX6854711,SRS5392913,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.78826,,0.16336,,0.97252,,0.48219,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54395,SRR10126301,SRX6854710,SRS5392912,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 03 G01,GSM4081187,,tissue:Brain|sorting:RG|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.245253335273735,RG 4 03 G01,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.245253335273735,GSM4081187,GSM4081187: RG 4 03 G01; Danio rerio; RNA Seq,GSM4081187,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081187,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24025_RG_4_03_G01_mod.bam,bam,30288280.0,398530.0,GSM4081187 r1,0:76,A:8102225;C:7392718;G:7404963;T:7388259;N:115,76,,,,8102225,7392718,7404963,7388259,115,SRX6854710,SRS5392912,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.58611,,0.06211,,0.99095,,0.56894,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54396,SRR10126300,SRX6854709,SRS5392911,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 03 H01,GSM4081186,,tissue:Brain|sorting:RG|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.540783502310504,RG 4 03 H01,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.540783502310504,GSM4081186,GSM4081186: RG 4 03 H01; Danio rerio; RNA Seq,GSM4081186,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081186,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24026_RG_4_03_H01_mod.bam,bam,55086776.0,724826.0,GSM4081186 r1,0:76,A:15030228;C:12501198;G:12598562;T:14956486;N:302,76,,,,15030228,12501198,12598562,14956486,302,SRX6854709,SRS5392911,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.80615,,0.13988,,0.95765,,0.48086,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54397,SRR10126299,SRX6854708,SRS5392910,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 03 E01,GSM4081185,,tissue:Brain|sorting:RG|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.0637304637280315,RG 4 03 E01,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.0637304637280315,GSM4081185,GSM4081185: RG 4 03 E01; Danio rerio; RNA Seq,GSM4081185,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081185,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24023_RG_4_03_E01.bam,bam,43745296.0,575596.0,GSM4081185 r1,0:76,A:11664185;C:10975964;G:10921062;T:10183883;N:202,76,,,,11664185,10975964,10921062,10183883,202,SRX6854708,SRS5392910,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.25729,,0.10073,,0.99813,,0.85282,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54398,SRR10126298,SRX6854707,SRS5392909,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 03 D01,GSM4081184,,tissue:Brain|sorting:RG|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.569502699214683,RG 4 03 D01,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.569502699214683,GSM4081184,GSM4081184: RG 4 03 D01; Danio rerio; RNA Seq,GSM4081184,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081184,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24022_RG_4_03_D01_mod.bam,bam,45673416.0,600966.0,GSM4081184 r1,0:76,A:12261353;C:10688092;G:10675712;T:12047986;N:273,76,,,,12261353,10688092,10675712,12047986,273,SRX6854707,SRS5392909,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.83933,,0.08001,,0.9653,,0.48949,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54399,SRR10126297,SRX6854706,SRS5392908,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 03 F01,GSM4081183,,tissue:Brain|sorting:RG|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.0898847052989515,RG 4 03 F01,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.0898847052989515,GSM4081183,GSM4081183: RG 4 03 F01; Danio rerio; RNA Seq,GSM4081183,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081183,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24024_RG_4_03_F01_mod.bam,bam,51495092.0,677567.0,GSM4081183 r1,0:76,A:13725202;C:12850216;G:12784293;T:12135098;N:283,76,,,,13725202,12850216,12784293,12135098,283,SRX6854706,SRS5392908,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.33847,,0.15231,,0.99845,,0.68863,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54400,SRR10126296,SRX6854705,SRS5392907,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 03 C01,GSM4081182,,tissue:Brain|sorting:RG|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.155483476006256,RG 4 03 C01,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.155483476006256,GSM4081182,GSM4081182: RG 4 03 C01; Danio rerio; RNA Seq,GSM4081182,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081182,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24021_RG_4_03_C01.bam,bam,29546368.0,388768.0,GSM4081182 r1,0:76,A:8324657;C:6832651;G:6875775;T:7513152;N:133,76,,,,8324657,6832651,6875775,7513152,133,SRX6854705,SRS5392907,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.43383,,0.15437,,0.99634,,0.49243,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54401,SRR10126295,SRX6854704,SRS5392906,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 03 B01,GSM4081181,,tissue:Brain|sorting:RG|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.615303809854487,RG 4 03 B01,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.615303809854487,GSM4081181,GSM4081181: RG 4 03 B01; Danio rerio; RNA Seq,GSM4081181,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081181,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24020_RG_4_03_B01_mod.bam,bam,60175432.0,791782.0,GSM4081181 r1,0:76,A:16514318;C:13627412;G:13665406;T:16368047;N:249,76,,,,16514318,13627412,13665406,16368047,249,SRX6854704,SRS5392906,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.85908,,0.10782,,0.96148,,0.51361,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54402,SRR10126294,SRX6854703,SRS5392905,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 03 A01,GSM4081180,,tissue:Brain|sorting:RG|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.570142657011503,RG 4 03 A01,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.570142657011503,GSM4081180,GSM4081180: RG 4 03 A01; Danio rerio; RNA Seq,GSM4081180,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081180,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24019_RG_4_03_A01_mod.bam,bam,38510568.0,506718.0,GSM4081180 r1,0:76,A:10747250;C:8632416;G:8694972;T:10435736;N:194,76,,,,10747250,8632416,8694972,10435736,194,SRX6854703,SRS5392905,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.852,,0.11594,,0.96924,,0.4745,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54403,SRR10126293,SRX6854702,SRS5392903,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 02 B12,GSM4081179,,tissue:Brain|sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.428431953922818,RG 4 02 B12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.428431953922818,GSM4081179,GSM4081179: RG 4 02 B12; Danio rerio; RNA Seq,GSM4081179,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081179,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24012_RG_4_02_B12_mod.bam,bam,23196948.0,305223.0,GSM4081179 r1,0:76,A:6650835;C:5125890;G:5156953;T:6263179;N:91,76,,,,6650835,5125890,5156953,6263179,91,SRX6854702,SRS5392903,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.68027,,0.08335,,0.99541,,0.78262,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54404,SRR10126292,SRX6854701,SRS5392904,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 02 C12,GSM4081178,,tissue:Brain|sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.256314554078489,RG 4 02 C12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.256314554078489,GSM4081178,GSM4081178: RG 4 02 C12; Danio rerio; RNA Seq,GSM4081178,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081178,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24013_RG_4_02_C12.bam,bam,20301196.0,267121.0,GSM4081178 r1,0:76,A:5819263;C:4507058;G:4523322;T:5451458;N:95,76,,,,5819263,4507058,4523322,5451458,95,SRX6854701,SRS5392904,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.50417,,0.05837,,0.9988,,0.96684,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54405,SRR10126291,SRX6854700,SRS5392902,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 02 D12,GSM4081177,,tissue:Brain|sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.491189003992584,RG 4 02 D12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.491189003992584,GSM4081177,GSM4081177: RG 4 02 D12; Danio rerio; RNA Seq,GSM4081177,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081177,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24014_RG_4_02_D12_mod.bam,bam,52577256.0,691806.0,GSM4081177 r1,0:76,A:14408204;C:11925559;G:11938551;T:14304703;N:239,76,,,,14408204,11925559,11938551,14304703,239,SRX6854700,SRS5392902,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.80575,,0.1619,,0.96516,,0.46709,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54406,SRR10126290,SRX6854699,SRS5392901,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 02 A12,GSM4081176,,tissue:Brain|sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.374689047966583,RG 4 02 A12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.374689047966583,GSM4081176,GSM4081176: RG 4 02 A12; Danio rerio; RNA Seq,GSM4081176,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081176,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24011_RG_4_02_A12_mod.bam,bam,24470556.0,321981.0,GSM4081176 r1,0:76,A:6855056;C:5618406;G:5599835;T:6397133;N:126,76,,,,6855056,5618406,5599835,6397133,126,SRX6854699,SRS5392901,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.64203,,0.08348,,0.99334,,0.65535,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54407,SRR10126289,SRX6854698,SRS5392900,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 02 H11,GSM4081175,,tissue:Brain|sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.0753273689206053,RG 4 02 H11,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.0753273689206053,GSM4081175,GSM4081175: RG 4 02 H11; Danio rerio; RNA Seq,GSM4081175,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081175,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24010_RG_4_02_H11.bam,bam,21619340.0,284465.0,GSM4081175 r1,0:76,A:5849729;C:5318056;G:5286321;T:5165140;N:94,76,,,,5849729,5318056,5286321,5165140,94,SRX6854698,SRS5392900,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.26022,,0.12088,,0.99874,,0.73088,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54408,SRR10126288,SRX6854697,SRS5392899,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 02 G11,GSM4081174,,tissue:Brain|sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.454699812270569,RG 4 02 G11,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.454699812270569,GSM4081174,GSM4081174: RG 4 02 G11; Danio rerio; RNA Seq,GSM4081174,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081174,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24009_RG_4_02_G11_mod.bam,bam,25422228.0,334503.0,GSM4081174 r1,0:76,A:6982673;C:5930126;G:5939036;T:6570320;N:73,76,,,,6982673,5930126,5939036,6570320,73,SRX6854697,SRS5392899,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.74275,,0.06432,,0.98723,,0.57598,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54409,SRR10126287,SRX6854696,SRS5392898,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 02 G12,GSM4081173,,tissue:Brain|sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.584411223876839,RG 4 02 G12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.584411223876839,GSM4081173,GSM4081173: RG 4 02 G12; Danio rerio; RNA Seq,GSM4081173,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081173,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24017_RG_4_02_G12_mod.bam,bam,57923932.0,762157.0,GSM4081173 r1,0:76,A:15942052;C:13000252;G:13080471;T:15900882;N:275,76,,,,15942052,13000252,13080471,15900882,275,SRX6854696,SRS5392898,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.81908,,0.11496,,0.95735,,0.50954,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54410,SRR10126286,SRX6854695,SRS5392897,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 02 F12,GSM4081172,,tissue:Brain|sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.320746896029119,RG 4 02 F12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.320746896029119,GSM4081172,GSM4081172: RG 4 02 F12; Danio rerio; RNA Seq,GSM4081172,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081172,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24016_RG_4_02_F12.bam,bam,23468648.0,308798.0,GSM4081172 r1,0:76,A:7319180;C:4363209;G:4610283;T:7175855;N:121,76,,,,7319180,4363209,4610283,7175855,121,SRX6854695,SRS5392897,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.55485,,0.12886,,0.99872,,0.98508,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54411,SRR10126285,SRX6854694,SRS5392896,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 02 E12,GSM4081171,,tissue:Brain|sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.588827526294561,RG 4 02 E12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.588827526294561,GSM4081171,GSM4081171: RG 4 02 E12; Danio rerio; RNA Seq,GSM4081171,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081171,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24015_RG_4_02_E12_mod.bam,bam,58770876.0,773301.0,GSM4081171 r1,0:76,A:16791138;C:12494383;G:12618663;T:16866357;N:335,76,,,,16791138,12494383,12618663,16866357,335,SRX6854694,SRS5392896,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.85803,,0.2024,,0.9583,,0.56471,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54412,SRR10126284,SRX6854693,SRS5392895,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 02 F11,GSM4081170,,tissue:Brain|sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.324106247522213,RG 4 02 F11,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.324106247522213,GSM4081170,GSM4081170: RG 4 02 F11; Danio rerio; RNA Seq,GSM4081170,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081170,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24008_RG_4_02_F11.bam,bam,29330604.0,385929.0,GSM4081170 r1,0:76,A:8485315;C:6315690;G:6498851;T:8030598;N:150,76,,,,8485315,6315690,6498851,8030598,150,SRX6854693,SRS5392895,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.6157,,0.0926,,0.99677,,0.62475,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54413,SRR10126283,SRX6854692,SRS5392894,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 02 E11,GSM4081169,,tissue:Brain|sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.580370132771242,RG 4 02 E11,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.580370132771242,GSM4081169,GSM4081169: RG 4 02 E11; Danio rerio; RNA Seq,GSM4081169,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081169,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24007_RG_4_02_E11_mod.bam,bam,53053700.0,698075.0,GSM4081169 r1,0:76,A:14361081;C:12184584;G:12231766;T:14275990;N:279,76,,,,14361081,12184584,12231766,14275990,279,SRX6854692,SRS5392894,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.87764,,0.1324,,0.97137,,0.48975,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54414,SRR10126282,SRX6854691,SRS5392893,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 02 D11,GSM4081168,,tissue:Brain|sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.175915507364975,RG 4 02 D11,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.175915507364975,GSM4081168,GSM4081168: RG 4 02 D11; Danio rerio; RNA Seq,GSM4081168,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081168,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24006_RG_4_02_D11.bam,bam,26747136.0,351936.0,GSM4081168 r1,0:76,A:7566075;C:6116368;G:6185399;T:6879178;N:116,76,,,,7566075,6116368,6185399,6879178,116,SRX6854691,SRS5392893,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.4582,,0.13972,,0.99839,,0.60869,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54415,SRR10126281,SRX6854690,SRS5392892,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 02 H12,GSM4081167,,tissue:Brain|sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.641571006115169,RG 4 02 H12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.641571006115169,GSM4081167,GSM4081167: RG 4 02 H12; Danio rerio; RNA Seq,GSM4081167,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081167,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24018_RG_4_02_H12_mod.bam,bam,61286476.0,806401.0,GSM4081167 r1,0:76,A:16910460;C:13631719;G:13724446;T:17019529;N:322,76,,,,16910460,13631719,13724446,17019529,322,SRX6854690,SRS5392892,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.87214,,0.11436,,0.95946,,0.47007,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54416,SRR10126280,SRX6854689,SRS5392890,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,RG 4 02 C11,GSM4081166,,tissue:Brain|sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.38192650803246,RG 4 02 C11,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.38192650803246,GSM4081166,GSM4081166: RG 4 02 C11; Danio rerio; RNA Seq,GSM4081166,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081166,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24005_RG_4_02_C11.bam,bam,16595664.0,218364.0,GSM4081166 r1,0:76,A:4663104;C:3733046;G:3788322;T:4411110;N:82,76,,,,4663104,3733046,3788322,4411110,82,SRX6854689,SRS5392890,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.63386,,0.12677,,0.9974,,0.39862,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54417,SRR10126079,SRX6854688,SRS5392891,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 5 03 F12,GSM4081273,,tissue:Brain|sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.525010889856876,NBN 5 03 F12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.525010889856876,GSM4081273,GSM4081273: NBN 5 03 F12; Danio rerio; RNA Seq,GSM4081273,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081273,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24112_NBN_5_03_F12_mod.bam,bam,48823084.0,642409.0,GSM4081273 r1,0:76,A:13281310;C:11283844;G:11320552;T:12937124;N:254,76,,,,13281310,11283844,11320552,12937124,254,SRX6854688,SRS5392891,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.84855,,0.12882,,0.97011,,0.5031,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54418,SRR10126078,SRX6854687,SRS5392889,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 5 03 E12,GSM4081272,,tissue:Brain|sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.58888053902187,NBN 5 03 E12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.58888053902187,GSM4081272,GSM4081272: NBN 5 03 E12; Danio rerio; RNA Seq,GSM4081272,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081272,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24111_NBN_5_03_E12_mod.bam,bam,53368568.0,702218.0,GSM4081272 r1,0:76,A:14305398;C:12420925;G:12495590;T:14146395;N:260,76,,,,14305398,12420925,12495590,14146395,260,SRX6854687,SRS5392889,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.88543,,0.10092,,0.96493,,0.51049,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54419,SRR10126077,SRX6854686,SRS5392888,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 5 03 H12,GSM4081271,,tissue:Brain|sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.676307655192171,NBN 5 03 H12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.676307655192171,GSM4081271,GSM4081271: NBN 5 03 H12; Danio rerio; RNA Seq,GSM4081271,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081271,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24114_NBN_5_03_H12_mod.bam,bam,50399780.0,663155.0,GSM4081271 r1,0:76,A:14087482;C:11098672;G:11185255;T:14028118;N:253,76,,,,14087482,11098672,11185255,14028118,253,SRX6854686,SRS5392888,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.89616,,0.14239,,0.93754,,0.488,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54420,SRR10126076,SRX6854685,SRS5392887,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 5 03 G12,GSM4081270,,tissue:Brain|sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.469570262254911,NBN 5 03 G12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.469570262254911,GSM4081270,GSM4081270: NBN 5 03 G12; Danio rerio; RNA Seq,GSM4081270,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081270,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24113_NBN_5_03_G12_mod.bam,bam,39821416.0,523966.0,GSM4081270 r1,0:76,A:11006563;C:9116301;G:9155476;T:10542886;N:190,76,,,,11006563,9116301,9155476,10542886,190,SRX6854685,SRS5392887,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.79523,,0.15323,,0.97794,,0.4983,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54421,SRR10126075,SRX6854684,SRS5392886,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 5 03 B12,GSM4081269,,tissue:Brain|sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.606668639243757,NBN 5 03 B12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.606668639243757,GSM4081269,GSM4081269: NBN 5 03 B12; Danio rerio; RNA Seq,GSM4081269,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081269,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24108_NBN_5_03_B12_mod.bam,bam,49564996.0,652171.0,GSM4081269 r1,0:76,A:13457686;C:11463971;G:11462445;T:13180670;N:224,76,,,,13457686,11463971,11462445,13180670,224,SRX6854684,SRS5392886,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.8526,,0.10679,,0.95647,,0.47783,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54422,SRR10126074,SRX6854683,SRS5392885,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 5 03 C12,GSM4081268,,tissue:Brain|sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.504928000361481,NBN 5 03 C12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.504928000361481,GSM4081268,GSM4081268: NBN 5 03 C12; Danio rerio; RNA Seq,GSM4081268,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081268,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24109_NBN_5_03_C12_mod.bam,bam,53799868.0,707893.0,GSM4081268 r1,0:76,A:14477673;C:12676492;G:12642373;T:14003009;N:321,76,,,,14477673,12676492,12642373,14003009,321,SRX6854683,SRS5392885,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.83364,,0.12094,,0.96607,,0.50035,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54423,SRR10126073,SRX6854682,SRS5392884,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 5 03 D12,GSM4081267,,tissue:Brain|sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.580831314940795,NBN 5 03 D12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.580831314940795,GSM4081267,GSM4081267: NBN 5 03 D12; Danio rerio; RNA Seq,GSM4081267,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081267,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24110_NBN_5_03_D12_mod.bam,bam,62659492.0,824467.0,GSM4081267 r1,0:76,A:17501184;C:13903981;G:13981600;T:17272412;N:315,76,,,,17501184,13903981,13981600,17272412,315,SRX6854682,SRS5392884,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.84637,,0.16833,,0.94176,,0.51092,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54424,SRR10126072,SRX6854681,SRS5392883,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 5 03 A12,GSM4081266,,tissue:Brain|sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.601561083260848,NBN 5 03 A12,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.601561083260848,GSM4081266,GSM4081266: NBN 5 03 A12; Danio rerio; RNA Seq,GSM4081266,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081266,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24107_NBN_5_03_A12_mod.bam,bam,49451984.0,650684.0,GSM4081266 r1,0:76,A:13859171;C:10940822;G:10987740;T:13664031;N:220,76,,,,13859171,10940822,10987740,13664031,220,SRX6854681,SRS5392883,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.87251,,0.1665,,0.94491,,0.48105,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54425,SRR10126071,SRX6854680,SRS5392882,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 5 03 H11,GSM4081265,,tissue:Brain|sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.55113188683118,NBN 5 03 H11,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.55113188683118,GSM4081265,GSM4081265: NBN 5 03 H11; Danio rerio; RNA Seq,GSM4081265,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081265,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24106_NBN_5_03_H11_mod.bam,bam,45911372.0,604097.0,GSM4081265 r1,0:76,A:12937055;C:10127940;G:10124771;T:12721382;N:224,76,,,,12937055,10127940,10124771,12721382,224,SRX6854680,SRS5392882,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.83064,,0.18688,,0.94038,,0.48867,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System
54426,SRR10126070,SRX6854679,SRS5392881,SRP221784,PRJNA565778,Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain,GSE137525,Transcriptome Analysis,Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain,,pubmed:31908317,,NBN 5 03 F11,GSM4081264,,tissue:Brain|sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.620118980345189,NBN 5 03 F11,"FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "" a"" ""/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf"" "" s"" ""2"" "" o"" ""genecount/bfx811.GRCz10.e87.txt"" "" Q"" ""1"" "" T"" ""8"" ""  tmpDir"" ""/tmp/418815.1.ngs.q"" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.",Brain,,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,,sorting:NBN|FISH id:bfx855 03|batch:bfx855|fraction mapped:0.620118980345189,GSM4081264,GSM4081264: NBN 5 03 F11; Danio rerio; RNA Seq,GSM4081264,,1,adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.,GEO Accession:GSM4081264,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP221784,,intentional duplicate|dangling references:treat as unmapped,L24104_NBN_5_03_F11_mod.bam,bam,54050744.0,711194.0,GSM4081264 r1,0:76,A:14547427;C:12569309;G:12552401;T:14381328;N:279,76,,,,14547427,12569309,12552401,14381328,279,SRX6854679,SRS5392881,SRA962624,GEO,"Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems",1,0.87911,,0.10227,,0.96745,,0.50866,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2019-09-16,Adult,Adult,Brain,Nervous System