RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

500 rows where devstage_curation = "Undetermined" and tissue_curation = "Kidney"

✎ View and edit SQL

This data as json, CSV (advanced)

technology 7

experiment.library_selection 3

devstage_curation_coarse 3

experiment.platform 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Kidney · 500 ✖

experiment.library_strategy 1

experiment.library_source 1

devstage_curation 1

  • Undetermined · 500 ✖
Link 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
11158 11158 ERR10047721 ERX9587609 ERS12570320 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Mutant Female 4 MF4 SAMEA110472297 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472297|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29737|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29737|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:372 85553 MF4 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 EF12_1.fq.gz EF12_2.fq.gz fastq fastq 9295860000.0 30986200.0 ena RUN TAB 10 08 2022 10:54:39:372 85554 0:150 1:150 A:2456629138;C:2211534829;G:2202795083;T:2424808616;N:92334 150 150     2456629138 2211534829 2202795083 2424808616 92334 ERX9587609 ERS12570320 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.94791 0.94821 0.05293 0.05316 0.71285 0.71267 0.5054 0.50686 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11159 11159 ERR10047720 ERX9587608 ERS12570319 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Mutant Female 3 MF3 SAMEA110472296 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472296|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29736|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29736|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:372 85551 MF3 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 EF11_1.fq.gz EF11_2.fq.gz fastq fastq 9515997600.0 31719992.0 ena RUN TAB 10 08 2022 10:54:39:372 85552 0:150 1:150 A:2541032543;C:2239204827;G:2227356932;T:2508310635;N:92663 150 150     2541032543 2239204827 2227356932 2508310635 92663 ERX9587608 ERS12570319 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95512 0.95547 0.06023 0.06014 0.70721 0.70658 0.51615 0.50766 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11160 11160 ERR10047719 ERX9587607 ERS12570318 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Mutant Female 2 MF2 SAMEA110472295 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472295|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29735|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29735|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:372 85549 MF2 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 EF10_1.fq.gz EF10_2.fq.gz fastq fastq 10394476500.0 34648255.0 ena RUN TAB 10 08 2022 10:54:39:372 85550 0:150 1:150 A:2789547305;C:2438564969;G:2423744267;T:2742517499;N:102460 150 150     2789547305 2438564969 2423744267 2742517499 102460 ERX9587607 ERS12570318 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95582 0.95591 0.06231 0.06252 0.70565 0.70715 0.51407 0.51477 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11161 11161 ERR10047718 ERX9587606 ERS12570317 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Mutant Female 1 MF1 SAMEA110472294 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472294|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29734|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29734|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:372 85547 MF1 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 EF9_1.fq.gz EF9_2.fq.gz fastq fastq 9531565200.0 31771884.0 ena RUN TAB 10 08 2022 10:54:39:372 85548 0:150 1:150 A:2534403521;C:2257857645;G:2242329348;T:2496889068;N:85618 150 150     2534403521 2257857645 2242329348 2496889068 85618 ERX9587606 ERS12570317 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95744 0.95773 0.05406 0.054 0.70703 0.70627 0.49691 0.49886 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11162 11162 ERR10047717 ERX9587605 ERS12570316 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Mutant Male 4 MM4 SAMEA110472293 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472293|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29733|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29733|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:371 85545 MM4 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 EM16_1.fq.gz EM16_2.fq.gz fastq fastq 9801781200.0 32672604.0 ena RUN TAB 10 08 2022 10:54:39:371 85546 0:150 1:150 A:2617469644;C:2307347982;G:2294965646;T:2581792895;N:205033 150 150     2617469644 2307347982 2294965646 2581792895 205033 ERX9587605 ERS12570316 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95755 0.95764 0.0539 0.05338 0.71587 0.71484 0.51048 0.52067 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11163 11163 ERR10047716 ERX9587604 ERS12570315 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Mutant Male 3 MM3 SAMEA110472292 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472292|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29732|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29732|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:371 85543 MM3 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 EM15_1.fq.gz EM15_2.fq.gz fastq fastq 9922431900.0 33074773.0 ena RUN TAB 10 08 2022 10:54:39:371 85544 0:150 1:150 A:2640289295;C:2345938205;G:2336699617;T:2599294368;N:210415 150 150     2640289295 2345938205 2336699617 2599294368 210415 ERX9587604 ERS12570315 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95894 0.95898 0.04903 0.04914 0.71346 0.71388 0.51462 0.51356 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11164 11164 ERR10047715 ERX9587603 ERS12570314 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Mutant Male 2 MM2 SAMEA110472291 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472291|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29731|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29731|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:371 85541 MM2 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 EM14_1.fq.gz EM14_2.fq.gz fastq fastq 9470081700.0 31566939.0 ena RUN TAB 10 08 2022 10:54:39:371 85542 0:150 1:150 A:2518757590;C:2239498890;G:2227790286;T:2483847148;N:187786 150 150     2518757590 2239498890 2227790286 2483847148 187786 ERX9587603 ERS12570314 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95826 0.95753 0.05166 0.05151 0.71827 0.71725 0.50776 0.50874 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11165 11165 ERR10047714 ERX9587602 ERS12570313 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Mutant Male 1 MM1 SAMEA110472290 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472290|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29730|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29730|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:371 85539 MM1 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 EM13_1.fq.gz EM13_2.fq.gz fastq fastq 9896066100.0 32986887.0 ena RUN TAB 10 08 2022 10:54:39:371 85540 0:150 1:150 A:2615586694;C:2355549418;G:2345987621;T:2578734637;N:207730 150 150     2615586694 2355549418 2345987621 2578734637 207730 ERX9587602 ERS12570313 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.96075 0.9607 0.04898 0.04814 0.71914 0.71762 0.50604 0.51092 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11166 11166 ERR10047713 ERX9587601 ERS12570312 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Wild type Female 4 WF4 SAMEA110472289 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472289|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29729|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29729|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:370 85537 WF4 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 WF4_1.fq.gz WF4_2.fq.gz fastq fastq 8902470600.0 29674902.0 ena RUN TAB 10 08 2022 10:54:39:370 85538 0:150 1:150 A:2387064218;C:2088721835;G:2083589487;T:2343005357;N:89703 150 150     2387064218 2088721835 2083589487 2343005357 89703 ERX9587601 ERS12570312 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95676 0.95666 0.0593 0.05927 0.70092 0.70337 0.49608 0.49899 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11167 11167 ERR10047712 ERX9587600 ERS12570311 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Wild type Female 3 WF3 SAMEA110472288 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472288|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29728|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29728|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:370 85535 WF3 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 WF3_1.fq.gz WF3_2.fq.gz fastq fastq 9063103800.0 30210346.0 ena RUN TAB 10 08 2022 10:54:39:370 85536 0:150 1:150 A:2432312114;C:2123240631;G:2111227574;T:2396247669;N:75812 150 150     2432312114 2123240631 2111227574 2396247669 75812 ERX9587600 ERS12570311 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95482 0.95494 0.06998 0.07003 0.70122 0.70228 0.50936 0.50507 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11168 11168 ERR10047711 ERX9587599 ERS12570310 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Wild type Female 2 WF2 SAMEA110472287 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472287|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29727|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29727|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:370 85533 WF2 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 WF2_1.fq.gz WF2_2.fq.gz fastq fastq 11904985800.0 39683286.0 ena RUN TAB 10 08 2022 10:54:39:370 85534 0:150 1:150 A:3185302826;C:2804829029;G:2783464897;T:3131272515;N:116533 150 150     3185302826 2804829029 2783464897 3131272515 116533 ERX9587599 ERS12570310 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95589 0.95646 0.058 0.05797 0.70457 0.70492 0.51464 0.5143 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11169 11169 ERR10047710 ERX9587598 ERS12570309 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Wild type Female 1 WF1 SAMEA110472286 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472286|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29726|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29726|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:370 85531 WF1 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 WF1_1.fq.gz WF1_2.fq.gz fastq fastq 9491977800.0 31639926.0 ena RUN TAB 10 08 2022 10:54:39:370 85532 0:150 1:150 A:2540140444;C:2236702404;G:2215435797;T:2499606420;N:92735 150 150     2540140444 2236702404 2215435797 2499606420 92735 ERX9587598 ERS12570309 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95868 0.95935 0.05681 0.05651 0.70487 0.70538 0.50749 0.50617 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11170 11170 ERR10047709 ERX9587597 ERS12570308 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Wild type Male 4 WM4 SAMEA110472285 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472285|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29725|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29725|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:369 85529 WM4 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 WM8_1.fq.gz WM8_2.fq.gz fastq fastq 9911994300.0 33039981.0 ena RUN TAB 10 08 2022 10:54:39:369 85530 0:150 1:150 A:2647417182;C:2332033790;G:2324021308;T:2608423782;N:98238 150 150     2647417182 2332033790 2324021308 2608423782 98238 ERX9587597 ERS12570308 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95754 0.95758 0.05322 0.05309 0.71936 0.71898 0.52558 0.52697 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11171 11171 ERR10047708 ERX9587596 ERS12570307 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Wild type Male 3 WM3 SAMEA110472284 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472284|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29724|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29724|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:369 85527 WM3 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 WM7_1.fq.gz WM7_2.fq.gz fastq fastq 10756015500.0 35853385.0 ena RUN TAB 10 08 2022 10:54:39:369 85528 0:150 1:150 A:2882486379;C:2526051573;G:2510570253;T:2836803943;N:103352 150 150     2882486379 2526051573 2510570253 2836803943 103352 ERX9587596 ERS12570307 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95343 0.9538 0.055 0.05491 0.71784 0.71883 0.53419 0.52955 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11172 11172 ERR10047707 ERX9587595 ERS12570306 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Wild type Male 2 WM2 SAMEA110472283 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472283|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29723|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29723|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:369 85525 WM2 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 WM6_1.fq.gz WM6_2.fq.gz fastq fastq 8944434000.0 29814780.0 ena RUN TAB 10 08 2022 10:54:39:369 85526 0:150 1:150 A:2384550098;C:2112886362;G:2095147407;T:2351765069;N:85064 150 150     2384550098 2112886362 2095147407 2351765069 85064 ERX9587595 ERS12570306 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95717 0.95759 0.05527 0.05526 0.72009 0.72011 0.52634 0.52832 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11173 11173 ERR10047706 ERX9587594 ERS12570305 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Wild type Male 1 WM1 SAMEA110472282 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472282|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29722|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29722|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:368 85523 WM1 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 WM5_1.fq.gz WM5_2.fq.gz fastq fastq 9558564300.0 31861881.0 ena RUN TAB 10 08 2022 10:54:39:369 85524 0:150 1:150 A:2556941509;C:2249230277;G:2236855770;T:2515442411;N:94333 150 150     2556941509 2249230277 2236855770 2515442411 94333 ERX9587594 ERS12570305 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95505 0.95484 0.05372 0.05318 0.71798 0.71898 0.52584 0.52042 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
38296 38296 SRR1647681 SRX756916 SRS742120 SRP049663 PRJNA266803 Spring Varaemia of Carp Virus SVCV infection of adult zebrafish GSE63133 Transcriptome Analysis During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.   pubmed:25535281   24K GSM1541905   source name:head kidney|tissue:head kidney|disease state:24h post SVCV infection 24K Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... head kidney   Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:head kidney|disease state:24h post SVCV infection GSM1541905 GSM1541905: 24K; Danio rerio; RNA Seq GSM1541905   1 Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1541905 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP049663     24K_GTGAAA_L003_R1.fastq fastq 1020487560.0 20009560.0 GSM1541905 r1 0:51 A:266117014;C:246797067;G:240014464;T:267491299;N:67716 51       266117014 246797067 240014464 267491299 67716 SRX756916 SRS742120 SRA200717 GEO Institute of Hydrobiology, Chinese Academy of Sciences 1 0.92411   0.07686   0.68647   0.4627   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-11-10 Undetermined Adult Kidney Renal System
38297 38297 SRR1647680 SRX756915 SRS742117 SRP049663 PRJNA266803 Spring Varaemia of Carp Virus SVCV infection of adult zebrafish GSE63133 Transcriptome Analysis During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.   pubmed:25535281   6K GSM1541904   source name:head kidney|tissue:head kidney|disease state:6h post SVCV infection 6K Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... head kidney   Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:head kidney|disease state:6h post SVCV infection GSM1541904 GSM1541904: 6K; Danio rerio; RNA Seq GSM1541904   1 Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1541904 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP049663     6K_GTCCGC_L003_R1.fastq fastq 929436036.0 18224236.0 GSM1541904 r1 0:51 A:242005719;C:225485975;G:219890494;T:241993975;N:59873 51       242005719 225485975 219890494 241993975 59873 SRX756915 SRS742117 SRA200717 GEO Institute of Hydrobiology, Chinese Academy of Sciences 1 0.92547   0.09105   0.69264   0.49166   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-11-10 Undetermined Adult Kidney Renal System
38298 38298 SRR1647679 SRX756914 SRS742116 SRP049663 PRJNA266803 Spring Varaemia of Carp Virus SVCV infection of adult zebrafish GSE63133 Transcriptome Analysis During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.   pubmed:25535281   0K GSM1541903   source name:head kidney|tissue:head kidney|disease state:un infected 0K Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... head kidney   Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:head kidney|disease state:un infected GSM1541903 GSM1541903: 0K; Danio rerio; RNA Seq GSM1541903   1 Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1541903 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP049663     0K_CCGTCC_L003_R1.fastq fastq 1077979095.0 21136845.0 GSM1541903 r1 0:51 A:280277150;C:261348733;G:255721013;T:280562071;N:70128 51       280277150 261348733 255721013 280562071 70128 SRX756914 SRS742116 SRA200717 GEO Institute of Hydrobiology, Chinese Academy of Sciences 1 0.92545   0.08181   0.68373   0.49408   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-11-10 Undetermined Adult Kidney Renal System
42599 42599 SRR5810682 SRX2989237 SRS2341160 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 2 GSM2696104   source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes inDrop sequencing of multiple samples 2 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696104 GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq GSM2696104   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696104 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     inDrop_v3_run2_R1.fastq.gz fastq 23315853588.0 382227108.0 GSM2696104 r1 0:61 1:0 A:6573828142;C:5137891481;G:5021324431;T:6582457296;N:352238 61 0     6573828142 5137891481 5021324431 6582457296 352238 SRX2989237 SRS2341160 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.83828   0.08537   0.83552   0.56658   61   B   usable mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42600 42600 SRR5810683 SRX2989237 SRS2341160 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 2 GSM2696104   source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes inDrop sequencing of multiple samples 2 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696104 GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq GSM2696104   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696104 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     inDrop_v3_run2_R2.fastq.gz fastq 3057816864.0 382227108.0 GSM2696104 r2 0:0 1:8 A:743619897;C:720488231;G:1031094190;T:562297818;N:316728 0 8     743619897 720488231 1031094190 562297818 316728 SRX2989237 SRS2341160 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0   0.0   1.0       8   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42601 42601 SRR5810684 SRX2989237 SRS2341160 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 2 GSM2696104   source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes inDrop sequencing of multiple samples 2 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696104 GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq GSM2696104   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696104 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     inDrop_v3_run2_R3.fastq.gz fastq 3057816864.0 382227108.0 GSM2696104 r3 0:8 A:913664473;C:577895371;G:646194239;T:918893384;N:1169397 8       913664473 577895371 646194239 918893384 1169397 SRX2989237 SRS2341160 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0   0.0   1.0       8   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42602 42602 SRR5810685 SRX2989237 SRS2341160 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 2 GSM2696104   source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes inDrop sequencing of multiple samples 2 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696104 GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq GSM2696104   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696104 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     inDrop_v3_run2_R4.fastq.gz fastq 5351179512.0 382227108.0 GSM2696104 r4 0:14 A:1351470715;C:1294400719;G:1379073889;T:1322397488;N:3836701 14       1351470715 1294400719 1379073889 1322397488 3836701 SRX2989237 SRS2341160 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0   0.0   1.0       14   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42603 42603 SRR5810678 SRX2989236 SRS2341159 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 1 GSM2696103   source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes inDrop sequencing of multiple samples 1 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696103 GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq GSM2696103   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696103 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     inDrop_v3_run1_R1.fastq.gz fastq 26868371039.0 440465099.0 GSM2696103 r1 0:61 1:0 A:7598044404;C:5948542485;G:5746339343;T:7575168754;N:276053 61 0     7598044404 5948542485 5746339343 7575168754 276053 SRX2989236 SRS2341159 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.83437   0.08222   0.82658   0.54569   61   B   usable mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42604 42604 SRR5810679 SRX2989236 SRS2341159 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 1 GSM2696103   source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes inDrop sequencing of multiple samples 1 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696103 GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq GSM2696103   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696103 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     inDrop_v3_run1_R2.fastq.gz fastq 3523720792.0 440465099.0 GSM2696103 r2 0:0 1:8 A:892841722;C:781074758;G:1176856476;T:672376743;N:571093 0 8     892841722 781074758 1176856476 672376743 571093 SRX2989236 SRS2341159 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0   0.0   1.0       8   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42605 42605 SRR5810680 SRX2989236 SRS2341159 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 1 GSM2696103   source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes inDrop sequencing of multiple samples 1 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696103 GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq GSM2696103   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696103 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     inDrop_v3_run1_R3.fastq.gz fastq 3523720792.0 440465099.0 GSM2696103 r3 0:8 A:1016854893;C:682256486;G:759860179;T:1063129659;N:1619575 8       1016854893 682256486 759860179 1063129659 1619575 SRX2989236 SRS2341159 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0   0.0   1.0       8   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42606 42606 SRR5810681 SRX2989236 SRS2341159 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 1 GSM2696103   source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes inDrop sequencing of multiple samples 1 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696103 GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq GSM2696103   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696103 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     inDrop_v3_run1_R4.fastq.gz fastq 6166511386.0 440465099.0 GSM2696103 r4 0:14 A:1513770161;C:1469643118;G:1669791951;T:1509862301;N:3443855 14       1513770161 1469643118 1669791951 1509862301 3443855 SRX2989236 SRS2341159 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0   0.0   1.0       14   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42607 42607 SRR5810676 SRX2989235 SRS2341158 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2 GSM2696102   source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs GSM2696102 GSM2696102: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2; Danio rerio; RNA Seq GSM2696102   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696102 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     PRKDC2_R1.fastq.gz fastq 1987929396.0 55220261.0 GSM2696102 r1 0:36 1:0 A:506372087;C:413396954;G:415448050;T:652683387;N:28918 36 0     506372087 413396954 415448050 652683387 28918 SRX2989235 SRS2341158 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.86587   0.12447   0.80336   0.54126   36   B   usable mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42608 42608 SRR5810677 SRX2989235 SRS2341158 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2 GSM2696102   source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs GSM2696102 GSM2696102: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2; Danio rerio; RNA Seq GSM2696102   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696102 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     PRKDC2_R2.fastq.gz fastq 2761013050.0 55220261.0 GSM2696102 r2 0:0 1:50 A:554483675;C:506568509;G:721419849;T:974751566;N:3789451 0 50     554483675 506568509 721419849 974751566 3789451 SRX2989235 SRS2341158 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.00796   0.0077   0.99961   0.78947   50   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42609 42609 SRR5810674 SRX2989234 SRS2341157 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1 GSM2696101   source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs GSM2696101 GSM2696101: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1; Danio rerio; RNA Seq GSM2696101   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696101 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     PRKDC1_R1.fastq.gz fastq 1549442736.0 43040076.0 GSM2696101 r1 0:36 1:0 A:402261661;C:326108405;G:319637981;T:501413963;N:20726 36 0     402261661 326108405 319637981 501413963 20726 SRX2989234 SRS2341157 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.84263   0.11449   0.79464   0.57001   36   B   usable mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42610 42610 SRR5810675 SRX2989234 SRS2341157 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1 GSM2696101   source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs GSM2696101 GSM2696101: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1; Danio rerio; RNA Seq GSM2696101   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696101 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     PRKDC1_R2.fastq.gz fastq 2152003800.0 43040076.0 GSM2696101 r2 0:0 1:50 A:432547886;C:403759182;G:561234660;T:751564536;N:2897536 0 50     432547886 403759182 561234660 751564536 2897536 SRX2989234 SRS2341157 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.00796   0.00773   0.99971   0.82758   50   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42611 42611 SRR5810672 SRX2989233 SRS2341156 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of WT sample animal #2 GSM2696100   source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype inDrop sequencing of WT sample animal #2 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype GSM2696100 GSM2696100: inDrop sequencing of WT sample animal #2; Danio rerio; RNA Seq GSM2696100   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696100 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     WT2_R1.fastq.gz fastq 3202042500.0 88945625.0 GSM2696100 r1 0:36 1:0 A:821476951;C:657776656;G:665293293;T:1057448635;N:46965 36 0     821476951 657776656 665293293 1057448635 46965 SRX2989233 SRS2341156 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.84222   0.12969   0.80683   0.53542   36   B   usable mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42612 42612 SRR5810673 SRX2989233 SRS2341156 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of WT sample animal #2 GSM2696100   source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype inDrop sequencing of WT sample animal #2 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype GSM2696100 GSM2696100: inDrop sequencing of WT sample animal #2; Danio rerio; RNA Seq GSM2696100   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696100 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     WT2_R2.fastq.gz fastq 4447281250.0 88945625.0 GSM2696100 r2 0:0 1:50 A:880464480;C:827380868;G:1171423978;T:1561925150;N:6086774 0 50     880464480 827380868 1171423978 1561925150 6086774 SRX2989233 SRS2341156 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.00782   0.0075   0.99947   0.91666   50   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42613 42613 SRR5810670 SRX2989232 SRS2341155 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of WT sample animal #1 GSM2696099   source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype inDrop sequencing of WT sample animal #1 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype GSM2696099 GSM2696099: inDrop sequencing of WT sample animal #1; Danio rerio; RNA Seq GSM2696099   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696099 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     WT1_R1.fastq.gz fastq 3313205496.0 92033486.0 GSM2696099 r1 0:36 1:0 A:858288917;C:693848400;G:675650809;T:1085369048;N:48322 36 0     858288917 693848400 675650809 1085369048 48322 SRX2989232 SRS2341155 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.8771   0.13918   0.81115   0.59004   36   B   usable mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42614 42614 SRR5810671 SRX2989232 SRS2341155 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of WT sample animal #1 GSM2696099   source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype inDrop sequencing of WT sample animal #1 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype GSM2696099 GSM2696099: inDrop sequencing of WT sample animal #1; Danio rerio; RNA Seq GSM2696099   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696099 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     WT1_R2.fastq.gz fastq 4601674300.0 92033486.0 GSM2696099 r2 0:0 1:50 A:914884703;C:856837987;G:1192418010;T:1631240786;N:6292814 0 50     914884703 856837987 1192418010 1631240786 6292814 SRX2989232 SRS2341155 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0063   0.00598   0.99959   0.8913   50   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42615 42615 SRR5810949 SRX2989499 SRS2341423 SRP111341 PRJNA393430 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq] GSE100912 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   IL2RGA rep3 bulkRNA GSM2696362   source name:whole kidney marrow|tissue:kidney marrow|genotype:IL2RGA IL2RGA rep3 bulkRNA Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.   tissue:kidney marrow|genotype:IL2RGA GSM2696362 GSM2696362: IL2RGA rep3 bulkRNA; Danio rerio; RNA Seq GSM2696362   1 Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in. GEO Accession:GSM2696362 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP111341     IL2RGA_rep3.bam bam 800560362.0 7848631.0 GSM2696362 r1 0:51 1:51 A:204943188;C:193859822;G:198825795;T:202880780;N:50777 51 51     204943188 193859822 198825795 202880780 50777 SRX2989499 SRS2341423 SRA584590 GEO Pathology, Massachusetts General Hospital 2 0.9537 0.95854 0.14459 0.14217 0.72297 0.72165 0.53136 0.5294 51 51 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext sc bulk bulk   United States 2017-07-07 Undetermined Adult Kidney Renal System
42616 42616 SRR5810948 SRX2989498 SRS2341422 SRP111341 PRJNA393430 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq] GSE100912 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   IL2RGA rep2 bulkRNA GSM2696361   source name:whole kidney marrow|tissue:kidney marrow|genotype:IL2RGA IL2RGA rep2 bulkRNA Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.   tissue:kidney marrow|genotype:IL2RGA GSM2696361 GSM2696361: IL2RGA rep2 bulkRNA; Danio rerio; RNA Seq GSM2696361   1 Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in. GEO Accession:GSM2696361 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP111341     IL2RGA_rep2.bam bam 1103288814.0 10816557.0 GSM2696361 r1 0:51 1:51 A:296109551;C:253391201;G:259742934;T:293977435;N:67693 51 51     296109551 253391201 259742934 293977435 67693 SRX2989498 SRS2341422 SRA584590 GEO Pathology, Massachusetts General Hospital 2 0.93568 0.946 0.07751 0.07604 0.67568 0.67616 0.49311 0.49081 51 51 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext sc bulk bulk   United States 2017-07-07 Undetermined Adult Kidney Renal System
42617 42617 SRR5810947 SRX2989497 SRS2341420 SRP111341 PRJNA393430 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq] GSE100912 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   IL2RGA rep1 bulkRNA GSM2696360   source name:whole kidney marrow|tissue:kidney marrow|genotype:IL2RGA IL2RGA rep1 bulkRNA Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.   tissue:kidney marrow|genotype:IL2RGA GSM2696360 GSM2696360: IL2RGA rep1 bulkRNA; Danio rerio; RNA Seq GSM2696360   1 Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in. GEO Accession:GSM2696360 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP111341     IL2RGA_rep1.bam bam 661646358.0 6486729.0 GSM2696360 r1 0:51 1:51 A:169428837;C:164616195;G:161161362;T:166407987;N:31977 51 51     169428837 164616195 161161362 166407987 31977 SRX2989497 SRS2341420 SRA584590 GEO Pathology, Massachusetts General Hospital 2 0.91331 0.93442 0.06212 0.06166 0.69915 0.69964 0.4776 0.5104 51 51 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext sc bulk bulk   United States 2017-07-07 Undetermined Adult Kidney Renal System
42618 42618 SRR5810946 SRX2989496 SRS2341419 SRP111341 PRJNA393430 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq] GSE100912 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   PRKDC.IL2RGA rep3 bulkRNA GSM2696359   source name:whole kidney marrow|tissue:kidney marrow|genotype:PRKDC;IL2RGA PRKDC.IL2RGA rep3 bulkRNA Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.   tissue:kidney marrow|genotype:PRKDC;IL2RGA GSM2696359 GSM2696359: PRKDC.IL2RGA rep3 bulkRNA; Danio rerio; RNA Seq GSM2696359   1 Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in. GEO Accession:GSM2696359 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP111341     PRKDC.IL2RGA_rep3.bam bam 887363484.0 8699642.0 GSM2696359 r1 0:51 1:51 A:236785705;C:205238782;G:210240418;T:235045073;N:53506 51 51     236785705 205238782 210240418 235045073 53506 SRX2989496 SRS2341419 SRA584590 GEO Pathology, Massachusetts General Hospital 2 0.92505 0.93893 0.07173 0.07011 0.71461 0.71435 0.48699 0.49848 51 51 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext sc bulk bulk   United States 2017-07-07 Undetermined Adult Kidney Renal System
42619 42619 SRR5810945 SRX2989495 SRS2341417 SRP111341 PRJNA393430 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq] GSE100912 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   PRKDC.IL2RGA rep2 bulkRNA GSM2696358   source name:whole kidney marrow|tissue:kidney marrow|genotype:PRKDC;IL2RGA PRKDC.IL2RGA rep2 bulkRNA Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.   tissue:kidney marrow|genotype:PRKDC;IL2RGA GSM2696358 GSM2696358: PRKDC.IL2RGA rep2 bulkRNA; Danio rerio; RNA Seq GSM2696358   1 Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in. GEO Accession:GSM2696358 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP111341     PRKDC.IL2RGA_rep2.bam bam 1243263312.0 12188856.0 GSM2696358 r1 0:51 1:51 A:335332471;C:284322063;G:289732846;T:333799129;N:76803 51 51     335332471 284322063 289732846 333799129 76803 SRX2989495 SRS2341417 SRA584590 GEO Pathology, Massachusetts General Hospital 2 0.93625 0.94489 0.08706 0.08568 0.68956 0.69067 0.49006 0.48855 51 51 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext sc bulk bulk   United States 2017-07-07 Undetermined Adult Kidney Renal System
42620 42620 SRR5810944 SRX2989494 SRS2341418 SRP111341 PRJNA393430 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq] GSE100912 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   PRKDC.IL2RGA rep1 bulkRNA GSM2696357   source name:whole kidney marrow|tissue:kidney marrow|genotype:PRKDC;IL2RGA PRKDC.IL2RGA rep1 bulkRNA Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.   tissue:kidney marrow|genotype:PRKDC;IL2RGA GSM2696357 GSM2696357: PRKDC.IL2RGA rep1 bulkRNA; Danio rerio; RNA Seq GSM2696357   1 Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in. GEO Accession:GSM2696357 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP111341     PRKDC.IL2RGA_rep1.bam bam 1186402800.0 11631400.0 GSM2696357 r1 0:51 1:51 A:318338106;C:272405192;G:278795626;T:316790310;N:73566 51 51     318338106 272405192 278795626 316790310 73566 SRX2989494 SRS2341418 SRA584590 GEO Pathology, Massachusetts General Hospital 2 0.93146 0.94427 0.06375 0.0617 0.69664 0.69566 0.48745 0.47922 51 51 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext sc bulk bulk   United States 2017-07-07 Undetermined Adult Kidney Renal System
42621 42621 SRR5810943 SRX2989493 SRS2341416 SRP111341 PRJNA393430 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq] GSE100912 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   PRKDC rep3 bulkRNA GSM2696356   source name:whole kidney marrow|tissue:kidney marrow|genotype:PRKDC PRKDC rep3 bulkRNA Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.   tissue:kidney marrow|genotype:PRKDC GSM2696356 GSM2696356: PRKDC rep3 bulkRNA; Danio rerio; RNA Seq GSM2696356   1 Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in. GEO Accession:GSM2696356 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP111341     PRKDC_rep3.bam bam 1086096306.0 10648003.0 GSM2696356 r1 0:51 1:51 A:290117045;C:250914550;G:254803671;T:289025322;N:1235718 51 51     290117045 250914550 254803671 289025322 1235718 SRX2989493 SRS2341416 SRA584590 GEO Pathology, Massachusetts General Hospital 2 0.93491 0.92916 0.13346 0.12712 0.69974 0.69996 0.49518 0.48499 51 51 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext sc bulk bulk   United States 2017-07-07 Undetermined Adult Kidney Renal System
42622 42622 SRR5810942 SRX2989492 SRS2341415 SRP111341 PRJNA393430 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq] GSE100912 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   PRKDC rep2 bulkRNA GSM2696355   source name:whole kidney marrow|tissue:kidney marrow|genotype:PRKDC PRKDC rep2 bulkRNA Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.   tissue:kidney marrow|genotype:PRKDC GSM2696355 GSM2696355: PRKDC rep2 bulkRNA; Danio rerio; RNA Seq GSM2696355   1 Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in. GEO Accession:GSM2696355 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP111341     PRKDC_rep2.bam bam 1295111136.0 12697168.0 GSM2696355 r1 0:51 1:51 A:347365385;C:295754109;G:304296998;T:346181142;N:1513502 51 51     347365385 295754109 304296998 346181142 1513502 SRX2989492 SRS2341415 SRA584590 GEO Pathology, Massachusetts General Hospital 2 0.93286 0.923 0.13571 0.1291 0.70512 0.70796 0.49872 0.49014 51 51 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext sc bulk bulk   United States 2017-07-07 Undetermined Adult Kidney Renal System
42623 42623 SRR5810941 SRX2989491 SRS2341414 SRP111341 PRJNA393430 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq] GSE100912 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   PRKDC rep1 bulkRNA GSM2696354   source name:whole kidney marrow|tissue:kidney marrow|genotype:PRKDC PRKDC rep1 bulkRNA Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.   tissue:kidney marrow|genotype:PRKDC GSM2696354 GSM2696354: PRKDC rep1 bulkRNA; Danio rerio; RNA Seq GSM2696354   1 Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in. GEO Accession:GSM2696354 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP111341     PRKDC_rep1.bam bam 1144774866.0 11223283.0 GSM2696354 r1 0:51 1:51 A:307919037;C:260831758;G:268914919;T:305733316;N:1375836 51 51     307919037 260831758 268914919 305733316 1375836 SRX2989491 SRS2341414 SRA584590 GEO Pathology, Massachusetts General Hospital 2 0.93261 0.92672 0.12175 0.11566 0.704 0.70597 0.49649 0.49333 51 51 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext sc bulk bulk   United States 2017-07-07 Undetermined Adult Kidney Renal System
42624 42624 SRR5810940 SRX2989490 SRS2341413 SRP111341 PRJNA393430 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq] GSE100912 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   WT rep3 bulkRNA GSM2696353   source name:whole kidney marrow|tissue:kidney marrow|genotype:wildtype WT rep3 bulkRNA Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.   tissue:kidney marrow|genotype:wildtype GSM2696353 GSM2696353: WT rep3 bulkRNA; Danio rerio; RNA Seq GSM2696353   1 Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in. GEO Accession:GSM2696353 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP111341     WT_rep3.bam bam 1222568532.0 11985966.0 GSM2696353 r1 0:51 1:51 A:325706008;C:281709574;G:290313610;T:323399233;N:1440107 51 51     325706008 281709574 290313610 323399233 1440107 SRX2989490 SRS2341413 SRA584590 GEO Pathology, Massachusetts General Hospital 2 0.92438 0.92382 0.11926 0.11474 0.69934 0.70116 0.50348 0.50642 51 51 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext sc bulk bulk   United States 2017-07-07 Undetermined Adult Kidney Renal System
42625 42625 SRR5810939 SRX2989489 SRS2341412 SRP111341 PRJNA393430 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq] GSE100912 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   WT rep2 bulkRNA GSM2696352   source name:whole kidney marrow|tissue:kidney marrow|genotype:wildtype WT rep2 bulkRNA Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.   tissue:kidney marrow|genotype:wildtype GSM2696352 GSM2696352: WT rep2 bulkRNA; Danio rerio; RNA Seq GSM2696352   1 Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in. GEO Accession:GSM2696352 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP111341     WT_rep2.bam bam 1169509356.0 11465778.0 GSM2696352 r1 0:51 1:51 A:311703416;C:268894082;G:278866430;T:308727612;N:1317816 51 51     311703416 268894082 278866430 308727612 1317816 SRX2989489 SRS2341412 SRA584590 GEO Pathology, Massachusetts General Hospital 2 0.91371 0.92007 0.1137 0.10922 0.70735 0.7093 0.49742 0.49982 51 51 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext sc bulk bulk   United States 2017-07-07 Undetermined Adult Kidney Renal System
42626 42626 SRR5810938 SRX2989488 SRS2341411 SRP111341 PRJNA393430 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq] GSE100912 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   WT rep1 bulkRNA GSM2696351   source name:whole kidney marrow|tissue:kidney marrow|genotype:wildtype WT rep1 bulkRNA Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.   tissue:kidney marrow|genotype:wildtype GSM2696351 GSM2696351: WT rep1 bulkRNA; Danio rerio; RNA Seq GSM2696351   1 Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® PolyA mRNA Magnetic Isolation Module followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in. GEO Accession:GSM2696351 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP111341     WT_rep1.bam bam 1371866442.0 13449671.0 GSM2696351 r1 0:51 1:51 A:360833799;C:320009757;G:330603707;T:358760329;N:1658850 51 51     360833799 320009757 330603707 358760329 1658850 SRX2989488 SRS2341411 SRA584590 GEO Pathology, Massachusetts General Hospital 2 0.94532 0.93582 0.11053 0.10605 0.70686 0.70869 0.48301 0.4993 51 51 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext sc bulk bulk   United States 2017-07-07 Undetermined Adult Kidney Renal System
42627 42627 SRR5810931 SRX2989483 SRS2341405 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.D12 GSM2696350   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.D12 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696350 GSM2696350: Runx123 GFP.P1.D12; Danio rerio; RNA Seq GSM2696350   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696350 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.D12.bam bam 80381537.0 1070203.0 GSM2696350 r1 0:37.55 1:37.56 A:21289298;C:18976641;G:18646654;T:21447816;N:21128 37 37     21289298 18976641 18646654 21447816 21128 SRX2989483 SRS2341405 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.87699 0.87627 0.08393 0.08323 0.94385 0.94432 0.47664 0.47751 37 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42628 42628 SRR5810930 SRX2989482 SRS2341406 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.D11 GSM2696349   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.D11 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696349 GSM2696349: Runx123 GFP.P1.D11; Danio rerio; RNA Seq GSM2696349   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696349 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.D11.bam bam 110475987.0 1471507.0 GSM2696349 r1 0:37.54 1:37.54 A:28733566;C:26637046;G:26164058;T:28909002;N:32315 37 37     28733566 26637046 26164058 28909002 32315 SRX2989482 SRS2341406 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.86384 0.86659 0.0745 0.07357 0.95026 0.95069 0.43802 0.44268 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42629 42629 SRR5810929 SRX2989481 SRS2341404 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.D10 GSM2696348   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.D10 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696348 GSM2696348: Runx123 GFP.P1.D10; Danio rerio; RNA Seq GSM2696348   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696348 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.D10.bam bam 64029006.0 852803.0 GSM2696348 r1 0:37.54 1:37.54 A:16672853;C:15398688;G:15154223;T:16784255;N:18987 37 37     16672853 15398688 15154223 16784255 18987 SRX2989481 SRS2341404 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.86959 0.86933 0.07603 0.07599 0.95371 0.95426 0.42353 0.46566 36 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42630 42630 SRR5810928 SRX2989480 SRS2341403 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.D09 GSM2696347   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.D09 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696347 GSM2696347: Runx123 GFP.P1.D09; Danio rerio; RNA Seq GSM2696347   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696347 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.D09.bam bam 47224779.0 627954.0 GSM2696347 r1 0:37.60 1:37.60 A:13328909;C:10314542;G:10086676;T:13486101;N:8551 37 37     13328909 10314542 10086676 13486101 8551 SRX2989480 SRS2341403 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91771 0.91801 0.2846 0.28357 0.98382 0.98441 0.51864 0.48968 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42631 42631 SRR5810927 SRX2989479 SRS2341402 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.D07 GSM2696346   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.D07 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696346 GSM2696346: Runx123 GFP.P1.D07; Danio rerio; RNA Seq GSM2696346   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696346 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.D07.bam bam 95937754.0 1276149.0 GSM2696346 r1 0:37.59 1:37.59 A:26235960;C:21834939;G:21328613;T:26519033;N:19209 37 37     26235960 21834939 21328613 26519033 19209 SRX2989479 SRS2341402 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91901 0.9191 0.21301 0.21363 0.97569 0.97636 0.50099 0.48645 38 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42632 42632 SRR5810926 SRX2989478 SRS2341401 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.D05 GSM2696345   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.D05 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696345 GSM2696345: Runx123 GFP.P1.D05; Danio rerio; RNA Seq GSM2696345   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696345 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.D05.bam bam 63200305.0 841042.0 GSM2696345 r1 0:37.57 1:37.57 A:16679985;C:14999740;G:14596412;T:16911795;N:12373 37 37     16679985 14999740 14596412 16911795 12373 SRX2989478 SRS2341401 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.92517 0.92801 0.09142 0.09164 0.92423 0.92476 0.49349 0.50932 38 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42633 42633 SRR5810925 SRX2989477 SRS2341400 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.D04 GSM2696344   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.D04 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696344 GSM2696344: Runx123 GFP.P1.D04; Danio rerio; RNA Seq GSM2696344   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696344 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.D04.bam bam 116667635.0 1552599.0 GSM2696344 r1 0:37.57 1:37.57 A:30673358;C:27825004;G:27081912;T:31064756;N:22605 37 37     30673358 27825004 27081912 31064756 22605 SRX2989477 SRS2341400 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.92555 0.92526 0.07819 0.07883 0.90179 0.9026 0.50917 0.4991 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42634 42634 SRR5810924 SRX2989476 SRS2341397 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.D03 GSM2696343   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.D03 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696343 GSM2696343: Runx123 GFP.P1.D03; Danio rerio; RNA Seq GSM2696343   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696343 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.D03.bam bam 17871672.0 237645.0 GSM2696343 r1 0:37.60 1:37.60 A:5018355;C:3926970;G:3841973;T:5081075;N:3299 37 37     5018355 3926970 3841973 5081075 3299 SRX2989476 SRS2341397 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91431 0.91617 0.27987 0.27943 0.9811 0.98177 0.46989 0.47788 38 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42635 42635 SRR5810923 SRX2989475 SRS2341399 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.D02 GSM2696342   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.D02 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696342 GSM2696342: Runx123 GFP.P1.D02; Danio rerio; RNA Seq GSM2696342   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696342 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.D02.bam bam 5910004.0 78559.0 GSM2696342 r1 0:37.62 1:37.61 A:1696500;C:1262727;G:1225976;T:1723800;N:1001 37 37     1696500 1262727 1225976 1723800 1001 SRX2989475 SRS2341399 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.90278 0.90711 0.30589 0.30762 0.98514 0.98537 0.53428 0.50422 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42636 42636 SRR5810922 SRX2989474 SRS2341396 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.D01 GSM2696341   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.D01 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696341 GSM2696341: Runx123 GFP.P1.D01; Danio rerio; RNA Seq GSM2696341   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696341 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.D01.bam bam 80127770.0 1066187.0 GSM2696341 r1 0:37.58 1:37.58 A:21326419;C:18808312;G:18299957;T:21677439;N:15643 37 37     21326419 18808312 18299957 21677439 15643 SRX2989474 SRS2341396 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.92107 0.92092 0.13232 0.13185 0.94757 0.94882 0.51086 0.51778 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42637 42637 SRR5810921 SRX2989473 SRS2341398 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.C12 GSM2696340   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.C12 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696340 GSM2696340: Runx123 GFP.P1.C12; Danio rerio; RNA Seq GSM2696340   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696340 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.C12.bam bam 111631740.0 1485455.0 GSM2696340 r1 0:37.57 1:37.58 A:29772997;C:26221160;G:25531927;T:30084216;N:21440 37 37     29772997 26221160 25531927 30084216 21440 SRX2989473 SRS2341398 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.92285 0.92236 0.08777 0.08728 0.90433 0.90526 0.50931 0.51179 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42638 42638 SRR5810920 SRX2989472 SRS2341395 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.C11 GSM2696339   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.C11 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696339 GSM2696339: Runx123 GFP.P1.C11; Danio rerio; RNA Seq GSM2696339   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696339 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.C11.bam bam 88068314.0 1172143.0 GSM2696339 r1 0:37.57 1:37.57 A:23113672;C:21054221;G:20500170;T:23381662;N:18589 37 37     23113672 21054221 20500170 23381662 18589 SRX2989472 SRS2341395 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91721 0.91633 0.05241 0.05228 0.95501 0.95491 0.52219 0.51522 38 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42639 42639 SRR5810919 SRX2989471 SRS2341394 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.C10 GSM2696338   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.C10 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696338 GSM2696338: Runx123 GFP.P1.C10; Danio rerio; RNA Seq GSM2696338   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696338 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.C10.bam bam 38361252.0 510997.0 GSM2696338 r1 0:37.54 1:37.54 A:9899029;C:9318645;G:9172551;T:9959598;N:11429 37 37     9899029 9318645 9172551 9959598 11429 SRX2989471 SRS2341394 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.86389 0.86228 0.05704 0.05555 0.97699 0.97731 0.44695 0.44501 37 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42640 42640 SRR5810918 SRX2989470 SRS2341392 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.C09 GSM2696337   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.C09 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696337 GSM2696337: Runx123 GFP.P1.C09; Danio rerio; RNA Seq GSM2696337   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696337 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.C09.bam bam 68798519.0 914900.0 GSM2696337 r1 0:37.60 1:37.60 A:19292535;C:15146911;G:14826092;T:19520460;N:12521 37 37     19292535 15146911 14826092 19520460 12521 SRX2989470 SRS2341392 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91662 0.91722 0.28132 0.28066 0.98334 0.9834 0.45843 0.45913 38 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42641 42641 SRR5810917 SRX2989469 SRS2341393 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.C07 GSM2696336   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.C07 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696336 GSM2696336: Runx123 GFP.P1.C07; Danio rerio; RNA Seq GSM2696336   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696336 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.C07.bam bam 132672266.0 1765198.0 GSM2696336 r1 0:37.58 1:37.58 A:35515458;C:30979554;G:30191689;T:35959966;N:25599 37 37     35515458 30979554 30191689 35959966 25599 SRX2989469 SRS2341393 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.9221 0.92377 0.13303 0.13251 0.94659 0.94744 0.48291 0.484 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42642 42642 SRR5810916 SRX2989468 SRS2341391 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.C06 GSM2696335   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.C06 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696335 GSM2696335: Runx123 GFP.P1.C06; Danio rerio; RNA Seq GSM2696335   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696335 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.C06.bam bam 84779265.0 1127489.0 GSM2696335 r1 0:37.59 1:37.60 A:23538252;C:18907613;G:18492124;T:23826770;N:14506 37 37     23538252 18907613 18492124 23826770 14506 SRX2989468 SRS2341391 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91446 0.91456 0.26601 0.26665 0.98494 0.98514 0.51766 0.52126 37 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42643 42643 SRR5810915 SRX2989467 SRS2341390 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.C05 GSM2696334   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.C05 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696334 GSM2696334: Runx123 GFP.P1.C05; Danio rerio; RNA Seq GSM2696334   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696334 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.C05.bam bam 80373171.0 1069341.0 GSM2696334 r1 0:37.58 1:37.58 A:21548703;C:18732066;G:18228538;T:21847949;N:15915 37 37     21548703 18732066 18228538 21847949 15915 SRX2989467 SRS2341390 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.92431 0.92384 0.14745 0.14636 0.94933 0.94929 0.49522 0.48798 37 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42644 42644 SRR5810914 SRX2989466 SRS2341388 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.C04 GSM2696333   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.C04 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696333 GSM2696333: Runx123 GFP.P1.C04; Danio rerio; RNA Seq GSM2696333   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696333 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.C04.bam bam 124894345.0 1662046.0 GSM2696333 r1 0:37.57 1:37.57 A:32951583;C:29685078;G:28861190;T:33372638;N:23856 37 37     32951583 29685078 28861190 33372638 23856 SRX2989466 SRS2341388 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.92688 0.92681 0.08279 0.08229 0.92064 0.92155 0.52192 0.52012 38 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42645 42645 SRR5810913 SRX2989465 SRS2341387 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.C03 GSM2696332   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.C03 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696332 GSM2696332: Runx123 GFP.P1.C03; Danio rerio; RNA Seq GSM2696332   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696332 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.C03.bam bam 52251566.0 695041.0 GSM2696332 r1 0:37.59 1:37.59 A:14281983;C:11886324;G:11596671;T:14476869;N:9719 37 37     14281983 11886324 11596671 14476869 9719 SRX2989465 SRS2341387 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91524 0.9151 0.18959 0.1887 0.96067 0.96077 0.45598 0.49671 37 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42646 42646 SRR5810912 SRX2989464 SRS2341389 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.C02 GSM2696331   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.C02 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696331 GSM2696331: Runx123 GFP.P1.C02; Danio rerio; RNA Seq GSM2696331   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696331 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.C02.bam bam 12001376.0 159695.0 GSM2696331 r1 0:37.58 1:37.58 A:3192413;C:2820081;G:2753190;T:3233261;N:2431 37 37     3192413 2820081 2753190 3233261 2431 SRX2989464 SRS2341389 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.92637 0.92622 0.10813 0.10815 0.93515 0.93531 0.50246 0.50502 38 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42647 42647 SRR5810911 SRX2989463 SRS2341386 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.C01 GSM2696330   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.C01 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696330 GSM2696330: Runx123 GFP.P1.C01; Danio rerio; RNA Seq GSM2696330   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696330 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.C01.bam bam 144381060.0 1921438.0 GSM2696330 r1 0:37.57 1:37.57 A:38239042;C:34184469;G:33246899;T:38682767;N:27883 37 37     38239042 34184469 33246899 38682767 27883 SRX2989463 SRS2341386 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.92638 0.92732 0.06569 0.06584 0.92301 0.92358 0.50911 0.4995 37 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42648 42648 SRR5810910 SRX2989462 SRS2341385 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.B12 GSM2696329   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.B12 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696329 GSM2696329: Runx123 GFP.P1.B12; Danio rerio; RNA Seq GSM2696329   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696329 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.B12.bam bam 117198871.0 1559287.0 GSM2696329 r1 0:37.58 1:37.58 A:31816554;C:26929456;G:26203100;T:32227582;N:22179 37 37     31816554 26929456 26203100 32227582 22179 SRX2989462 SRS2341385 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.9156 0.91553 0.13034 0.1312 0.93785 0.93874 0.51145 0.50275 37 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42649 42649 SRR5810909 SRX2989461 SRS2341384 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.B10 GSM2696328   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.B10 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696328 GSM2696328: Runx123 GFP.P1.B10; Danio rerio; RNA Seq GSM2696328   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696328 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.B10.bam bam 81830143.0 1088700.0 GSM2696328 r1 0:37.58 1:37.58 A:22083784;C:18952625;G:18451060;T:22326965;N:15709 37 37     22083784 18952625 18451060 22326965 15709 SRX2989461 SRS2341384 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.92296 0.92455 0.13679 0.13773 0.95361 0.95432 0.48069 0.48697 37 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42650 42650 SRR5810908 SRX2989460 SRS2341383 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.B08 GSM2696327   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.B08 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696327 GSM2696327: Runx123 GFP.P1.B08; Danio rerio; RNA Seq GSM2696327   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696327 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.B08.bam bam 142205131.0 1893127.0 GSM2696327 r1 0:37.56 1:37.56 A:37131753;C:34113884;G:33438831;T:37487774;N:32889 37 37     37131753 34113884 33438831 37487774 32889 SRX2989460 SRS2341383 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.89693 0.89889 0.10925 0.10945 0.94369 0.94424 0.50241 0.50502 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42651 42651 SRR5810907 SRX2989459 SRS2341382 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.B05 GSM2696326   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.B05 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696326 GSM2696326: Runx123 GFP.P1.B05; Danio rerio; RNA Seq GSM2696326   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696326 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.B05.bam bam 126983826.0 1690889.0 GSM2696326 r1 0:37.55 1:37.55 A:33026361;C:30589990;G:30037590;T:33298071;N:31814 37 37     33026361 30589990 30037590 33298071 31814 SRX2989459 SRS2341382 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.89076 0.89215 0.06876 0.06832 0.94554 0.94681 0.47848 0.46333 38 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42652 42652 SRR5810906 SRX2989458 SRS2341381 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.B04 GSM2696325   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.B04 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696325 GSM2696325: Runx123 GFP.P1.B04; Danio rerio; RNA Seq GSM2696325   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696325 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.B04.bam bam 122544174.0 1630177.0 GSM2696325 r1 0:37.59 1:37.59 A:33125816;C:28259989;G:27509174;T:33626259;N:22936 37 37     33125816 28259989 27509174 33626259 22936 SRX2989458 SRS2341381 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91867 0.91774 0.16669 0.16691 0.95739 0.95816 0.46968 0.48233 37 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42653 42653 SRR5810905 SRX2989457 SRS2341380 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.B03 GSM2696324   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.B03 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696324 GSM2696324: Runx123 GFP.P1.B03; Danio rerio; RNA Seq GSM2696324   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696324 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.B03.bam bam 62836732.0 835736.0 GSM2696324 r1 0:37.59 1:37.59 A:17345816;C:14088789;G:13765145;T:17625439;N:11543 37 37     17345816 14088789 13765145 17625439 11543 SRX2989457 SRS2341380 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91135 0.91164 0.22828 0.23 0.95657 0.95799 0.48254 0.48557 37 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42654 42654 SRR5810904 SRX2989456 SRS2341379 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.B02 GSM2696323   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.B02 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696323 GSM2696323: Runx123 GFP.P1.B02; Danio rerio; RNA Seq GSM2696323   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696323 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.B02.bam bam 55579726.0 739325.0 GSM2696323 r1 0:37.59 1:37.59 A:15158695;C:12732111;G:12337350;T:15341128;N:10442 37 37     15158695 12732111 12337350 15341128 10442 SRX2989456 SRS2341379 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.9206 0.92564 0.12141 0.12123 0.932 0.93261 0.52491 0.53084 36 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42655 42655 SRR5810903 SRX2989455 SRS2341378 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.B01 GSM2696322   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.B01 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696322 GSM2696322: Runx123 GFP.P1.B01; Danio rerio; RNA Seq GSM2696322   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696322 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.B01.bam bam 97175306.0 1292997.0 GSM2696322 r1 0:37.58 1:37.58 A:25961006;C:22751707;G:22103012;T:26340740;N:18841 37 37     25961006 22751707 22103012 26340740 18841 SRX2989455 SRS2341378 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91993 0.92006 0.1164 0.11549 0.94077 0.94194 0.52856 0.52534 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42656 42656 SRR5810902 SRX2989454 SRS2341376 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.A11 GSM2696321   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.A11 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696321 GSM2696321: Runx123 GFP.P1.A11; Danio rerio; RNA Seq GSM2696321   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696321 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.A11.bam bam 55671938.0 740250.0 GSM2696321 r1 0:37.60 1:37.60 A:15655840;C:12190990;G:11931748;T:15883734;N:9626 37 37     15655840 12190990 11931748 15883734 9626 SRX2989454 SRS2341376 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.90289 0.90262 0.32668 0.32572 0.97074 0.97086 0.5031 0.51683 38 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42657 42657 SRR5810901 SRX2989453 SRS2341377 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.A09 GSM2696320   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.A09 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696320 GSM2696320: Runx123 GFP.P1.A09; Danio rerio; RNA Seq GSM2696320   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696320 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.A09.bam bam 179417367.0 2387224.0 GSM2696320 r1 0:37.58 1:37.58 A:48292938;C:41636027;G:40587884;T:48866235;N:34283 37 37     48292938 41636027 40587884 48866235 34283 SRX2989453 SRS2341377 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.92302 0.92326 0.13644 0.13752 0.94779 0.94862 0.48378 0.49265 38 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42658 42658 SRR5810900 SRX2989452 SRS2341375 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.A08 GSM2696319   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.A08 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696319 GSM2696319: Runx123 GFP.P1.A08; Danio rerio; RNA Seq GSM2696319   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696319 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.A08.bam bam 159126189.0 2117119.0 GSM2696319 r1 0:37.58 1:37.58 A:43149278;C:36645757;G:35730147;T:43570177;N:30830 37 37     43149278 36645757 35730147 43570177 30830 SRX2989452 SRS2341375 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91867 0.91766 0.14618 0.14712 0.96019 0.96187 0.48834 0.4962 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42659 42659 SRR5810899 SRX2989451 SRS2341374 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.A07 GSM2696318   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.A07 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696318 GSM2696318: Runx123 GFP.P1.A07; Danio rerio; RNA Seq GSM2696318   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696318 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.A07.bam bam 58771551.0 781510.0 GSM2696318 r1 0:37.60 1:37.60 A:16473933;C:12912665;G:12629036;T:16745570;N:10347 37 37     16473933 12912665 12629036 16745570 10347 SRX2989451 SRS2341374 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.90899 0.90998 0.27862 0.27924 0.98504 0.98608 0.45606 0.46747 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42660 42660 SRR5810898 SRX2989450 SRS2341373 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.A06 GSM2696317   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.A06 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696317 GSM2696317: Runx123 GFP.P1.A06; Danio rerio; RNA Seq GSM2696317   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696317 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.A06.bam bam 140233110.0 1865323.0 GSM2696317 r1 0:37.59 1:37.59 A:38560492;C:31737880;G:30971443;T:38937194;N:26101 37 37     38560492 31737880 30971443 38937194 26101 SRX2989450 SRS2341373 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91848 0.91824 0.23265 0.23216 0.97262 0.9726 0.48014 0.48002 37 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42661 42661 SRR5810897 SRX2989449 SRS2341372 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.A05 GSM2696316   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.A05 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696316 GSM2696316: Runx123 GFP.P1.A05; Danio rerio; RNA Seq GSM2696316   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696316 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.A05.bam bam 124170196.0 1651790.0 GSM2696316 r1 0:37.59 1:37.59 A:34062267;C:28219948;G:27555733;T:34308702;N:23546 37 37     34062267 28219948 27555733 34308702 23546 SRX2989449 SRS2341372 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.9207 0.9201 0.17897 0.17898 0.95455 0.9553 0.49553 0.49608 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42662 42662 SRR5810896 SRX2989448 SRS2341371 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.A04 GSM2696315   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.A04 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696315 GSM2696315: Runx123 GFP.P1.A04; Danio rerio; RNA Seq GSM2696315   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696315 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.A04.bam bam 150251742.0 1999217.0 GSM2696315 r1 0:37.58 1:37.58 A:40047183;C:35282116;G:34306907;T:40586886;N:28650 37 37     40047183 35282116 34306907 40586886 28650 SRX2989448 SRS2341371 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.92398 0.92406 0.13217 0.1313 0.94414 0.9447 0.50222 0.50658 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42663 42663 SRR5810895 SRX2989447 SRS2341369 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.A03 GSM2696314   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.A03 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696314 GSM2696314: Runx123 GFP.P1.A03; Danio rerio; RNA Seq GSM2696314   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696314 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.A03.bam bam 102838133.0 1368212.0 GSM2696314 r1 0:37.58 1:37.58 A:27916613;C:23679845;G:23064232;T:28156982;N:20461 37 37     27916613 23679845 23064232 28156982 20461 SRX2989447 SRS2341369 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.92121 0.92192 0.12738 0.12845 0.94838 0.94909 0.48807 0.49988 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42664 42664 SRR5810894 SRX2989446 SRS2341370 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.A02 GSM2696313   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.A02 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696313 GSM2696313: Runx123 GFP.P1.A02; Danio rerio; RNA Seq GSM2696313   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696313 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.A02.bam bam 37280197.0 495818.0 GSM2696313 r1 0:37.59 1:37.60 A:10319799;C:8371049;G:8123905;T:10458151;N:7293 37 37     10319799 8371049 8123905 10458151 7293 SRX2989446 SRS2341370 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.913 0.91779 0.17824 0.17822 0.96495 0.96611 0.51175 0.51518 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42665 42665 SRR5810893 SRX2989445 SRS2341368 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   Runx123 GFP.P1.A01 GSM2696312   source name:whole kidney marrow|tissue:kidney marrow Runx123 GFP.P1.A01 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696312 GSM2696312: Runx123 GFP.P1.A01; Danio rerio; RNA Seq GSM2696312   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696312 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     Runx123_GFP.P1.A01.bam bam 75636367.0 1006419.0 GSM2696312 r1 0:37.58 1:37.58 A:20057115;C:17816438;G:17336922;T:20410910;N:14982 37 37     20057115 17816438 17336922 20410910 14982 SRX2989445 SRS2341368 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.92197 0.92171 0.13753 0.13713 0.94767 0.94823 0.52196 0.51719 38 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42666 42666 SRR5810892 SRX2989444 SRS2341366 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   rag2 GFP.P2.D12 GSM2696311   source name:whole kidney marrow|tissue:kidney marrow rag2 GFP.P2.D12 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696311 GSM2696311: rag2 GFP.P2.D12; Danio rerio; RNA Seq GSM2696311   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696311 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     rag2_GFP.P2.D12.bam bam 18336287.0 243806.0 GSM2696311 r1 0:37.61 1:37.60 A:5238158;C:3941841;G:3849809;T:5303266;N:3213 37 37     5238158 3941841 3849809 5303266 3213 SRX2989444 SRS2341366 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.90498 0.90585 0.28323 0.28433 0.98031 0.98086 0.47103 0.45526 37 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42667 42667 SRR5810891 SRX2989443 SRS2341367 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   rag2 GFP.P2.D11 GSM2696310   source name:whole kidney marrow|tissue:kidney marrow rag2 GFP.P2.D11 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696310 GSM2696310: rag2 GFP.P2.D11; Danio rerio; RNA Seq GSM2696310   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696310 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     rag2_GFP.P2.D11.bam bam 105860026.0 1408098.0 GSM2696310 r1 0:37.59 1:37.59 A:29590883;C:23482079;G:22917678;T:29849840;N:19546 37 37     29590883 23482079 22917678 29849840 19546 SRX2989443 SRS2341367 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91232 0.91086 0.21168 0.21274 0.97686 0.97761 0.50363 0.49791 38 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42668 42668 SRR5810890 SRX2989442 SRS2341365 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   rag2 GFP.P2.D10 GSM2696309   source name:whole kidney marrow|tissue:kidney marrow rag2 GFP.P2.D10 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696309 GSM2696309: rag2 GFP.P2.D10; Danio rerio; RNA Seq GSM2696309   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696309 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     rag2_GFP.P2.D10.bam bam 113396448.0 1508550.0 GSM2696309 r1 0:37.58 1:37.59 A:31048855;C:25782613;G:25159308;T:31385416;N:20256 37 37     31048855 25782613 25159308 31385416 20256 SRX2989442 SRS2341365 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.9238 0.92418 0.17217 0.17365 0.97926 0.97964 0.47951 0.47658 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42669 42669 SRR5810889 SRX2989441 SRS2341363 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   rag2 GFP.P2.D09 GSM2696308   source name:whole kidney marrow|tissue:kidney marrow rag2 GFP.P2.D09 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696308 GSM2696308: rag2 GFP.P2.D09; Danio rerio; RNA Seq GSM2696308   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696308 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     rag2_GFP.P2.D09.bam bam 79322046.0 1054999.0 GSM2696308 r1 0:37.59 1:37.59 A:22150256;C:17580460;G:17121788;T:22454972;N:14570 37 37     22150256 17580460 17121788 22454972 14570 SRX2989441 SRS2341363 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91629 0.91611 0.24413 0.24557 0.98319 0.98411 0.45659 0.46601 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42670 42670 SRR5810888 SRX2989440 SRS2341364 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   rag2 GFP.P2.D08 GSM2696307   source name:whole kidney marrow|tissue:kidney marrow rag2 GFP.P2.D08 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696307 GSM2696307: rag2 GFP.P2.D08; Danio rerio; RNA Seq GSM2696307   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696307 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     rag2_GFP.P2.D08.bam bam 97315108.0 1293526.0 GSM2696307 r1 0:37.61 1:37.62 A:28277708;C:20425852;G:20047156;T:28548795;N:15597 37 37     28277708 20425852 20047156 28548795 15597 SRX2989440 SRS2341364 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.88795 0.88723 0.3754 0.37563 0.9627 0.96319 0.5016 0.50183 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42671 42671 SRR5810887 SRX2989439 SRS2341362 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   rag2 GFP.P2.D07 GSM2696306   source name:whole kidney marrow|tissue:kidney marrow rag2 GFP.P2.D07 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696306 GSM2696306: rag2 GFP.P2.D07; Danio rerio; RNA Seq GSM2696306   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696306 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     rag2_GFP.P2.D07.bam bam 25814611.0 343345.0 GSM2696306 r1 0:37.59 1:37.59 A:7160379;C:5767559;G:5618492;T:7263400;N:4781 37 37     7160379 5767559 5618492 7263400 4781 SRX2989439 SRS2341362 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91094 0.91044 0.23203 0.23267 0.98161 0.982 0.5025 0.4792 37 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42672 42672 SRR5810886 SRX2989438 SRS2341361 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   rag2 GFP.P2.D06 GSM2696305   source name:whole kidney marrow|tissue:kidney marrow rag2 GFP.P2.D06 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696305 GSM2696305: rag2 GFP.P2.D06; Danio rerio; RNA Seq GSM2696305   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696305 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     rag2_GFP.P2.D06.bam bam 141381372.0 1880842.0 GSM2696305 r1 0:37.58 1:37.58 A:38780204;C:32095151;G:31245396;T:39233572;N:27049 37 37     38780204 32095151 31245396 39233572 27049 SRX2989438 SRS2341361 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91983 0.91897 0.15478 0.15471 0.9666 0.96773 0.47909 0.4824 37 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42673 42673 SRR5810885 SRX2989437 SRS2341360 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   rag2 GFP.P2.D05 GSM2696304   source name:whole kidney marrow|tissue:kidney marrow rag2 GFP.P2.D05 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696304 GSM2696304: rag2 GFP.P2.D05; Danio rerio; RNA Seq GSM2696304   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696304 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     rag2_GFP.P2.D05.bam bam 15226605.0 202462.0 GSM2696304 r1 0:37.60 1:37.61 A:4335596;C:3292087;G:3205961;T:4390270;N:2691 37 37     4335596 3292087 3205961 4390270 2691 SRX2989437 SRS2341360 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91107 0.91265 0.25537 0.25586 0.98443 0.98581 0.4967 0.48642 38 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42674 42674 SRR5810884 SRX2989436 SRS2341359 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   rag2 GFP.P2.D04 GSM2696303   source name:whole kidney marrow|tissue:kidney marrow rag2 GFP.P2.D04 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696303 GSM2696303: rag2 GFP.P2.D04; Danio rerio; RNA Seq GSM2696303   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696303 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     rag2_GFP.P2.D04.bam bam 106079832.0 1411328.0 GSM2696303 r1 0:37.58 1:37.58 A:28894435;C:24306423;G:23644014;T:29214896;N:20064 37 37     28894435 24306423 23644014 29214896 20064 SRX2989436 SRS2341359 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.9227 0.92237 0.13726 0.13735 0.9553 0.95647 0.49331 0.49947 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42675 42675 SRR5810883 SRX2989435 SRS2341358 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   rag2 GFP.P2.D03 GSM2696302   source name:whole kidney marrow|tissue:kidney marrow rag2 GFP.P2.D03 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696302 GSM2696302: rag2 GFP.P2.D03; Danio rerio; RNA Seq GSM2696302   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696302 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     rag2_GFP.P2.D03.bam bam 21289941.0 283156.0 GSM2696302 r1 0:37.59 1:37.59 A:5938700;C:4726083;G:4610632;T:6010768;N:3758 37 37     5938700 4726083 4610632 6010768 3758 SRX2989435 SRS2341358 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91069 0.911 0.20523 0.20574 0.9825 0.98267 0.52786 0.52592 37 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42676 42676 SRR5810882 SRX2989434 SRS2341356 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   rag2 GFP.P2.D02 GSM2696301   source name:whole kidney marrow|tissue:kidney marrow rag2 GFP.P2.D02 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696301 GSM2696301: rag2 GFP.P2.D02; Danio rerio; RNA Seq GSM2696301   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696301 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     rag2_GFP.P2.D02.bam bam 130831699.0 1740981.0 GSM2696301 r1 0:37.57 1:37.58 A:35439280;C:30110780;G:29373364;T:35882908;N:25367 37 37     35439280 30110780 29373364 35882908 25367 SRX2989434 SRS2341356 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91951 0.91958 0.07134 0.07239 0.95982 0.96035 0.47198 0.46193 36 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42677 42677 SRR5810881 SRX2989433 SRS2341357 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   rag2 GFP.P2.D01 GSM2696300   source name:whole kidney marrow|tissue:kidney marrow rag2 GFP.P2.D01 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696300 GSM2696300: rag2 GFP.P2.D01; Danio rerio; RNA Seq GSM2696300   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696300 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     rag2_GFP.P2.D01.bam bam 72216876.0 960467.0 GSM2696300 r1 0:37.59 1:37.60 A:20300075;C:15865991;G:15492398;T:20545211;N:13201 37 37     20300075 15865991 15492398 20545211 13201 SRX2989433 SRS2341357 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91121 0.91013 0.25023 0.25089 0.98413 0.98386 0.5025 0.50723 37 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42678 42678 SRR5810880 SRX2989432 SRS2341355 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   rag2 GFP.P2.C12 GSM2696299   source name:whole kidney marrow|tissue:kidney marrow rag2 GFP.P2.C12 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696299 GSM2696299: rag2 GFP.P2.C12; Danio rerio; RNA Seq GSM2696299   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696299 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     rag2_GFP.P2.C12.bam bam 22373523.0 297634.0 GSM2696299 r1 0:37.59 1:37.59 A:6088784;C:5104577;G:4981100;T:6194997;N:4065 37 37     6088784 5104577 4981100 6194997 4065 SRX2989432 SRS2341355 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91311 0.91533 0.20964 0.21002 0.9792 0.97928 0.4834 0.47212 38 37 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System
42679 42679 SRR5810879 SRX2989431 SRS2341354 SRP111340 PRJNA393431 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq] GSE100911 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   rag2 GFP.P2.C11 GSM2696298   source name:whole kidney marrow|tissue:kidney marrow rag2 GFP.P2.C11 Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts whole kidney marrow   Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.   tissue:kidney marrow GSM2696298 GSM2696298: rag2 GFP.P2.C11; Danio rerio; RNA Seq GSM2696298   1 Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in 80°C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. GEO Accession:GSM2696298 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP111340     rag2_GFP.P2.C11.bam bam 78810745.0 1048392.0 GSM2696298 r1 0:37.59 1:37.59 A:21634279;C:17846551;G:17407357;T:21908404;N:14154 37 37     21634279 17846551 17407357 21908404 14154 SRX2989431 SRS2341354 SRA584588 GEO Pathology, Massachusetts General Hospital 2 0.91212 0.91267 0.21149 0.21231 0.978 0.97786 0.48227 0.47875 38 38 B B biological fallback assumption illumina nextseq full_length random_priming unknown sc single_cell_plate smartseq   United States 2017-07-07 Undetermined Adult Kidney Renal System

Next page

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;