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
156,DRR067143,DRX061087,DRS034141,DRP003275,PRJDB4941,Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum,DRP003275,Other,An RNA seq analysis was performed using zebrafish granule cells  Purkinje cells  IO neurons  and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.,,,,Zebrafish RNA seq for Bergmann glial cells using Tg line SAGFFLF251A sample 2,SAMD00057666,,sample name:Zebrafish 251A 02|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center  Nagoya University|tissue type:cerebellum|cell type:bergmann glial cells|dev stage:14 dpf|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 1500 paired end sequencing of SAMD00057666,DRX061087,1,1,Quartz seq for low amount total RNA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003275,Illumina HiSeq 1500 paired end sequencing of SAMD00057666,,,,2040373922.0,10100861.0,DRR067143,0:101 1:101,A:577691972;C:445051245;G:472607289;T:544962357;N:61059,101,101,,,577691972,445051245,472607289,544962357,61059,DRX061087,DRS034141,DRA004955,RIKEN_CLST_DBFDI|Phyloinformatics Unit,RIKEN CLST,2,0.83407,0.83802,0.12612,0.12666,0.73675,0.74079,0.4948,0.49282,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,quartzseq,,Japan,2016-09-19,Larval,Larval,Brain,Nervous System
157,DRR067142,DRX061086,DRS034140,DRP003275,PRJDB4941,Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum,DRP003275,Other,An RNA seq analysis was performed using zebrafish granule cells  Purkinje cells  IO neurons  and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.,,,,Zebrafish RNA seq for Bergmann glial cells using Tg line SAGFFLF251A sample 1,SAMD00057665,,sample name:Zebrafish 251A 01|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center  Nagoya University|tissue type:cerebellum|cell type:bergmann glial cells|dev stage:14 dpf|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 1500 paired end sequencing of SAMD00057665,DRX061086,1,1,Quartz seq for low amount total RNA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003275,Illumina HiSeq 1500 paired end sequencing of SAMD00057665,,,,2033951534.0,10069067.0,DRR067142,0:101 1:101,A:589558269;C:431084184;G:460501802;T:552746498;N:60781,101,101,,,589558269,431084184,460501802,552746498,60781,DRX061086,DRS034140,DRA004955,RIKEN_CLST_DBFDI|Phyloinformatics Unit,RIKEN CLST,2,0.8958,0.90339,0.13764,0.1385,0.72563,0.72865,0.49373,0.49916,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,quartzseq,,Japan,2016-09-19,Larval,Larval,Brain,Nervous System
158,DRR067141,DRX061085,DRS034139,DRP003275,PRJDB4941,Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum,DRP003275,Other,An RNA seq analysis was performed using zebrafish granule cells  Purkinje cells  IO neurons  and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.,,,,Zebrafish RNA seq for Purkinje cells using Tg line aldoca:GAP Venus sample 3,SAMD00057664,,sample name:Zebrafish aldoca 03|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center  Nagoya University|tissue type:cerebellum|cell type:purkinje cells|dev stage:14 dpf|replicate:biological replicate 3,,,,,,,,,Illumina HiSeq 1500 paired end sequencing of SAMD00057664,DRX061085,1,1,Quartz seq for low amount total RNA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003275,Illumina HiSeq 1500 paired end sequencing of SAMD00057664,,,,1931908608.0,9563904.0,DRR067141,0:101 1:101,A:558444394;C:409856521;G:429168864;T:534380258;N:58571,101,101,,,558444394,409856521,429168864,534380258,58571,DRX061085,DRS034139,DRA004955,RIKEN_CLST_DBFDI|Phyloinformatics Unit,RIKEN CLST,2,0.88632,0.89109,0.15695,0.15773,0.75694,0.7599,0.46875,0.49236,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,quartzseq,,Japan,2016-09-19,Larval,Larval,Brain,Nervous System
159,DRR067140,DRX061084,DRS034138,DRP003275,PRJDB4941,Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum,DRP003275,Other,An RNA seq analysis was performed using zebrafish granule cells  Purkinje cells  IO neurons  and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.,,,,Zebrafish RNA seq for Purkinje cells using Tg line aldoca:GAP Venus sample 2,SAMD00057663,,sample name:Zebrafish aldoca 02|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center  Nagoya University|tissue type:cerebellum|cell type:purkinje cells|dev stage:14 dpf|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 1500 paired end sequencing of SAMD00057663,DRX061084,1,1,Quartz seq for low amount total RNA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003275,Illumina HiSeq 1500 paired end sequencing of SAMD00057663,,,,1851108406.0,9163903.0,DRR067140,0:101 1:101,A:537339104;C:390802782;G:416335529;T:506575762;N:55229,101,101,,,537339104,390802782,416335529,506575762,55229,DRX061084,DRS034138,DRA004955,RIKEN_CLST_DBFDI|Phyloinformatics Unit,RIKEN CLST,2,0.9055,0.91341,0.1515,0.15333,0.76495,0.76719,0.49219,0.49012,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,quartzseq,,Japan,2016-09-19,Larval,Larval,Brain,Nervous System
160,DRR067139,DRX061083,DRS034137,DRP003275,PRJDB4941,Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum,DRP003275,Other,An RNA seq analysis was performed using zebrafish granule cells  Purkinje cells  IO neurons  and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.,,,,Zebrafish RNA seq for Purkinje cells using Tg line aldoca:GAP Venus sample 1,SAMD00057662,,sample name:Zebrafish aldoca 01|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center  Nagoya University|tissue type:cerebellum|cell type:purkinje cells|dev stage:14 dpf|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 1500 paired end sequencing of SAMD00057662,DRX061083,1,1,Quartz seq for low amount total RNA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003275,Illumina HiSeq 1500 paired end sequencing of SAMD00057662,,,,2000078962.0,9901381.0,DRR067139,0:101 1:101,A:583169141;C:420603631;G:446949308;T:549297272;N:59610,101,101,,,583169141,420603631,446949308,549297272,59610,DRX061083,DRS034137,DRA004955,RIKEN_CLST_DBFDI|Phyloinformatics Unit,RIKEN CLST,2,0.9056,0.90932,0.15092,0.15179,0.76173,0.7654,0.49028,0.49604,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,quartzseq,,Japan,2016-09-19,Larval,Larval,Brain,Nervous System
161,DRR067138,DRX061082,DRS034136,DRP003275,PRJDB4941,Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum,DRP003275,Other,An RNA seq analysis was performed using zebrafish granule cells  Purkinje cells  IO neurons  and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.,,,,Zebrafish RNA seq for granule cells using Tg line gSA2AzGFF152B sample 2,SAMD00057661,,sample name:Zebrafish 152B 02|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center  Nagoya University|tissue type:cerebellum|cell type:granule cells|dev stage:14 dpf|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 1500 paired end sequencing of SAMD00057661,DRX061082,1,1,Quartz seq for low amount total RNA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003275,Illumina HiSeq 1500 paired end sequencing of SAMD00057661,,,,1997432156.0,9888278.0,DRR067138,0:101 1:101,A:578466824;C:423038930;G:449779231;T:546086391;N:60780,101,101,,,578466824,423038930,449779231,546086391,60780,DRX061082,DRS034136,DRA004955,RIKEN_CLST_DBFDI|Phyloinformatics Unit,RIKEN CLST,2,0.90322,0.91109,0.1463,0.14811,0.75452,0.75633,0.48303,0.48557,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,quartzseq,,Japan,2016-09-19,Larval,Larval,Brain,Nervous System
162,DRR067137,DRX061081,DRS034135,DRP003275,PRJDB4941,Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum,DRP003275,Other,An RNA seq analysis was performed using zebrafish granule cells  Purkinje cells  IO neurons  and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.,,,,Zebrafish RNA seq for granule cells using Tg line gSA2AzGFF152B sample 1,SAMD00057660,,sample name:Zebrafish 152B 01|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center  Nagoya University|tissue type:cerebellum|cell type:granule cells|dev stage:14 dpf|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 1500 paired end sequencing of SAMD00057660,DRX061081,1,1,Quartz seq for low amount total RNA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003275,Illumina HiSeq 1500 paired end sequencing of SAMD00057660,,,,1908437218.0,9447709.0,DRR067137,0:101 1:101,A:552150223;C:401993096;G:427236477;T:527000978;N:56444,101,101,,,552150223,401993096,427236477,527000978,56444,DRX061081,DRS034135,DRA004955,RIKEN_CLST_DBFDI|Phyloinformatics Unit,RIKEN CLST,2,0.90474,0.91043,0.17336,0.17401,0.76108,0.76359,0.483,0.48537,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,quartzseq,,Japan,2016-09-19,Larval,Larval,Brain,Nervous System
163,DRR067136,DRX061080,DRS034134,DRP003275,PRJDB4941,Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum,DRP003275,Other,An RNA seq analysis was performed using zebrafish granule cells  Purkinje cells  IO neurons  and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.,,,,Zebrafish RNA seq for Inferior olive nuclei using Tg line hspGFFDMC28C sample 3,SAMD00057659,,sample name:Zebrafish 28C 03|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center  Nagoya University|tissue type:hindbrain|cell type:inferior olive nuclei|dev stage:14 dpf|replicate:biological replicate 3,,,,,,,,,Illumina HiSeq 1500 paired end sequencing of SAMD00057659,DRX061080,1,1,Quartz seq for low amount total RNA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003275,Illumina HiSeq 1500 paired end sequencing of SAMD00057659,,,,1982971178.0,9816689.0,DRR067136,0:101 1:101,A:504064758;C:488246993;G:520130333;T:470469799;N:59295,101,101,,,504064758,488246993,520130333,470469799,59295,DRX061080,DRS034134,DRA004955,RIKEN_CLST_DBFDI|Phyloinformatics Unit,RIKEN CLST,2,0.53386,0.54375,0.06072,0.06189,0.76351,0.76641,0.4872,0.48857,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,quartzseq,,Japan,2016-09-19,Larval,Larval,Brain,Nervous System
164,DRR067135,DRX061079,DRS034133,DRP003275,PRJDB4941,Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum,DRP003275,Other,An RNA seq analysis was performed using zebrafish granule cells  Purkinje cells  IO neurons  and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.,,,,Zebrafish RNA seq for Inferior olive nuclei using Tg line hspGFFDMC28C sample 2,SAMD00057658,,sample name:Zebrafish 28C 02|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center  Nagoya University|tissue type:hindbrain|cell type:inferior olive nuclei|dev stage:14 dpf|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 1500 paired end sequencing of SAMD00057658,DRX061079,1,1,Quartz seq for low amount total RNA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003275,Illumina HiSeq 1500 paired end sequencing of SAMD00057658,,,,1961048320.0,9708160.0,DRR067135,0:101 1:101,A:557469151;C:424691789;G:455244994;T:523583601;N:58785,101,101,,,557469151,424691789,455244994,523583601,58785,DRX061079,DRS034133,DRA004955,RIKEN_CLST_DBFDI|Phyloinformatics Unit,RIKEN CLST,2,0.84854,0.8526,0.10311,0.1042,0.75227,0.75499,0.49321,0.49435,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,quartzseq,,Japan,2016-09-19,Larval,Larval,Brain,Nervous System
165,DRR067134,DRX061078,DRS034132,DRP003275,PRJDB4941,Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum,DRP003275,Other,An RNA seq analysis was performed using zebrafish granule cells  Purkinje cells  IO neurons  and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.,,,,Zebrafish RNA seq for Inferior olive nuclei using Tg line hspGFFDMC28C sample 1,SAMD00057657,,sample name:Zebrafish 28C 01|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center  Nagoya University|tissue type:hindbrain|cell type:inferior olive nuclei|dev stage:14 dpf|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 1500 paired end sequencing of SAMD00057657,DRX061078,1,1,Quartz seq for low amount total RNA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003275,Illumina HiSeq 1500 paired end sequencing of SAMD00057657,,,,1931802760.0,9563380.0,DRR067134,0:101 1:101,A:546501397;C:422500710;G:452200521;T:510543489;N:56643,101,101,,,546501397,422500710,452200521,510543489,56643,DRX061078,DRS034132,DRA004955,RIKEN_CLST_DBFDI|Phyloinformatics Unit,RIKEN CLST,2,0.85439,0.85613,0.09867,0.09897,0.76871,0.77082,0.48943,0.48936,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,quartzseq,,Japan,2016-09-19,Larval,Larval,Brain,Nervous System
166,DRR067133,DRX061077,DRS034131,DRP003275,PRJDB4941,Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum,DRP003275,Other,An RNA seq analysis was performed using zebrafish granule cells  Purkinje cells  IO neurons  and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.,,,,Zebrafish RNA seq for eurydendroid cells using Tg line hspzGFFgDMC156A sample 2,SAMD00057656,,sample name:Zebrafish 156A 02|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center  Nagoya University|tissue type:cerebellum|cell type:eurydendroid cells|dev stage:14 dpf|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 1500 paired end sequencing of SAMD00057656,DRX061077,1,1,Quartz seq for low amount total RNA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003275,Illumina HiSeq 1500 paired end sequencing of SAMD00057656,,,,2054289096.0,10169748.0,DRR067133,0:101 1:101,A:563764176;C:464768863;G:497506420;T:528187503;N:62134,101,101,,,563764176,464768863,497506420,528187503,62134,DRX061077,DRS034131,DRA004955,RIKEN_CLST_DBFDI|Phyloinformatics Unit,RIKEN CLST,2,0.69311,0.6968,0.12309,0.12389,0.76428,0.76676,0.48379,0.48227,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,quartzseq,,Japan,2016-09-19,Larval,Larval,Brain,Nervous System
167,DRR067132,DRX061076,DRS034130,DRP003275,PRJDB4941,Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum,DRP003275,Other,An RNA seq analysis was performed using zebrafish granule cells  Purkinje cells  IO neurons  and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.,,,,Zebrafish RNA seq for eurydendroid cells using Tg line hspzGFFgDMC156A sample 1,SAMD00057655,,sample name:Zebrafish 156A 01|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center  Nagoya University|tissue type:cerebellum|cell type:eurydendroid cells|dev stage:14 dpf|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 1500 paired end sequencing of SAMD00057655,DRX061076,1,1,Quartz seq for low amount total RNA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003275,Illumina HiSeq 1500 paired end sequencing of SAMD00057655,,,,2152665722.0,10656761.0,DRR067132,0:101 1:101,A:585252781;C:495382257;G:522677749;T:549287359;N:65576,101,101,,,585252781,495382257,522677749,549287359,65576,DRX061076,DRS034130,DRA004955,RIKEN_CLST_DBFDI|Phyloinformatics Unit,RIKEN CLST,2,0.67771,0.68253,0.12949,0.1303,0.77216,0.77542,0.4951,0.49452,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,quartzseq,,Japan,2016-09-19,Larval,Larval,Brain,Nervous System
52867,SRR9320540,SRX6088057,SRS4989404,SRP201776,PRJNA549478,Gene expression analysis of hematopoietic stem/progenitor cells in the zebrafish kidney,GSE132927,Transcriptome Analysis,Hematopoietic stem cells HSCs maintain the entire blood system throughout the life and are utilized for a therapeutic component of blood diseases. The zebrafish is an elegant genetic model for the study of hematopoiesis due to its many unique advantages. We have developed the method to isolate zebrafish HSCs by a combination of two HSC related transgenic lines  gata2a:GFP and runx1:mCherry. In this study  we performed RNA seq analysis in three distinct hematopoietic cell populations in the adult kidney  gata2a+ runx1+ cells HSCs  gata2a  runx1+ cells erythroid  and/or myeloid primed progenitors  and gata2a+ runx1  cells lymphoid primed progenitors. Overall design: mRNA profiles of isolated gata2a+ runx1+ cells  gata2a  runx1+ cells  and gata2a+ runx1  cells in the zebrafish kidney were generated by Quartz seq using Illumina NextSeq500.,,pubmed:31578390,,gata2a+ runx1 ,GSM3896451,,source name:lymphoid primed progenitors|tissue:Sorted cells from the kidney|cell type:gata2a+ runx1 |age:adult|genotype:wild type,gata2a+ runx1 ,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,lymphoid primed progenitors,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,tissue:Sorted cells from the kidney|cell type:gata2a+ runx1 |age:adult|genotype:wild type,GSM3896451,GSM3896451: gata2a+ runx1 ; Danio rerio; RNA Seq,GSM3896451,,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP201776,,,gata2a+_runx1-_R2.fastq.gz gata2a+_runx1-_R1.fastq.gz,fastq fastq,3262502100.0,10875007.0,GSM3896451 r1,0:150 1:150,A:832656373;C:815169099;G:759749436;T:854690002;N:237190,150,150,,,832656373,815169099,759749436,854690002,237190,SRX6088057,SRS4989404,SRA900579,GEO,Kanazawa University,2,0.92596,0.92513,0.0638,0.06526,0.77264,0.77644,0.47852,0.47703,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2019-06-18,Adult,Adult,Kidney,Renal System
52868,SRR9320539,SRX6088056,SRS4989403,SRP201776,PRJNA549478,Gene expression analysis of hematopoietic stem/progenitor cells in the zebrafish kidney,GSE132927,Transcriptome Analysis,Hematopoietic stem cells HSCs maintain the entire blood system throughout the life and are utilized for a therapeutic component of blood diseases. The zebrafish is an elegant genetic model for the study of hematopoiesis due to its many unique advantages. We have developed the method to isolate zebrafish HSCs by a combination of two HSC related transgenic lines  gata2a:GFP and runx1:mCherry. In this study  we performed RNA seq analysis in three distinct hematopoietic cell populations in the adult kidney  gata2a+ runx1+ cells HSCs  gata2a  runx1+ cells erythroid  and/or myeloid primed progenitors  and gata2a+ runx1  cells lymphoid primed progenitors. Overall design: mRNA profiles of isolated gata2a+ runx1+ cells  gata2a  runx1+ cells  and gata2a+ runx1  cells in the zebrafish kidney were generated by Quartz seq using Illumina NextSeq500.,,pubmed:31578390,,gata2a  runx1+,GSM3896450,,source name:erythroid  and/or myeloid primed progenitors|tissue:Sorted cells from the kidney|cell type:gata2a  runx1+|age:adult|genotype:wild type,gata2a  runx1+,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,erythroid  and/or myeloid primed progenitors,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,tissue:Sorted cells from the kidney|cell type:gata2a  runx1+|age:adult|genotype:wild type,GSM3896450,GSM3896450: gata2a  runx1+; Danio rerio; RNA Seq,GSM3896450,,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP201776,,,gata2a-_runx1+_R1.fastq.gz gata2a-_runx1+_R2.fastq.gz,fastq fastq,3020091000.0,10066970.0,GSM3896450 r1,0:150 1:150,A:767222151;C:757037823;G:716904952;T:778714622;N:211452,150,150,,,767222151,757037823,716904952,778714622,211452,SRX6088056,SRS4989403,SRA900579,GEO,Kanazawa University,2,0.94127,0.94225,0.05481,0.05688,0.7867,0.79097,0.49005,0.47682,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2019-06-18,Adult,Adult,Kidney,Renal System
52869,SRR9320538,SRX6088055,SRS4989402,SRP201776,PRJNA549478,Gene expression analysis of hematopoietic stem/progenitor cells in the zebrafish kidney,GSE132927,Transcriptome Analysis,Hematopoietic stem cells HSCs maintain the entire blood system throughout the life and are utilized for a therapeutic component of blood diseases. The zebrafish is an elegant genetic model for the study of hematopoiesis due to its many unique advantages. We have developed the method to isolate zebrafish HSCs by a combination of two HSC related transgenic lines  gata2a:GFP and runx1:mCherry. In this study  we performed RNA seq analysis in three distinct hematopoietic cell populations in the adult kidney  gata2a+ runx1+ cells HSCs  gata2a  runx1+ cells erythroid  and/or myeloid primed progenitors  and gata2a+ runx1  cells lymphoid primed progenitors. Overall design: mRNA profiles of isolated gata2a+ runx1+ cells  gata2a  runx1+ cells  and gata2a+ runx1  cells in the zebrafish kidney were generated by Quartz seq using Illumina NextSeq500.,,pubmed:31578390,,gata2a+ runx1+,GSM3896449,,source name:HSCs|tissue:Sorted cells from the kidney|cell type:gata2a+ runx1+|age:adult|genotype:wild type,gata2a+ runx1+,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,HSCs,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,tissue:Sorted cells from the kidney|cell type:gata2a+ runx1+|age:adult|genotype:wild type,GSM3896449,GSM3896449: gata2a+ runx1+; Danio rerio; RNA Seq,GSM3896449,,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP201776,,,gata2a+_runx1+_R1.fastq.gz gata2a+_runx1+_R2.fastq.gz,fastq fastq,3011439900.0,10038133.0,GSM3896449 r1,0:150 1:150,A:779051405;C:744098139;G:706333868;T:781739857;N:216631,150,150,,,779051405,744098139,706333868,781739857,216631,SRX6088055,SRS4989402,SRA900579,GEO,Kanazawa University,2,0.93396,0.93416,0.06842,0.07131,0.77555,0.77885,0.47177,0.48081,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2019-06-18,Adult,Adult,Kidney,Renal System
53148,SRR9692022,SRX6451056,SRS5104327,SRP214773,PRJNA554788,Gene expression analysis in the zebrafish fractured scale,GSE134330,Transcriptome Analysis,Bone is a connective tissue which undergoes continuous remodeling  including bone resorption and formation by osteoclasts OCs and osteoblasts OBs  respectively. Recently  extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs  OCs  and bone matrix  providing an elegant model to visualize OC OB communication. Here  we developed a double transgenic zebrafish line  trap:GFP; osterix:mCherry  which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer  respectively. Utilizing this double transgenic line  in combination with Hoechst 33342 Hoe staining  we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry  GFP– mCh+ Hoehigh OB fraction  GFPlow mCh+ Hoehigh OC precursor pOC fraction  GFPhigh Hoehigh mature OC mOC fraction  and mCh+ Hoe– OB derived extracellular vesicle EV fraction. In this study  we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each  fraction. Overall design: mRNA profiles of isolated OBs  pOCs   mOCs  and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.,,pubmed:32327701,,EV 2,GSM3942348,,source name:osteoblast derived extracellular vesicles|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblast derived extracellular vesicles|molecule type:Amplified RNA,EV 2,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,osteoblast derived extracellular vesicles,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblast derived extracellular vesicles|molecule type:Amplified RNA,GSM3942348,GSM3942348: EV 2; Danio rerio; RNA Seq,GSM3942348,,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP214773,,,EV_2_R1.fastq.gz EV_2_R2.fastq.gz,fastq fastq,6759957000.0,22533190.0,GSM3942348 r1,0:150 1:150,A:1706593126;C:1699056754;G:1646763192;T:1707067337;N:476591,150,150,,,1706593126,1699056754,1646763192,1707067337,476591,SRX6451056,SRS5104327,SRA921382,GEO,Kanazawa University,2,0.94501,0.94549,0.02885,0.03033,0.80458,0.80957,0.48799,0.50474,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2019-07-16,Adult,Adult,Bone or Cartilage,Skeletal Element
53149,SRR9692021,SRX6451055,SRS5104326,SRP214773,PRJNA554788,Gene expression analysis in the zebrafish fractured scale,GSE134330,Transcriptome Analysis,Bone is a connective tissue which undergoes continuous remodeling  including bone resorption and formation by osteoclasts OCs and osteoblasts OBs  respectively. Recently  extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs  OCs  and bone matrix  providing an elegant model to visualize OC OB communication. Here  we developed a double transgenic zebrafish line  trap:GFP; osterix:mCherry  which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer  respectively. Utilizing this double transgenic line  in combination with Hoechst 33342 Hoe staining  we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry  GFP– mCh+ Hoehigh OB fraction  GFPlow mCh+ Hoehigh OC precursor pOC fraction  GFPhigh Hoehigh mature OC mOC fraction  and mCh+ Hoe– OB derived extracellular vesicle EV fraction. In this study  we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each  fraction. Overall design: mRNA profiles of isolated OBs  pOCs   mOCs  and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.,,pubmed:32327701,,EV 1,GSM3942347,,source name:osteoblast derived extracellular vesicles|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblast derived extracellular vesicles|molecule type:Amplified RNA,EV 1,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,osteoblast derived extracellular vesicles,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblast derived extracellular vesicles|molecule type:Amplified RNA,GSM3942347,GSM3942347: EV 1; Danio rerio; RNA Seq,GSM3942347,,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP214773,,,EV_1_R1.fastq.gz EV_1_R2.fastq.gz,fastq fastq,6368980200.0,21229934.0,GSM3942347 r1,0:150 1:150,A:1609224577;C:1593521490;G:1569729629;T:1596056057;N:448447,150,150,,,1609224577,1593521490,1569729629,1596056057,448447,SRX6451055,SRS5104326,SRA921382,GEO,Kanazawa University,2,0.93738,0.93601,0.02919,0.03087,0.79669,0.80312,0.50627,0.50567,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2019-07-16,Adult,Adult,Bone or Cartilage,Skeletal Element
53150,SRR9692020,SRX6451054,SRS5104325,SRP214773,PRJNA554788,Gene expression analysis in the zebrafish fractured scale,GSE134330,Transcriptome Analysis,Bone is a connective tissue which undergoes continuous remodeling  including bone resorption and formation by osteoclasts OCs and osteoblasts OBs  respectively. Recently  extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs  OCs  and bone matrix  providing an elegant model to visualize OC OB communication. Here  we developed a double transgenic zebrafish line  trap:GFP; osterix:mCherry  which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer  respectively. Utilizing this double transgenic line  in combination with Hoechst 33342 Hoe staining  we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry  GFP– mCh+ Hoehigh OB fraction  GFPlow mCh+ Hoehigh OC precursor pOC fraction  GFPhigh Hoehigh mature OC mOC fraction  and mCh+ Hoe– OB derived extracellular vesicle EV fraction. In this study  we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each  fraction. Overall design: mRNA profiles of isolated OBs  pOCs   mOCs  and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.,,pubmed:32327701,,mOC 2,GSM3942346,,source name:mature osteoclasts|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:mature osteoclasts|molecule type:Amplified RNA,mOC 2,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,mature osteoclasts,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:mature osteoclasts|molecule type:Amplified RNA,GSM3942346,GSM3942346: mOC 2; Danio rerio; RNA Seq,GSM3942346,,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP214773,,,mOC_2_R1.fastq.gz mOC_2_R2.fastq.gz,fastq fastq,3442034400.0,11473448.0,GSM3942346 r1,0:150 1:150,A:874790081;C:854584498;G:837659746;T:874907519;N:92556,150,150,,,874790081,854584498,837659746,874907519,92556,SRX6451054,SRS5104325,SRA921382,GEO,Kanazawa University,2,0.94546,0.94169,0.03234,0.03643,0.79845,0.81132,0.49852,0.47127,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2019-07-16,Adult,Adult,Undetermined,Undetermined
53151,SRR9692019,SRX6451053,SRS5104324,SRP214773,PRJNA554788,Gene expression analysis in the zebrafish fractured scale,GSE134330,Transcriptome Analysis,Bone is a connective tissue which undergoes continuous remodeling  including bone resorption and formation by osteoclasts OCs and osteoblasts OBs  respectively. Recently  extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs  OCs  and bone matrix  providing an elegant model to visualize OC OB communication. Here  we developed a double transgenic zebrafish line  trap:GFP; osterix:mCherry  which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer  respectively. Utilizing this double transgenic line  in combination with Hoechst 33342 Hoe staining  we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry  GFP– mCh+ Hoehigh OB fraction  GFPlow mCh+ Hoehigh OC precursor pOC fraction  GFPhigh Hoehigh mature OC mOC fraction  and mCh+ Hoe– OB derived extracellular vesicle EV fraction. In this study  we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each  fraction. Overall design: mRNA profiles of isolated OBs  pOCs   mOCs  and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.,,pubmed:32327701,,mOC 1,GSM3942345,,source name:mature osteoclasts|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:mature osteoclasts|molecule type:Amplified RNA,mOC 1,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,mature osteoclasts,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:mature osteoclasts|molecule type:Amplified RNA,GSM3942345,GSM3942345: mOC 1; Danio rerio; RNA Seq,GSM3942345,,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP214773,,,mOC_1_R1.fastq.gz mOC_1_R2.fastq.gz,fastq fastq,3725202300.0,12417341.0,GSM3942345 r1,0:150 1:150,A:939287270;C:932158020;G:913434023;T:940223484;N:99503,150,150,,,939287270,932158020,913434023,940223484,99503,SRX6451053,SRS5104324,SRA921382,GEO,Kanazawa University,2,0.95139,0.94882,0.0326,0.03471,0.79393,0.80507,0.4667,0.49924,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2019-07-16,Adult,Adult,Undetermined,Undetermined
53152,SRR9692018,SRX6451052,SRS5104323,SRP214773,PRJNA554788,Gene expression analysis in the zebrafish fractured scale,GSE134330,Transcriptome Analysis,Bone is a connective tissue which undergoes continuous remodeling  including bone resorption and formation by osteoclasts OCs and osteoblasts OBs  respectively. Recently  extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs  OCs  and bone matrix  providing an elegant model to visualize OC OB communication. Here  we developed a double transgenic zebrafish line  trap:GFP; osterix:mCherry  which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer  respectively. Utilizing this double transgenic line  in combination with Hoechst 33342 Hoe staining  we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry  GFP– mCh+ Hoehigh OB fraction  GFPlow mCh+ Hoehigh OC precursor pOC fraction  GFPhigh Hoehigh mature OC mOC fraction  and mCh+ Hoe– OB derived extracellular vesicle EV fraction. In this study  we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each  fraction. Overall design: mRNA profiles of isolated OBs  pOCs   mOCs  and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.,,pubmed:32327701,,pOC 2,GSM3942344,,source name:osteoclast precursors|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoclast precursors|molecule type:Amplified RNA,pOC 2,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,osteoclast precursors,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoclast precursors|molecule type:Amplified RNA,GSM3942344,GSM3942344: pOC 2; Danio rerio; RNA Seq,GSM3942344,,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP214773,,,pOC_2_R1.fastq.gz pOC_2_R2.fastq.gz,fastq fastq,8180901900.0,27269673.0,GSM3942344 r1,0:150 1:150,A:2045941714;C:2067950267;G:1981277316;T:2085490817;N:241786,150,150,,,2045941714,2067950267,1981277316,2085490817,241786,SRX6451052,SRS5104323,SRA921382,GEO,Kanazawa University,2,0.94075,0.93872,0.04606,0.04832,0.77847,0.78482,0.50377,0.50525,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2019-07-16,Adult,Adult,Undetermined,Undetermined
53153,SRR9692017,SRX6451051,SRS5104322,SRP214773,PRJNA554788,Gene expression analysis in the zebrafish fractured scale,GSE134330,Transcriptome Analysis,Bone is a connective tissue which undergoes continuous remodeling  including bone resorption and formation by osteoclasts OCs and osteoblasts OBs  respectively. Recently  extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs  OCs  and bone matrix  providing an elegant model to visualize OC OB communication. Here  we developed a double transgenic zebrafish line  trap:GFP; osterix:mCherry  which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer  respectively. Utilizing this double transgenic line  in combination with Hoechst 33342 Hoe staining  we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry  GFP– mCh+ Hoehigh OB fraction  GFPlow mCh+ Hoehigh OC precursor pOC fraction  GFPhigh Hoehigh mature OC mOC fraction  and mCh+ Hoe– OB derived extracellular vesicle EV fraction. In this study  we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each  fraction. Overall design: mRNA profiles of isolated OBs  pOCs   mOCs  and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.,,pubmed:32327701,,pOC 1,GSM3942343,,source name:osteoclast precursors|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoclast precursors|molecule type:Amplified RNA,pOC 1,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,osteoclast precursors,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoclast precursors|molecule type:Amplified RNA,GSM3942343,GSM3942343: pOC 1; Danio rerio; RNA Seq,GSM3942343,,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP214773,,,pOC_1_R1.fastq.gz pOC_1_R2.fastq.gz,fastq fastq,8119854000.0,27066180.0,GSM3942343 r1,0:150 1:150,A:2022941314;C:2067331062;G:1960663076;T:2068678318;N:240230,150,150,,,2022941314,2067331062,1960663076,2068678318,240230,SRX6451051,SRS5104322,SRA921382,GEO,Kanazawa University,2,0.94544,0.94406,0.04202,0.04348,0.77979,0.78624,0.50479,0.48269,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2019-07-16,Adult,Adult,Undetermined,Undetermined
53154,SRR9692016,SRX6451050,SRS5104321,SRP214773,PRJNA554788,Gene expression analysis in the zebrafish fractured scale,GSE134330,Transcriptome Analysis,Bone is a connective tissue which undergoes continuous remodeling  including bone resorption and formation by osteoclasts OCs and osteoblasts OBs  respectively. Recently  extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs  OCs  and bone matrix  providing an elegant model to visualize OC OB communication. Here  we developed a double transgenic zebrafish line  trap:GFP; osterix:mCherry  which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer  respectively. Utilizing this double transgenic line  in combination with Hoechst 33342 Hoe staining  we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry  GFP– mCh+ Hoehigh OB fraction  GFPlow mCh+ Hoehigh OC precursor pOC fraction  GFPhigh Hoehigh mature OC mOC fraction  and mCh+ Hoe– OB derived extracellular vesicle EV fraction. In this study  we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each  fraction. Overall design: mRNA profiles of isolated OBs  pOCs   mOCs  and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.,,pubmed:32327701,,OB 2,GSM3942342,,source name:osteoblasts|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblasts|molecule type:Amplified RNA,OB 2,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,osteoblasts,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblasts|molecule type:Amplified RNA,GSM3942342,GSM3942342: OB 2; Danio rerio; RNA Seq,GSM3942342,,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP214773,,,OB_2_R1.fastq.gz OB_2_R2.fastq.gz,fastq fastq,4566907200.0,15223024.0,GSM3942342 r1,0:150 1:150,A:1133280984;C:1162119484;G:1119861724;T:1151514772;N:130236,150,150,,,1133280984,1162119484,1119861724,1151514772,130236,SRX6451050,SRS5104321,SRA921382,GEO,Kanazawa University,2,0.9502,0.9473,0.0382,0.04036,0.77853,0.78719,0.47336,0.4862,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2019-07-16,Adult,Adult,Bone or Cartilage,Skeletal Element
53155,SRR9692015,SRX6451049,SRS5104320,SRP214773,PRJNA554788,Gene expression analysis in the zebrafish fractured scale,GSE134330,Transcriptome Analysis,Bone is a connective tissue which undergoes continuous remodeling  including bone resorption and formation by osteoclasts OCs and osteoblasts OBs  respectively. Recently  extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs  OCs  and bone matrix  providing an elegant model to visualize OC OB communication. Here  we developed a double transgenic zebrafish line  trap:GFP; osterix:mCherry  which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer  respectively. Utilizing this double transgenic line  in combination with Hoechst 33342 Hoe staining  we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry  GFP– mCh+ Hoehigh OB fraction  GFPlow mCh+ Hoehigh OC precursor pOC fraction  GFPhigh Hoehigh mature OC mOC fraction  and mCh+ Hoe– OB derived extracellular vesicle EV fraction. In this study  we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each  fraction. Overall design: mRNA profiles of isolated OBs  pOCs   mOCs  and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.,,pubmed:32327701,,OB 1,GSM3942341,,source name:osteoblasts|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblasts|molecule type:Amplified RNA,OB 1,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,osteoblasts,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblasts|molecule type:Amplified RNA,GSM3942341,GSM3942341: OB 1; Danio rerio; RNA Seq,GSM3942341,,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP214773,,,OB_1_R1.fastq.gz OB_1_R2.fastq.gz,fastq fastq,3924215700.0,13080719.0,GSM3942341 r1,0:150 1:150,A:983923789;C:989882668;G:965519773;T:984780602;N:108868,150,150,,,983923789,989882668,965519773,984780602,108868,SRX6451049,SRS5104320,SRA921382,GEO,Kanazawa University,2,0.95148,0.94857,0.03822,0.04077,0.77705,0.78729,0.48248,0.49117,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2019-07-16,Adult,Adult,Bone or Cartilage,Skeletal Element
66733,SRR16518314,SRX12721081,SRS10670484,SRP342508,PRJNA773247,Gene expression analysis of hematopoietic niche cells in the zebrafish kidney,GSE186298,Transcriptome Analysis,"The zebrafish is an excellent model for the study of hematopoiesis. The use of fluorescently labeled transgenic lines allows us to isolate various hematopoietic cell types. Moreover  transplantation and cell culture assays enable to test the ability for hematopoietic repopulation and differentiation in isolated hematopoietic cells. The zebrafish counterpart of the mammalian bone marrow is the kidney  termed the ""kidney marrow""  providing an attractive tool for studying hematopoietic niches. Here  we isolated two candidate niche cell populations from the zebrafish kidney  pericytes and sinusoidal endothelial cells. Sinusoidal endothelial cells have been shown to endocytose acetylated low density lipoprotein Ac LDL  whereas pericytes can be labeled by pdgfrb expression. Therefore  pericytes and sinusoidal endothelial cells were isolated by using pdfgrb:GFP and kdrl:Cerulean injected with Alexa Fluor 488 conjugated Ac LDL  respectively. In addition  we also utilized a cell line generated from the zebrafish kidney  zebrafish kidney stromal ZKS  which have been shown to support proliferation of various hematopoietic precursors Stachula et al.  2009. In this study  we performed RNA seq analysis using these three fractions to investigate the gene expression profile of each niche cell fraction. Three distinct conditions of gata2a:GFP+ runx1:mCherry+ DP hematopoietic stem/progenitor cells were also analyzed: uncultured gata2a+ runx1+ cells DP uncul  gata2a+ runx1+ cells co cultured with ZKS cells DP cocul  and gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo DP IW+Th. Overall design: mRNA profiles of isolated ZKS cells  pericytes  sinusoids  and gata2a+ runx1+ DP in the zebrafish kidney were generated by Quartz seq using Illumina NextSeq500.",,pubmed:35759948,,Ac LDL hi 2,GSM5643374,,source name:sinusoids|tissue:Sorted from the kidney|age:adult|genotype:wild type|cell type:sinusoids,Ac LDL hi 2,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Tags per million TPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Tags per million TPM values for each sample.,sinusoids,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using the RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer containing oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer containing oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer to amplify small size DNA containing complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using the Nextera XT DNA Library Preparation Kit illumina.,,tissue:Sorted from the kidney|age:adult|genotype:wild type|cell type:sinusoids,GSM5643374,GSM5643374: Ac LDL hi 2; Danio rerio; RNA Seq,GSM5643374 r1,GSM5643374,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using the RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer containing oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer containing oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer to amplify small size DNA containing complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using the Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP342508,,,Ac-LDL-hi-2_1.fq.gz Ac-LDL-hi-2_2.fq.gz,fastq fastq,6994471800.0,23314906.0,GSM5643374 r1,0:150 1:150,A:1758266999;C:1627906654;G:1814489014;T:1793694348;N:114785,150,150,,,1758266999,1627906654,1814489014,1793694348,114785,SRX12721081,SRS10670484,SRA1524642,Kanazawa University,Kanazawa University,2,0.94141,0.94076,0.07685,0.07754,0.80265,0.8029,0.49348,0.49936,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2021-10-21,Adult,Adult,Kidney,Renal System
66734,SRR16518315,SRX12721080,SRS10670483,SRP342508,PRJNA773247,Gene expression analysis of hematopoietic niche cells in the zebrafish kidney,GSE186298,Transcriptome Analysis,"The zebrafish is an excellent model for the study of hematopoiesis. The use of fluorescently labeled transgenic lines allows us to isolate various hematopoietic cell types. Moreover  transplantation and cell culture assays enable to test the ability for hematopoietic repopulation and differentiation in isolated hematopoietic cells. The zebrafish counterpart of the mammalian bone marrow is the kidney  termed the ""kidney marrow""  providing an attractive tool for studying hematopoietic niches. Here  we isolated two candidate niche cell populations from the zebrafish kidney  pericytes and sinusoidal endothelial cells. Sinusoidal endothelial cells have been shown to endocytose acetylated low density lipoprotein Ac LDL  whereas pericytes can be labeled by pdgfrb expression. Therefore  pericytes and sinusoidal endothelial cells were isolated by using pdfgrb:GFP and kdrl:Cerulean injected with Alexa Fluor 488 conjugated Ac LDL  respectively. In addition  we also utilized a cell line generated from the zebrafish kidney  zebrafish kidney stromal ZKS  which have been shown to support proliferation of various hematopoietic precursors Stachula et al.  2009. In this study  we performed RNA seq analysis using these three fractions to investigate the gene expression profile of each niche cell fraction. Three distinct conditions of gata2a:GFP+ runx1:mCherry+ DP hematopoietic stem/progenitor cells were also analyzed: uncultured gata2a+ runx1+ cells DP uncul  gata2a+ runx1+ cells co cultured with ZKS cells DP cocul  and gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo DP IW+Th. Overall design: mRNA profiles of isolated ZKS cells  pericytes  sinusoids  and gata2a+ runx1+ DP in the zebrafish kidney were generated by Quartz seq using Illumina NextSeq500.",,pubmed:35759948,,Ac LDL hi 1,GSM5643373,,source name:sinusoids|tissue:Sorted from the kidney|age:adult|genotype:wild type|cell type:sinusoids,Ac LDL hi 1,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Tags per million TPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Tags per million TPM values for each sample.,sinusoids,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using the RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer containing oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer containing oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer to amplify small size DNA containing complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using the Nextera XT DNA Library Preparation Kit illumina.,,tissue:Sorted from the kidney|age:adult|genotype:wild type|cell type:sinusoids,GSM5643373,GSM5643373: Ac LDL hi 1; Danio rerio; RNA Seq,GSM5643373 r1,GSM5643373,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using the RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer containing oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer containing oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer to amplify small size DNA containing complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using the Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP342508,,,Ac-LDL-hi-1_1.fq.gz Ac-LDL-hi-1_2.fq.gz,fastq fastq,5352974400.0,17843248.0,GSM5643373 r1,0:150 1:150,A:1359148172;C:1231019883;G:1385606834;T:1377113418;N:86093,150,150,,,1359148172,1231019883,1385606834,1377113418,86093,SRX12721080,SRS10670483,SRA1524642,Kanazawa University,Kanazawa University,2,0.94458,0.94286,0.09932,0.10018,0.74789,0.75006,0.48096,0.48099,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2021-10-21,Adult,Adult,Kidney,Renal System
66735,SRR16518316,SRX12721079,SRS10670481,SRP342508,PRJNA773247,Gene expression analysis of hematopoietic niche cells in the zebrafish kidney,GSE186298,Transcriptome Analysis,"The zebrafish is an excellent model for the study of hematopoiesis. The use of fluorescently labeled transgenic lines allows us to isolate various hematopoietic cell types. Moreover  transplantation and cell culture assays enable to test the ability for hematopoietic repopulation and differentiation in isolated hematopoietic cells. The zebrafish counterpart of the mammalian bone marrow is the kidney  termed the ""kidney marrow""  providing an attractive tool for studying hematopoietic niches. Here  we isolated two candidate niche cell populations from the zebrafish kidney  pericytes and sinusoidal endothelial cells. Sinusoidal endothelial cells have been shown to endocytose acetylated low density lipoprotein Ac LDL  whereas pericytes can be labeled by pdgfrb expression. Therefore  pericytes and sinusoidal endothelial cells were isolated by using pdfgrb:GFP and kdrl:Cerulean injected with Alexa Fluor 488 conjugated Ac LDL  respectively. In addition  we also utilized a cell line generated from the zebrafish kidney  zebrafish kidney stromal ZKS  which have been shown to support proliferation of various hematopoietic precursors Stachula et al.  2009. In this study  we performed RNA seq analysis using these three fractions to investigate the gene expression profile of each niche cell fraction. Three distinct conditions of gata2a:GFP+ runx1:mCherry+ DP hematopoietic stem/progenitor cells were also analyzed: uncultured gata2a+ runx1+ cells DP uncul  gata2a+ runx1+ cells co cultured with ZKS cells DP cocul  and gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo DP IW+Th. Overall design: mRNA profiles of isolated ZKS cells  pericytes  sinusoids  and gata2a+ runx1+ DP in the zebrafish kidney were generated by Quartz seq using Illumina NextSeq500.",,pubmed:35759948,,pdgfrb 2,GSM5643372,,source name:pericytes|tissue:Sorted from the kidney|age:adult|genotype:wild type|cell type:pericytes,pdgfrb 2,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Tags per million TPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Tags per million TPM values for each sample.,pericytes,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using the RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer containing oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer containing oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer to amplify small size DNA containing complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using the Nextera XT DNA Library Preparation Kit illumina.,,tissue:Sorted from the kidney|age:adult|genotype:wild type|cell type:pericytes,GSM5643372,GSM5643372: pdgfrb 2; Danio rerio; RNA Seq,GSM5643372 r1,GSM5643372,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using the RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer containing oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer containing oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer to amplify small size DNA containing complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using the Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP342508,,,pdgfrb-2_1.fq.gz pdgfrb-2_2.fq.gz,fastq fastq,4395253800.0,14650846.0,GSM5643372 r1,0:150 1:150,A:1043237389;C:1069231932;G:1194350025;T:1088346880;N:87574,150,150,,,1043237389,1069231932,1194350025,1088346880,87574,SRX12721079,SRS10670481,SRA1524642,Kanazawa University,Kanazawa University,2,0.94341,0.94412,0.12389,0.12419,0.76248,0.76201,0.46533,0.45218,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2021-10-21,Adult,Adult,Kidney,Renal System
66736,SRR16518317,SRX12721078,SRS10670487,SRP342508,PRJNA773247,Gene expression analysis of hematopoietic niche cells in the zebrafish kidney,GSE186298,Transcriptome Analysis,"The zebrafish is an excellent model for the study of hematopoiesis. The use of fluorescently labeled transgenic lines allows us to isolate various hematopoietic cell types. Moreover  transplantation and cell culture assays enable to test the ability for hematopoietic repopulation and differentiation in isolated hematopoietic cells. The zebrafish counterpart of the mammalian bone marrow is the kidney  termed the ""kidney marrow""  providing an attractive tool for studying hematopoietic niches. Here  we isolated two candidate niche cell populations from the zebrafish kidney  pericytes and sinusoidal endothelial cells. Sinusoidal endothelial cells have been shown to endocytose acetylated low density lipoprotein Ac LDL  whereas pericytes can be labeled by pdgfrb expression. Therefore  pericytes and sinusoidal endothelial cells were isolated by using pdfgrb:GFP and kdrl:Cerulean injected with Alexa Fluor 488 conjugated Ac LDL  respectively. In addition  we also utilized a cell line generated from the zebrafish kidney  zebrafish kidney stromal ZKS  which have been shown to support proliferation of various hematopoietic precursors Stachula et al.  2009. In this study  we performed RNA seq analysis using these three fractions to investigate the gene expression profile of each niche cell fraction. Three distinct conditions of gata2a:GFP+ runx1:mCherry+ DP hematopoietic stem/progenitor cells were also analyzed: uncultured gata2a+ runx1+ cells DP uncul  gata2a+ runx1+ cells co cultured with ZKS cells DP cocul  and gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo DP IW+Th. Overall design: mRNA profiles of isolated ZKS cells  pericytes  sinusoids  and gata2a+ runx1+ DP in the zebrafish kidney were generated by Quartz seq using Illumina NextSeq500.",,pubmed:35759948,,pdgfrb 1,GSM5643371,,source name:pericytes|tissue:Sorted from the kidney|age:adult|genotype:wild type|cell type:pericytes,pdgfrb 1,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Tags per million TPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Tags per million TPM values for each sample.,pericytes,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using the RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer containing oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer containing oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer to amplify small size DNA containing complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using the Nextera XT DNA Library Preparation Kit illumina.,,tissue:Sorted from the kidney|age:adult|genotype:wild type|cell type:pericytes,GSM5643371,GSM5643371: pdgfrb 1; Danio rerio; RNA Seq,GSM5643371 r1,GSM5643371,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using the RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer containing oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer containing oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer to amplify small size DNA containing complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using the Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP342508,,,pdgfrb-1_1.fq.gz pdgfrb-1_2.fq.gz,fastq fastq,4673934300.0,15579781.0,GSM5643371 r1,0:150 1:150,A:1100236513;C:1109153190;G:1328236996;T:1136213461;N:94140,150,150,,,1100236513,1109153190,1328236996,1136213461,94140,SRX12721078,SRS10670487,SRA1524642,Kanazawa University,Kanazawa University,2,0.94656,0.94514,0.13828,0.13839,0.75477,0.75497,0.45582,0.45404,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2021-10-21,Adult,Adult,Kidney,Renal System
66737,SRR16518318,SRX12721077,SRS10670482,SRP342508,PRJNA773247,Gene expression analysis of hematopoietic niche cells in the zebrafish kidney,GSE186298,Transcriptome Analysis,"The zebrafish is an excellent model for the study of hematopoiesis. The use of fluorescently labeled transgenic lines allows us to isolate various hematopoietic cell types. Moreover  transplantation and cell culture assays enable to test the ability for hematopoietic repopulation and differentiation in isolated hematopoietic cells. The zebrafish counterpart of the mammalian bone marrow is the kidney  termed the ""kidney marrow""  providing an attractive tool for studying hematopoietic niches. Here  we isolated two candidate niche cell populations from the zebrafish kidney  pericytes and sinusoidal endothelial cells. Sinusoidal endothelial cells have been shown to endocytose acetylated low density lipoprotein Ac LDL  whereas pericytes can be labeled by pdgfrb expression. Therefore  pericytes and sinusoidal endothelial cells were isolated by using pdfgrb:GFP and kdrl:Cerulean injected with Alexa Fluor 488 conjugated Ac LDL  respectively. In addition  we also utilized a cell line generated from the zebrafish kidney  zebrafish kidney stromal ZKS  which have been shown to support proliferation of various hematopoietic precursors Stachula et al.  2009. In this study  we performed RNA seq analysis using these three fractions to investigate the gene expression profile of each niche cell fraction. Three distinct conditions of gata2a:GFP+ runx1:mCherry+ DP hematopoietic stem/progenitor cells were also analyzed: uncultured gata2a+ runx1+ cells DP uncul  gata2a+ runx1+ cells co cultured with ZKS cells DP cocul  and gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo DP IW+Th. Overall design: mRNA profiles of isolated ZKS cells  pericytes  sinusoids  and gata2a+ runx1+ DP in the zebrafish kidney were generated by Quartz seq using Illumina NextSeq500.",,pubmed:35759948,,ZKS 2,GSM5643370,,source name:ZKS cells|tissue:Sorted from the kidney|age:adult|genotype:wild type|cell type:ZKS cells,ZKS 2,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Tags per million TPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Tags per million TPM values for each sample.,ZKS cells,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using the RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer containing oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer containing oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer to amplify small size DNA containing complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using the Nextera XT DNA Library Preparation Kit illumina.,,tissue:Sorted from the kidney|age:adult|genotype:wild type|cell type:ZKS cells,GSM5643370,GSM5643370: ZKS 2; Danio rerio; RNA Seq,GSM5643370 r1,GSM5643370,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using the RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer containing oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer containing oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer to amplify small size DNA containing complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using the Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP342508,,,ZKS-2_1.fq.gz ZKS-2_2.fq.gz,fastq fastq,4179795600.0,13932652.0,GSM5643370 r1,0:150 1:150,A:998158893;C:1020113109;G:1117249708;T:1044189609;N:84281,150,150,,,998158893,1020113109,1117249708,1044189609,84281,SRX12721077,SRS10670482,SRA1524642,Kanazawa University,Kanazawa University,2,0.95978,0.95964,0.06099,0.06067,0.77088,0.77059,0.48527,0.48549,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2021-10-21,Adult,Adult,Kidney,Renal System
66738,SRR16518319,SRX12721076,SRS10670480,SRP342508,PRJNA773247,Gene expression analysis of hematopoietic niche cells in the zebrafish kidney,GSE186298,Transcriptome Analysis,"The zebrafish is an excellent model for the study of hematopoiesis. The use of fluorescently labeled transgenic lines allows us to isolate various hematopoietic cell types. Moreover  transplantation and cell culture assays enable to test the ability for hematopoietic repopulation and differentiation in isolated hematopoietic cells. The zebrafish counterpart of the mammalian bone marrow is the kidney  termed the ""kidney marrow""  providing an attractive tool for studying hematopoietic niches. Here  we isolated two candidate niche cell populations from the zebrafish kidney  pericytes and sinusoidal endothelial cells. Sinusoidal endothelial cells have been shown to endocytose acetylated low density lipoprotein Ac LDL  whereas pericytes can be labeled by pdgfrb expression. Therefore  pericytes and sinusoidal endothelial cells were isolated by using pdfgrb:GFP and kdrl:Cerulean injected with Alexa Fluor 488 conjugated Ac LDL  respectively. In addition  we also utilized a cell line generated from the zebrafish kidney  zebrafish kidney stromal ZKS  which have been shown to support proliferation of various hematopoietic precursors Stachula et al.  2009. In this study  we performed RNA seq analysis using these three fractions to investigate the gene expression profile of each niche cell fraction. Three distinct conditions of gata2a:GFP+ runx1:mCherry+ DP hematopoietic stem/progenitor cells were also analyzed: uncultured gata2a+ runx1+ cells DP uncul  gata2a+ runx1+ cells co cultured with ZKS cells DP cocul  and gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo DP IW+Th. Overall design: mRNA profiles of isolated ZKS cells  pericytes  sinusoids  and gata2a+ runx1+ DP in the zebrafish kidney were generated by Quartz seq using Illumina NextSeq500.",,pubmed:35759948,,ZKS 1,GSM5643369,,source name:ZKS cells|tissue:Sorted from the kidney|age:adult|genotype:wild type|cell type:ZKS cells,ZKS 1,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Tags per million TPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Tags per million TPM values for each sample.,ZKS cells,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using the RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer containing oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer containing oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer to amplify small size DNA containing complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using the Nextera XT DNA Library Preparation Kit illumina.,,tissue:Sorted from the kidney|age:adult|genotype:wild type|cell type:ZKS cells,GSM5643369,GSM5643369: ZKS 1; Danio rerio; RNA Seq,GSM5643369 r1,GSM5643369,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using the RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer containing oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer containing oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer to amplify small size DNA containing complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using the Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP342508,,,ZKS-1_1.fq.gz ZKS-1_2.fq.gz,fastq fastq,4423714500.0,14745715.0,GSM5643369 r1,0:150 1:150,A:1071455088;C:1054123974;G:1209651151;T:1088394831;N:89456,150,150,,,1071455088,1054123974,1209651151,1088394831,89456,SRX12721076,SRS10670480,SRA1524642,Kanazawa University,Kanazawa University,2,0.95616,0.95652,0.07013,0.07004,0.76982,0.76938,0.48054,0.48396,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2021-10-21,Adult,Adult,Kidney,Renal System
66739,SRR19117214,SRX15184903,SRS12924346,SRP342508,PRJNA773247,Gene expression analysis of hematopoietic niche cells in the zebrafish kidney,GSE186298,Transcriptome Analysis,"The zebrafish is an excellent model for the study of hematopoiesis. The use of fluorescently labeled transgenic lines allows us to isolate various hematopoietic cell types. Moreover  transplantation and cell culture assays enable to test the ability for hematopoietic repopulation and differentiation in isolated hematopoietic cells. The zebrafish counterpart of the mammalian bone marrow is the kidney  termed the ""kidney marrow""  providing an attractive tool for studying hematopoietic niches. Here  we isolated two candidate niche cell populations from the zebrafish kidney  pericytes and sinusoidal endothelial cells. Sinusoidal endothelial cells have been shown to endocytose acetylated low density lipoprotein Ac LDL  whereas pericytes can be labeled by pdgfrb expression. Therefore  pericytes and sinusoidal endothelial cells were isolated by using pdfgrb:GFP and kdrl:Cerulean injected with Alexa Fluor 488 conjugated Ac LDL  respectively. In addition  we also utilized a cell line generated from the zebrafish kidney  zebrafish kidney stromal ZKS  which have been shown to support proliferation of various hematopoietic precursors Stachula et al.  2009. In this study  we performed RNA seq analysis using these three fractions to investigate the gene expression profile of each niche cell fraction. Three distinct conditions of gata2a:GFP+ runx1:mCherry+ DP hematopoietic stem/progenitor cells were also analyzed: uncultured gata2a+ runx1+ cells DP uncul  gata2a+ runx1+ cells co cultured with ZKS cells DP cocul  and gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo DP IW+Th. Overall design: mRNA profiles of isolated ZKS cells  pericytes  sinusoids  and gata2a+ runx1+ DP in the zebrafish kidney were generated by Quartz seq using Illumina NextSeq500.",,pubmed:35759948,,DP IW+Th 2,GSM6111983,,source name:gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo|tissue:Sorted from the kidney|age:adult|genotype:wild type|treatment:gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo,DP IW+Th 2,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Tags per million TPM were calculated using the Subread ver. 1.6.4. Assembly: GRCz11 Supplementary files format and content: Tags per million TPM values for each sample.,gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,tissue:Sorted from the kidney|age:adult|genotype:wild type|treatment:gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo,GSM6111983,GSM6111983: DP IW+Th 2; Danio rerio; RNA Seq,GSM6111983 r1,GSM6111983,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP342508,,loader:fastq load.py,DP_IW+Th_2_L1_1.fq.gz DP_IW+Th_2_L1_2.fq.gz,fastq fastq,8969949600.0,29899832.0,GSM6111983 r1,0:150 1:150,A:2214657919;C:2139450844;G:2332885774;T:2282841671;N:113392,150,150,,,2214657919,2139450844,2332885774,2282841671,113392,SRX15184903,SRS12924346,SRA1415793,Kanazawa University,Kanazawa University,2,0.91433,0.91342,0.11652,0.11712,0.87765,0.87817,0.46807,0.47014,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2022-05-06,Adult,Adult,Kidney,Renal System
66740,SRR19117217,SRX15184902,SRS12924345,SRP342508,PRJNA773247,Gene expression analysis of hematopoietic niche cells in the zebrafish kidney,GSE186298,Transcriptome Analysis,"The zebrafish is an excellent model for the study of hematopoiesis. The use of fluorescently labeled transgenic lines allows us to isolate various hematopoietic cell types. Moreover  transplantation and cell culture assays enable to test the ability for hematopoietic repopulation and differentiation in isolated hematopoietic cells. The zebrafish counterpart of the mammalian bone marrow is the kidney  termed the ""kidney marrow""  providing an attractive tool for studying hematopoietic niches. Here  we isolated two candidate niche cell populations from the zebrafish kidney  pericytes and sinusoidal endothelial cells. Sinusoidal endothelial cells have been shown to endocytose acetylated low density lipoprotein Ac LDL  whereas pericytes can be labeled by pdgfrb expression. Therefore  pericytes and sinusoidal endothelial cells were isolated by using pdfgrb:GFP and kdrl:Cerulean injected with Alexa Fluor 488 conjugated Ac LDL  respectively. In addition  we also utilized a cell line generated from the zebrafish kidney  zebrafish kidney stromal ZKS  which have been shown to support proliferation of various hematopoietic precursors Stachula et al.  2009. In this study  we performed RNA seq analysis using these three fractions to investigate the gene expression profile of each niche cell fraction. Three distinct conditions of gata2a:GFP+ runx1:mCherry+ DP hematopoietic stem/progenitor cells were also analyzed: uncultured gata2a+ runx1+ cells DP uncul  gata2a+ runx1+ cells co cultured with ZKS cells DP cocul  and gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo DP IW+Th. Overall design: mRNA profiles of isolated ZKS cells  pericytes  sinusoids  and gata2a+ runx1+ DP in the zebrafish kidney were generated by Quartz seq using Illumina NextSeq500.",,pubmed:35759948,,DP IW+Th 1,GSM6111982,,source name:gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo|tissue:Sorted from the kidney|age:adult|genotype:wild type|treatment:gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo,DP IW+Th 1,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Tags per million TPM were calculated using the Subread ver. 1.6.4. Assembly: GRCz11 Supplementary files format and content: Tags per million TPM values for each sample.,gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,tissue:Sorted from the kidney|age:adult|genotype:wild type|treatment:gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo,GSM6111982,GSM6111982: DP IW+Th 1; Danio rerio; RNA Seq,GSM6111982 r1,GSM6111982,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP342508,,loader:fastq load.py,DP_IW+Th_1_L1_1.fq.gz DP_IW+Th_1_L1_2.fq.gz,fastq fastq,9669542400.0,32231808.0,GSM6111982 r1,0:150 1:150,A:2372090263;C:2321922668;G:2513943265;T:2461463769;N:122435,150,150,,,2372090263,2321922668,2513943265,2461463769,122435,SRX15184902,SRS12924345,SRA1415793,Kanazawa University,Kanazawa University,2,0.91161,0.91093,0.1272,0.12807,0.87036,0.8704,0.48064,0.48231,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2022-05-06,Adult,Adult,Kidney,Renal System
66741,SRR19117215,SRX15184901,SRS12924344,SRP342508,PRJNA773247,Gene expression analysis of hematopoietic niche cells in the zebrafish kidney,GSE186298,Transcriptome Analysis,"The zebrafish is an excellent model for the study of hematopoiesis. The use of fluorescently labeled transgenic lines allows us to isolate various hematopoietic cell types. Moreover  transplantation and cell culture assays enable to test the ability for hematopoietic repopulation and differentiation in isolated hematopoietic cells. The zebrafish counterpart of the mammalian bone marrow is the kidney  termed the ""kidney marrow""  providing an attractive tool for studying hematopoietic niches. Here  we isolated two candidate niche cell populations from the zebrafish kidney  pericytes and sinusoidal endothelial cells. Sinusoidal endothelial cells have been shown to endocytose acetylated low density lipoprotein Ac LDL  whereas pericytes can be labeled by pdgfrb expression. Therefore  pericytes and sinusoidal endothelial cells were isolated by using pdfgrb:GFP and kdrl:Cerulean injected with Alexa Fluor 488 conjugated Ac LDL  respectively. In addition  we also utilized a cell line generated from the zebrafish kidney  zebrafish kidney stromal ZKS  which have been shown to support proliferation of various hematopoietic precursors Stachula et al.  2009. In this study  we performed RNA seq analysis using these three fractions to investigate the gene expression profile of each niche cell fraction. Three distinct conditions of gata2a:GFP+ runx1:mCherry+ DP hematopoietic stem/progenitor cells were also analyzed: uncultured gata2a+ runx1+ cells DP uncul  gata2a+ runx1+ cells co cultured with ZKS cells DP cocul  and gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo DP IW+Th. Overall design: mRNA profiles of isolated ZKS cells  pericytes  sinusoids  and gata2a+ runx1+ DP in the zebrafish kidney were generated by Quartz seq using Illumina NextSeq500.",,pubmed:35759948,,DP cocul 2,GSM6111981,,source name:gata2a+ runx1+ cells co cultured with ZKS cells|tissue:Sorted from the kidney|age:adult|genotype:wild type|treatment:gata2a+ runx1+ cells co cultured with ZKS cells,DP cocul 2,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Tags per million TPM were calculated using the Subread ver. 1.6.4. Assembly: GRCz11 Supplementary files format and content: Tags per million TPM values for each sample.,gata2a+ runx1+ cells co cultured with ZKS cells,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,tissue:Sorted from the kidney|age:adult|genotype:wild type|treatment:gata2a+ runx1+ cells co cultured with ZKS cells,GSM6111981,GSM6111981: DP cocul 2; Danio rerio; RNA Seq,GSM6111981 r1,GSM6111981,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP342508,,loader:fastq load.py,DP_cocul_2_L1_1.fq.gz DP_cocul_2_L1_2.fq.gz,fastq fastq,9886327200.0,32954424.0,GSM6111981 r1,0:150 1:150,A:2404667221;C:2405733394;G:2582890033;T:2492911405;N:125147,150,150,,,2404667221,2405733394,2582890033,2492911405,125147,SRX15184901,SRS12924344,SRA1415793,Kanazawa University,Kanazawa University,2,0.93134,0.93104,0.07833,0.07872,0.86912,0.86931,0.48907,0.48985,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2022-05-06,Adult,Adult,Kidney,Renal System
66742,SRR19117216,SRX15184900,SRS12924343,SRP342508,PRJNA773247,Gene expression analysis of hematopoietic niche cells in the zebrafish kidney,GSE186298,Transcriptome Analysis,"The zebrafish is an excellent model for the study of hematopoiesis. The use of fluorescently labeled transgenic lines allows us to isolate various hematopoietic cell types. Moreover  transplantation and cell culture assays enable to test the ability for hematopoietic repopulation and differentiation in isolated hematopoietic cells. The zebrafish counterpart of the mammalian bone marrow is the kidney  termed the ""kidney marrow""  providing an attractive tool for studying hematopoietic niches. Here  we isolated two candidate niche cell populations from the zebrafish kidney  pericytes and sinusoidal endothelial cells. Sinusoidal endothelial cells have been shown to endocytose acetylated low density lipoprotein Ac LDL  whereas pericytes can be labeled by pdgfrb expression. Therefore  pericytes and sinusoidal endothelial cells were isolated by using pdfgrb:GFP and kdrl:Cerulean injected with Alexa Fluor 488 conjugated Ac LDL  respectively. In addition  we also utilized a cell line generated from the zebrafish kidney  zebrafish kidney stromal ZKS  which have been shown to support proliferation of various hematopoietic precursors Stachula et al.  2009. In this study  we performed RNA seq analysis using these three fractions to investigate the gene expression profile of each niche cell fraction. Three distinct conditions of gata2a:GFP+ runx1:mCherry+ DP hematopoietic stem/progenitor cells were also analyzed: uncultured gata2a+ runx1+ cells DP uncul  gata2a+ runx1+ cells co cultured with ZKS cells DP cocul  and gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo DP IW+Th. Overall design: mRNA profiles of isolated ZKS cells  pericytes  sinusoids  and gata2a+ runx1+ DP in the zebrafish kidney were generated by Quartz seq using Illumina NextSeq500.",,pubmed:35759948,,DP cocul 1,GSM6111980,,source name:gata2a+ runx1+ cells co cultured with ZKS cells|tissue:Sorted from the kidney|age:adult|genotype:wild type|treatment:gata2a+ runx1+ cells co cultured with ZKS cells,DP cocul 1,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Tags per million TPM were calculated using the Subread ver. 1.6.4. Assembly: GRCz11 Supplementary files format and content: Tags per million TPM values for each sample.,gata2a+ runx1+ cells co cultured with ZKS cells,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,tissue:Sorted from the kidney|age:adult|genotype:wild type|treatment:gata2a+ runx1+ cells co cultured with ZKS cells,GSM6111980,GSM6111980: DP cocul 1; Danio rerio; RNA Seq,GSM6111980 r1,GSM6111980,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP342508,,loader:fastq load.py,DP_cocul_1_L1_1.fq.gz DP_cocul_1_L1_2.fq.gz,fastq fastq,8155126500.0,27183755.0,GSM6111980 r1,0:150 1:150,A:2030269245;C:1956730134;G:2116603885;T:2051419869;N:103367,150,150,,,2030269245,1956730134,2116603885,2051419869,103367,SRX15184900,SRS12924343,SRA1415793,Kanazawa University,Kanazawa University,2,0.89139,0.89027,0.10447,0.10496,0.87562,0.87629,0.47824,0.45494,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2022-05-06,Adult,Adult,Kidney,Renal System
66743,SRR19117218,SRX15184899,SRS12924342,SRP342508,PRJNA773247,Gene expression analysis of hematopoietic niche cells in the zebrafish kidney,GSE186298,Transcriptome Analysis,"The zebrafish is an excellent model for the study of hematopoiesis. The use of fluorescently labeled transgenic lines allows us to isolate various hematopoietic cell types. Moreover  transplantation and cell culture assays enable to test the ability for hematopoietic repopulation and differentiation in isolated hematopoietic cells. The zebrafish counterpart of the mammalian bone marrow is the kidney  termed the ""kidney marrow""  providing an attractive tool for studying hematopoietic niches. Here  we isolated two candidate niche cell populations from the zebrafish kidney  pericytes and sinusoidal endothelial cells. Sinusoidal endothelial cells have been shown to endocytose acetylated low density lipoprotein Ac LDL  whereas pericytes can be labeled by pdgfrb expression. Therefore  pericytes and sinusoidal endothelial cells were isolated by using pdfgrb:GFP and kdrl:Cerulean injected with Alexa Fluor 488 conjugated Ac LDL  respectively. In addition  we also utilized a cell line generated from the zebrafish kidney  zebrafish kidney stromal ZKS  which have been shown to support proliferation of various hematopoietic precursors Stachula et al.  2009. In this study  we performed RNA seq analysis using these three fractions to investigate the gene expression profile of each niche cell fraction. Three distinct conditions of gata2a:GFP+ runx1:mCherry+ DP hematopoietic stem/progenitor cells were also analyzed: uncultured gata2a+ runx1+ cells DP uncul  gata2a+ runx1+ cells co cultured with ZKS cells DP cocul  and gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo DP IW+Th. Overall design: mRNA profiles of isolated ZKS cells  pericytes  sinusoids  and gata2a+ runx1+ DP in the zebrafish kidney were generated by Quartz seq using Illumina NextSeq500.",,pubmed:35759948,,DP uncul 2,GSM6111979,,source name:uncultured gata2a+ runx1+ cells|tissue:Sorted from the kidney|age:adult|genotype:wild type|treatment:uncultured gata2a+ runx1+ cells,DP uncul 2,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Tags per million TPM were calculated using the Subread ver. 1.6.4. Assembly: GRCz11 Supplementary files format and content: Tags per million TPM values for each sample.,uncultured gata2a+ runx1+ cells,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,tissue:Sorted from the kidney|age:adult|genotype:wild type|treatment:uncultured gata2a+ runx1+ cells,GSM6111979,GSM6111979: DP uncul 2; Danio rerio; RNA Seq,GSM6111979 r1,GSM6111979,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP342508,,loader:fastq load.py,DP_uncul_2_L1_1.fq.gz DP_uncul_2_L1_2.fq.gz,fastq fastq,9011330400.0,30037768.0,GSM6111979 r1,0:150 1:150,A:2194903966;C:2190545401;G:2357703031;T:2268063634;N:114368,150,150,,,2194903966,2190545401,2357703031,2268063634,114368,SRX15184899,SRS12924342,SRA1415793,Kanazawa University,Kanazawa University,2,0.93907,0.93919,0.07706,0.07749,0.83903,0.83915,0.47122,0.49535,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2022-05-06,Adult,Adult,Kidney,Renal System
66744,SRR19117219,SRX15184898,SRS12924341,SRP342508,PRJNA773247,Gene expression analysis of hematopoietic niche cells in the zebrafish kidney,GSE186298,Transcriptome Analysis,"The zebrafish is an excellent model for the study of hematopoiesis. The use of fluorescently labeled transgenic lines allows us to isolate various hematopoietic cell types. Moreover  transplantation and cell culture assays enable to test the ability for hematopoietic repopulation and differentiation in isolated hematopoietic cells. The zebrafish counterpart of the mammalian bone marrow is the kidney  termed the ""kidney marrow""  providing an attractive tool for studying hematopoietic niches. Here  we isolated two candidate niche cell populations from the zebrafish kidney  pericytes and sinusoidal endothelial cells. Sinusoidal endothelial cells have been shown to endocytose acetylated low density lipoprotein Ac LDL  whereas pericytes can be labeled by pdgfrb expression. Therefore  pericytes and sinusoidal endothelial cells were isolated by using pdfgrb:GFP and kdrl:Cerulean injected with Alexa Fluor 488 conjugated Ac LDL  respectively. In addition  we also utilized a cell line generated from the zebrafish kidney  zebrafish kidney stromal ZKS  which have been shown to support proliferation of various hematopoietic precursors Stachula et al.  2009. In this study  we performed RNA seq analysis using these three fractions to investigate the gene expression profile of each niche cell fraction. Three distinct conditions of gata2a:GFP+ runx1:mCherry+ DP hematopoietic stem/progenitor cells were also analyzed: uncultured gata2a+ runx1+ cells DP uncul  gata2a+ runx1+ cells co cultured with ZKS cells DP cocul  and gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo DP IW+Th. Overall design: mRNA profiles of isolated ZKS cells  pericytes  sinusoids  and gata2a+ runx1+ DP in the zebrafish kidney were generated by Quartz seq using Illumina NextSeq500.",,pubmed:35759948,,DP uncul 1,GSM6111978,,source name:uncultured gata2a+ runx1+ cells|tissue:Sorted from the kidney|age:adult|genotype:wild type|treatment:uncultured gata2a+ runx1+ cells,DP uncul 1,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Tags per million TPM were calculated using the Subread ver. 1.6.4. Assembly: GRCz11 Supplementary files format and content: Tags per million TPM values for each sample.,uncultured gata2a+ runx1+ cells,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,tissue:Sorted from the kidney|age:adult|genotype:wild type|treatment:uncultured gata2a+ runx1+ cells,GSM6111978,GSM6111978: DP uncul 1; Danio rerio; RNA Seq,GSM6111978 r1,GSM6111978,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP342508,,loader:fastq load.py,DP_uncul_1_L1_1.fq.gz DP_uncul_1_L1_2.fq.gz,fastq fastq,9150386700.0,30501289.0,GSM6111978 r1,0:150 1:150,A:2223358030;C:2191244858;G:2448935477;T:2286732767;N:115568,150,150,,,2223358030,2191244858,2448935477,2286732767,115568,SRX15184898,SRS12924341,SRA1415793,Kanazawa University,Kanazawa University,2,0.93895,0.93783,0.07402,0.07389,0.83715,0.8368,0.49173,0.49347,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2022-05-06,Adult,Adult,Kidney,Renal System