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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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
47861,SRR6908751,SRX3856810,SRS3100403,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM9 unenriched,GSM3070148,,tissue:WKM9 unenriched|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM9 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM9 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070148,GSM3070148: WKM9 unenriched; Danio rerio; RNA Seq,GSM3070148,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070148,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_unenriched_L001_R1_001.fastq.gz WKM9_unenriched_L001_R2_001.fastq.gz,fastq fastq,1346805481.0,8925729.0,GSM3070148 r1,0:75.41 1:75.48,A:389424098;C:209314278;G:233588167;T:514471922;N:7016,75,75,,,389424098,209314278,233588167,514471922,7016,SRX3856810,SRS3100403,SRA675960,GEO,Hubrecht Institute,2,0.43527,0.79133,0.35777,0.52091,0.95361,0.87156,0.48343,0.54164,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47862,SRR6908752,SRX3856810,SRS3100403,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM9 unenriched,GSM3070148,,tissue:WKM9 unenriched|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM9 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM9 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070148,GSM3070148: WKM9 unenriched; Danio rerio; RNA Seq,GSM3070148,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070148,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_unenriched_L002_R1_001.fastq.gz WKM9_unenriched_L002_R2_001.fastq.gz,fastq fastq,1325332076.0,8783303.0,GSM3070148 r2,0:75.41 1:75.48,A:380077587;C:204687058;G:234896688;T:505666915;N:3828,75,75,,,380077587,204687058,234896688,505666915,3828,SRX3856810,SRS3100403,SRA675960,GEO,Hubrecht Institute,2,0.42931,0.78191,0.35315,0.51028,0.95787,0.87493,0.49522,0.49685,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47863,SRR6908753,SRX3856810,SRS3100403,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM9 unenriched,GSM3070148,,tissue:WKM9 unenriched|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM9 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM9 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070148,GSM3070148: WKM9 unenriched; Danio rerio; RNA Seq,GSM3070148,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070148,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_unenriched_L003_R1_001.fastq.gz WKM9_unenriched_L003_R2_001.fastq.gz,fastq fastq,1209174922.0,8013226.0,GSM3070148 r3,0:75.42 1:75.47,A:347525516;C:187142186;G:212384943;T:462099359;N:22918,75,75,,,347525516,187142186,212384943,462099359,22918,SRX3856810,SRS3100403,SRA675960,GEO,Hubrecht Institute,2,0.4232,0.78709,0.34991,0.51583,0.9614,0.88215,0.50753,0.49857,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47864,SRR6908754,SRX3856810,SRS3100403,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM9 unenriched,GSM3070148,,tissue:WKM9 unenriched|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM9 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM9 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070148,GSM3070148: WKM9 unenriched; Danio rerio; RNA Seq,GSM3070148,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070148,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_unenriched_L004_R1_001.fastq.gz WKM9_unenriched_L004_R2_001.fastq.gz,fastq fastq,1177710986.0,7804805.0,GSM3070148 r4,0:75.42 1:75.47,A:337640779;C:180611864;G:209653010;T:449785638;N:19695,75,75,,,337640779,180611864,209653010,449785638,19695,SRX3856810,SRS3100403,SRA675960,GEO,Hubrecht Institute,2,0.42938,0.78452,0.35813,0.51351,0.96435,0.89035,0.46765,0.55409,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47865,SRR6908747,SRX3856809,SRS3100401,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM9 monocytes,GSM3070147,,tissue:WKM9 monocytes|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes,WKM9 monocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM9 monocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070147,GSM3070147: WKM9 monocytes; Danio rerio; RNA Seq,GSM3070147,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070147,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_monocytes_L001_R1_001.fastq.gz WKM9_monocytes_L001_R2_001.fastq.gz,fastq fastq,1661471905.0,11011987.0,GSM3070147 r1,0:75.40 1:75.48,A:483808436;C:239092096;G:277634836;T:660929005;N:7532,75,75,,,483808436,239092096,277634836,660929005,7532,SRX3856809,SRS3100401,SRA675960,GEO,Hubrecht Institute,2,0.36065,0.81129,0.26031,0.39596,0.96376,0.87584,0.46482,0.51218,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47866,SRR6908748,SRX3856809,SRS3100401,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM9 monocytes,GSM3070147,,tissue:WKM9 monocytes|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes,WKM9 monocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM9 monocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070147,GSM3070147: WKM9 monocytes; Danio rerio; RNA Seq,GSM3070147,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070147,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_monocytes_L002_R1_001.fastq.gz WKM9_monocytes_L002_R2_001.fastq.gz,fastq fastq,1643858405.0,10895074.0,GSM3070147 r2,0:75.40 1:75.48,A:474610672;C:235181134;G:281183851;T:652878617;N:4131,75,75,,,474610672,235181134,281183851,652878617,4131,SRX3856809,SRS3100401,SRA675960,GEO,Hubrecht Institute,2,0.35844,0.80892,0.26121,0.38966,0.96631,0.88008,0.45688,0.49263,74,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47867,SRR6908749,SRX3856809,SRS3100401,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM9 monocytes,GSM3070147,,tissue:WKM9 monocytes|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes,WKM9 monocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM9 monocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070147,GSM3070147: WKM9 monocytes; Danio rerio; RNA Seq,GSM3070147,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070147,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_monocytes_L003_R1_001.fastq.gz WKM9_monocytes_L003_R2_001.fastq.gz,fastq fastq,1503593728.0,9965072.0,GSM3070147 r3,0:75.41 1:75.48,A:435191543;C:215315484;G:255248972;T:597807800;N:29929,75,75,,,435191543,215315484,255248972,597807800,29929,SRX3856809,SRS3100401,SRA675960,GEO,Hubrecht Institute,2,0.3504,0.80674,0.25495,0.3888,0.96974,0.88402,0.4596,0.50684,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47868,SRR6908750,SRX3856809,SRS3100401,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM9 monocytes,GSM3070147,,tissue:WKM9 monocytes|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes,WKM9 monocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM9 monocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070147,GSM3070147: WKM9 monocytes; Danio rerio; RNA Seq,GSM3070147,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070147,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_monocytes_L004_R1_001.fastq.gz WKM9_monocytes_L004_R2_001.fastq.gz,fastq fastq,1474164037.0,9770113.0,GSM3070147 r4,0:75.41 1:75.48,A:425654229;C:209255453;G:253849148;T:585380972;N:24235,75,75,,,425654229,209255453,253849148,585380972,24235,SRX3856809,SRS3100401,SRA675960,GEO,Hubrecht Institute,2,0.36215,0.81922,0.26584,0.39594,0.97096,0.89171,0.46223,0.51731,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47873,SRR6908739,SRX3856807,SRS3100399,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM8 unenriched,GSM3070145,,tissue:WKM8 unenriched|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM8 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM8 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070145,GSM3070145: WKM8 unenriched; Danio rerio; RNA Seq,GSM3070145,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070145,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM8_unenriched_L001_R1_001.fastq.gz WKM8_unenriched_L001_R2_001.fastq.gz,fastq fastq,1667087336.0,11048469.0,GSM3070145 r1,0:75.40 1:75.49,A:475560256;C:240713376;G:276116899;T:674689422;N:7383,75,75,,,475560256,240713376,276116899,674689422,7383,SRX3856807,SRS3100399,SRA675960,GEO,Hubrecht Institute,2,0.39157,0.8295,0.26694,0.3429,0.95806,0.85117,0.47471,0.5079,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47874,SRR6908740,SRX3856807,SRS3100399,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM8 unenriched,GSM3070145,,tissue:WKM8 unenriched|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM8 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM8 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070145,GSM3070145: WKM8 unenriched; Danio rerio; RNA Seq,GSM3070145,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070145,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM8_unenriched_L002_R1_001.fastq.gz WKM8_unenriched_L002_R2_001.fastq.gz,fastq fastq,1643985440.0,10895186.0,GSM3070145 r2,0:75.40 1:75.49,A:465022994;C:236298663;G:278363355;T:664296206;N:4222,75,75,,,465022994,236298663,278363355,664296206,4222,SRX3856807,SRS3100399,SRA675960,GEO,Hubrecht Institute,2,0.38307,0.82794,0.26079,0.33908,0.95966,0.85573,0.47886,0.53225,76,74,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47875,SRR6908741,SRX3856807,SRS3100399,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM8 unenriched,GSM3070145,,tissue:WKM8 unenriched|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM8 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM8 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070145,GSM3070145: WKM8 unenriched; Danio rerio; RNA Seq,GSM3070145,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070145,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM8_unenriched_L003_R1_001.fastq.gz WKM8_unenriched_L003_R2_001.fastq.gz,fastq fastq,1497995831.0,9927192.0,GSM3070145 r3,0:75.41 1:75.48,A:423994108;C:216014805;G:251009522;T:606949772;N:27624,75,75,,,423994108,216014805,251009522,606949772,27624,SRX3856807,SRS3100399,SRA675960,GEO,Hubrecht Institute,2,0.37662,0.82297,0.26009,0.33859,0.96382,0.8616,0.4713,0.53853,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47876,SRR6908742,SRX3856807,SRS3100399,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM8 unenriched,GSM3070145,,tissue:WKM8 unenriched|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM8 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM8 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070145,GSM3070145: WKM8 unenriched; Danio rerio; RNA Seq,GSM3070145,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070145,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM8_unenriched_L004_R1_001.fastq.gz WKM8_unenriched_L004_R2_001.fastq.gz,fastq fastq,1462948321.0,9695189.0,GSM3070145 r4,0:75.41 1:75.48,A:413526172;C:209432303;G:247960945;T:592005236;N:23665,75,75,,,413526172,209432303,247960945,592005236,23665,SRX3856807,SRS3100399,SRA675960,GEO,Hubrecht Institute,2,0.39195,0.83802,0.26623,0.34329,0.96301,0.86659,0.47028,0.53168,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47877,SRR6908735,SRX3856806,SRS3100398,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM8 monocytes,GSM3070144,,tissue:WKM8 monocytes|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes,WKM8 monocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM8 monocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070144,GSM3070144: WKM8 monocytes; Danio rerio; RNA Seq,GSM3070144,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070144,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM8_monocytes_L001_R1_001.fastq.gz WKM8_monocytes_L001_R2_001.fastq.gz,fastq fastq,930630033.0,6164203.0,GSM3070144 r1,0:75.50 1:75.47,A:258982746;C:129522885;G:148763386;T:393303395;N:57621,75,75,,,258982746,129522885,148763386,393303395,57621,SRX3856806,SRS3100398,SRA675960,GEO,Hubrecht Institute,2,0.32023,0.84288,0.2067,0.29948,0.98628,0.9247,0.4816,0.56903,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47878,SRR6908736,SRX3856806,SRS3100398,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM8 monocytes,GSM3070144,,tissue:WKM8 monocytes|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes,WKM8 monocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM8 monocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070144,GSM3070144: WKM8 monocytes; Danio rerio; RNA Seq,GSM3070144,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070144,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM8_monocytes_L002_R1_001.fastq.gz WKM8_monocytes_L002_R2_001.fastq.gz,fastq fastq,840139689.0,5565664.0,GSM3070144 r2,0:75.50 1:75.45,A:236179715;C:116541374;G:133572472;T:353806731;N:39397,75,75,,,236179715,116541374,133572472,353806731,39397,SRX3856806,SRS3100398,SRA675960,GEO,Hubrecht Institute,2,0.28608,0.81641,0.18643,0.30235,0.99159,0.94799,0.46036,0.51728,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47879,SRR6908737,SRX3856806,SRS3100398,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM8 monocytes,GSM3070144,,tissue:WKM8 monocytes|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes,WKM8 monocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM8 monocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070144,GSM3070144: WKM8 monocytes; Danio rerio; RNA Seq,GSM3070144,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070144,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM8_monocytes_L003_R2_001.fastq.gz WKM8_monocytes_L003_R1_001.fastq.gz,fastq fastq,829094700.0,5491203.0,GSM3070144 r3,0:75.52 1:75.47,A:229473245;C:115123563;G:132541877;T:351944469;N:11546,75,75,,,229473245,115123563,132541877,351944469,11546,SRX3856806,SRS3100398,SRA675960,GEO,Hubrecht Institute,2,0.27624,0.83541,0.18571,0.30162,0.99358,0.93693,0.46624,0.58337,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47880,SRR6908738,SRX3856806,SRS3100398,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM8 monocytes,GSM3070144,,tissue:WKM8 monocytes|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes,WKM8 monocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM8 monocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070144,GSM3070144: WKM8 monocytes; Danio rerio; RNA Seq,GSM3070144,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070144,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM8_monocytes_L004_R1_001.fastq.gz WKM8_monocytes_L004_R2_001.fastq.gz,fastq fastq,717316840.0,4751642.0,GSM3070144 r4,0:75.51 1:75.45,A:201002776;C:99055550;G:115888860;T:301362855;N:6799,75,75,,,201002776,99055550,115888860,301362855,6799,SRX3856806,SRS3100398,SRA675960,GEO,Hubrecht Institute,2,0.24919,0.82101,0.16961,0.29185,0.99543,0.94882,0.43582,0.58134,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47885,SRR6908727,SRX3856804,SRS3100396,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM7 unenriched,GSM3070142,,tissue:WKM7 unenriched|FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM7 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM7 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070142,GSM3070142: WKM7 unenriched; Danio rerio; RNA Seq,GSM3070142,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070142,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM7_unenriched_L001_R1_001.fastq.gz WKM7_unenriched_L001_R2_001.fastq.gz,fastq fastq,1470115941.0,9738991.0,GSM3070142 r1,0:75.44 1:75.51,A:398948568;C:202294647;G:231760451;T:636827163;N:285112,75,75,,,398948568,202294647,231760451,636827163,285112,SRX3856804,SRS3100396,SRA675960,GEO,Hubrecht Institute,2,0.40309,0.87046,0.32221,0.26166,0.99233,0.84327,0.29642,0.52123,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47886,SRR6908728,SRX3856804,SRS3100396,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM7 unenriched,GSM3070142,,tissue:WKM7 unenriched|FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM7 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM7 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070142,GSM3070142: WKM7 unenriched; Danio rerio; RNA Seq,GSM3070142,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070142,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM7_unenriched_L002_R1_001.fastq.gz WKM7_unenriched_L002_R2_001.fastq.gz,fastq fastq,1461695240.0,9683144.0,GSM3070142 r2,0:75.44 1:75.51,A:394008699;C:201030493;G:233919014;T:632480364;N:256670,75,75,,,394008699,201030493,233919014,632480364,256670,SRX3856804,SRS3100396,SRA675960,GEO,Hubrecht Institute,2,0.38758,0.86795,0.30719,0.26558,0.99255,0.84607,0.30994,0.51718,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47887,SRR6908729,SRX3856804,SRS3100396,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM7 unenriched,GSM3070142,,tissue:WKM7 unenriched|FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM7 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM7 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070142,GSM3070142: WKM7 unenriched; Danio rerio; RNA Seq,GSM3070142,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070142,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM7_unenriched_L003_R1_001.fastq.gz WKM7_unenriched_L003_R2_001.fastq.gz,fastq fastq,1418045610.0,9393861.0,GSM3070142 r3,0:75.45 1:75.51,A:383399208;C:195487055;G:222663120;T:616484616;N:11611,75,75,,,383399208,195487055,222663120,616484616,11611,SRX3856804,SRS3100396,SRA675960,GEO,Hubrecht Institute,2,0.41019,0.87176,0.32985,0.2642,0.99338,0.8452,0.2589,0.52225,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47888,SRR6908730,SRX3856804,SRS3100396,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM7 unenriched,GSM3070142,,tissue:WKM7 unenriched|FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM7 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM7 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070142,GSM3070142: WKM7 unenriched; Danio rerio; RNA Seq,GSM3070142,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070142,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM7_unenriched_L004_R1_001.fastq.gz WKM7_unenriched_L004_R2_001.fastq.gz,fastq fastq,1401330195.0,9283131.0,GSM3070142 r4,0:75.44 1:75.51,A:376049927;C:192808560;G:224900456;T:607563117;N:8135,75,75,,,376049927,192808560,224900456,607563117,8135,SRX3856804,SRS3100396,SRA675960,GEO,Hubrecht Institute,2,0.40071,0.86588,0.31811,0.26185,0.99263,0.84569,0.27227,0.5224,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47889,SRR6908723,SRX3856803,SRS3100395,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM7 monocytes,GSM3070141,,tissue:WKM7 monocytes|FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes,WKM7 monocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM7 monocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070141,GSM3070141: WKM7 monocytes; Danio rerio; RNA Seq,GSM3070141,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070141,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM7_monocytes_L001_R1_001.fastq.gz WKM7_monocytes_L001_R2_001.fastq.gz,fastq fastq,1791125985.0,11864169.0,GSM3070141 r1,0:75.46 1:75.51,A:485867889;C:238293947;G:271424293;T:795194496;N:345360,75,75,,,485867889,238293947,271424293,795194496,345360,SRX3856803,SRS3100395,SRA675960,GEO,Hubrecht Institute,2,0.42246,0.87038,0.34993,0.25475,0.99302,0.86906,0.3,0.50725,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47890,SRR6908724,SRX3856803,SRS3100395,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM7 monocytes,GSM3070141,,tissue:WKM7 monocytes|FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes,WKM7 monocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM7 monocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070141,GSM3070141: WKM7 monocytes; Danio rerio; RNA Seq,GSM3070141,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070141,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM7_monocytes_L002_R1_001.fastq.gz WKM7_monocytes_L002_R2_001.fastq.gz,fastq fastq,1792721494.0,11874637.0,GSM3070141 r2,0:75.46 1:75.51,A:482977185;C:238180503;G:276068534;T:795172908;N:322364,75,75,,,482977185,238180503,276068534,795172908,322364,SRX3856803,SRS3100395,SRA675960,GEO,Hubrecht Institute,2,0.42187,0.86585,0.347,0.25727,0.99261,0.86983,0.32168,0.51044,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47891,SRR6908725,SRX3856803,SRS3100395,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM7 monocytes,GSM3070141,,tissue:WKM7 monocytes|FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes,WKM7 monocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM7 monocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070141,GSM3070141: WKM7 monocytes; Danio rerio; RNA Seq,GSM3070141,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070141,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM7_monocytes_L003_R1_001.fastq.gz WKM7_monocytes_L003_R2_001.fastq.gz,fastq fastq,1726273948.0,11434355.0,GSM3070141 r3,0:75.46 1:75.51,A:466721054;C:229970045;G:260445487;T:769123115;N:14247,75,75,,,466721054,229970045,260445487,769123115,14247,SRX3856803,SRS3100395,SRA675960,GEO,Hubrecht Institute,2,0.43817,0.86963,0.36713,0.25464,0.99409,0.87136,0.28011,0.50765,75,73,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47892,SRR6908726,SRX3856803,SRS3100395,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM7 monocytes,GSM3070141,,tissue:WKM7 monocytes|FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes,WKM7 monocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM7 monocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM7|cell type:whole kidney marrow single cells|cell subtype:monocytes,GSM3070141,GSM3070141: WKM7 monocytes; Danio rerio; RNA Seq,GSM3070141,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070141,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM7_monocytes_L004_R1_001.fastq.gz WKM7_monocytes_L004_R2_001.fastq.gz,fastq fastq,1706923699.0,11306267.0,GSM3070141 r4,0:75.46 1:75.51,A:458067525;C:226793433;G:263424046;T:758628361;N:10334,75,75,,,458067525,226793433,263424046,758628361,10334,SRX3856803,SRS3100395,SRA675960,GEO,Hubrecht Institute,2,0.42414,0.86508,0.34964,0.25009,0.99375,0.87198,0.28225,0.51467,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47893,SRR6908717,SRX3856802,SRS3100394,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM6 unenriched,GSM3070140,,tissue:WKM6 unenriched|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM6 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM6 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070140,GSM3070140: WKM6 unenriched; Danio rerio; RNA Seq,GSM3070140,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070140,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM6_unenriched_L001_R1_001.fastq.gz WKM6_unenriched_L001_R2_001.fastq.gz,fastq fastq,1091182818.0,7228537.0,GSM3070140 r1,0:75.49 1:75.46,A:305460604;C:155608830;G:177642198;T:452400520;N:70666,75,75,,,305460604,155608830,177642198,452400520,70666,SRX3856802,SRS3100394,SRA675960,GEO,Hubrecht Institute,2,0.32983,0.81725,0.21464,0.30328,0.98524,0.91348,0.47654,0.51388,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47894,SRR6908718,SRX3856802,SRS3100394,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM6 unenriched,GSM3070140,,tissue:WKM6 unenriched|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM6 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM6 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070140,GSM3070140: WKM6 unenriched; Danio rerio; RNA Seq,GSM3070140,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070140,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM6_unenriched_L002_R1_001.fastq.gz WKM6_unenriched_L002_R2_001.fastq.gz,fastq fastq,992904107.0,6578507.0,GSM3070140 r2,0:75.49 1:75.44,A:280993567;C:141013446;G:160470422;T:410379926;N:46746,75,75,,,280993567,141013446,160470422,410379926,46746,SRX3856802,SRS3100394,SRA675960,GEO,Hubrecht Institute,2,0.3103,0.79506,0.20764,0.30662,0.99076,0.94178,0.49304,0.53389,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47895,SRR6908720,SRX3856802,SRS3100394,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM6 unenriched,GSM3070140,,tissue:WKM6 unenriched|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM6 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM6 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070140,GSM3070140: WKM6 unenriched; Danio rerio; RNA Seq,GSM3070140,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070140,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM6_unenriched_L003_R1_001.fastq.gz WKM6_unenriched_L003_R2_001.fastq.gz,fastq fastq,967648040.0,6409722.0,GSM3070140 r3,0:75.51 1:75.46,A:269841606;C:137530059;G:157502274;T:402760480;N:13621,75,75,,,269841606,137530059,157502274,402760480,13621,SRX3856802,SRS3100394,SRA675960,GEO,Hubrecht Institute,2,0.304,0.80424,0.20488,0.29857,0.99383,0.92894,0.44008,0.5232,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47896,SRR6908722,SRX3856802,SRS3100394,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM6 unenriched,GSM3070140,,tissue:WKM6 unenriched|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM6 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM6 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070140,GSM3070140: WKM6 unenriched; Danio rerio; RNA Seq,GSM3070140,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070140,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM6_unenriched_L004_R1_001.fastq.gz WKM6_unenriched_L004_R2_001.fastq.gz,fastq fastq,843966623.0,5591352.0,GSM3070140 r4,0:75.50 1:75.44,A:238568640;C:119216971;G:138770810;T:347402234;N:7968,75,75,,,238568640,119216971,138770810,347402234,7968,SRX3856802,SRS3100394,SRA675960,GEO,Hubrecht Institute,2,0.28014,0.78908,0.18667,0.29821,0.99496,0.94424,0.46594,0.52932,75,72,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47901,SRR6908709,SRX3856800,SRS3100392,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM5 unenriched,GSM3070138,,tissue:WKM5 unenriched|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM5 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM5 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070138,GSM3070138: WKM5 unenriched; Danio rerio; RNA Seq,GSM3070138,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070138,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM5_unenriched_L001_R1_001.fastq.gz WKM5_unenriched_L001_R2_001.fastq.gz,fastq fastq,1616915014.0,10719306.0,GSM3070138 r1,0:75.41 1:75.43,A:470483106;C:225755405;G:263766190;T:656561040;N:349273,75,75,,,470483106,225755405,263766190,656561040,349273,SRX3856800,SRS3100392,SRA675960,GEO,Hubrecht Institute,2,0.10729,0.72403,0.07307,0.20274,0.99017,0.84524,0.5068,0.51693,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47902,SRR6908710,SRX3856800,SRS3100392,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM5 unenriched,GSM3070138,,tissue:WKM5 unenriched|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM5 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM5 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070138,GSM3070138: WKM5 unenriched; Danio rerio; RNA Seq,GSM3070138,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070138,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM5_unenriched_L002_R1_001.fastq.gz WKM5_unenriched_L002_R2_001.fastq.gz,fastq fastq,1573355252.0,10430670.0,GSM3070138 r2,0:75.40 1:75.44,A:458302389;C:217385315;G:261327273;T:636024406;N:315869,75,75,,,458302389,217385315,261327273,636024406,315869,SRX3856800,SRS3100392,SRA675960,GEO,Hubrecht Institute,2,0.11064,0.71559,0.07574,0.19872,0.98981,0.85005,0.45203,0.52838,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47903,SRR6908711,SRX3856800,SRS3100392,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM5 unenriched,GSM3070138,,tissue:WKM5 unenriched|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM5 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM5 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070138,GSM3070138: WKM5 unenriched; Danio rerio; RNA Seq,GSM3070138,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070138,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM5_unenriched_L003_R2_001.fastq.gz WKM5_unenriched_L003_R1_001.fastq.gz,fastq fastq,1566951274.0,10386628.0,GSM3070138 r3,0:75.42 1:75.44,A:451321309;C:220819392;G:256230144;T:638495895;N:84534,75,75,,,451321309,220819392,256230144,638495895,84534,SRX3856800,SRS3100392,SRA675960,GEO,Hubrecht Institute,2,0.10189,0.72988,0.07219,0.20488,0.99281,0.83899,0.46012,0.51971,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47904,SRR6908712,SRX3856800,SRS3100392,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM5 unenriched,GSM3070138,,tissue:WKM5 unenriched|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM5 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM5 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070138,GSM3070138: WKM5 unenriched; Danio rerio; RNA Seq,GSM3070138,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070138,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM5_unenriched_L004_R1_001.fastq.gz WKM5_unenriched_L004_R2_001.fastq.gz,fastq fastq,1470255063.0,9745929.0,GSM3070138 r4,0:75.41 1:75.45,A:425542718;C:206068561;G:242779977;T:595798063;N:65744,75,75,,,425542718,206068561,242779977,595798063,65744,SRX3856800,SRS3100392,SRA675960,GEO,Hubrecht Institute,2,0.10318,0.71368,0.07165,0.20008,0.99159,0.8508,0.46642,0.51043,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47909,SRR6908701,SRX3856798,SRS3100390,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM5 hspcs,GSM3070136,,tissue:WKM5 hspcs|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:hspcs,WKM5 hspcs,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM5 hspcs,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:hspcs,GSM3070136,GSM3070136: WKM5 hspcs; Danio rerio; RNA Seq,GSM3070136,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070136,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM5_hspcs_L001_R2_001.fastq.gz WKM5_hspcs_L001_R1_001.fastq.gz,fastq fastq,6064422368.0,40205564.0,GSM3070136 r1,0:75.42 1:75.41,A:1792101497;C:906329224;G:1061291018;T:2303411628;N:1289001,75,75,,,1792101497,906329224,1061291018,2303411628,1289001,SRX3856798,SRS3100390,SRA675960,GEO,Hubrecht Institute,2,0.07707,0.61908,0.04536,0.14979,0.98711,0.86186,0.54256,0.52115,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47910,SRR6908702,SRX3856798,SRS3100390,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM5 hspcs,GSM3070136,,tissue:WKM5 hspcs|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:hspcs,WKM5 hspcs,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM5 hspcs,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:hspcs,GSM3070136,GSM3070136: WKM5 hspcs; Danio rerio; RNA Seq,GSM3070136,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070136,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM5_hspcs_L002_R1_001.fastq.gz WKM5_hspcs_L002_R2_001.fastq.gz,fastq fastq,5921476240.0,39257421.0,GSM3070136 r2,0:75.41 1:75.43,A:1748991850;C:876000140;G:1055863619;T:2239402733;N:1217898,75,75,,,1748991850,876000140,1055863619,2239402733,1217898,SRX3856798,SRS3100390,SRA675960,GEO,Hubrecht Institute,2,0.08014,0.61413,0.04634,0.14581,0.98654,0.8717,0.51292,0.50066,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47911,SRR6908703,SRX3856798,SRS3100390,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM5 hspcs,GSM3070136,,tissue:WKM5 hspcs|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:hspcs,WKM5 hspcs,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM5 hspcs,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:hspcs,GSM3070136,GSM3070136: WKM5 hspcs; Danio rerio; RNA Seq,GSM3070136,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070136,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM5_hspcs_L003_R1_001.fastq.gz WKM5_hspcs_L003_R2_001.fastq.gz,fastq fastq,5866299339.0,38885339.0,GSM3070136 r3,0:75.43 1:75.43,A:1717556539;C:883848150;G:1028347614;T:2236229877;N:317159,75,75,,,1717556539,883848150,1028347614,2236229877,317159,SRX3856798,SRS3100390,SRA675960,GEO,Hubrecht Institute,2,0.06878,0.62531,0.04189,0.15336,0.99113,0.85888,0.5,0.51754,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47912,SRR6908704,SRX3856798,SRS3100390,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM5 hspcs,GSM3070136,,tissue:WKM5 hspcs|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:hspcs,WKM5 hspcs,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM5 hspcs,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:hspcs,GSM3070136,GSM3070136: WKM5 hspcs; Danio rerio; RNA Seq,GSM3070136,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070136,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM5_hspcs_L004_R1_001.fastq.gz WKM5_hspcs_L004_R2_001.fastq.gz,fastq fastq,5566177327.0,36895726.0,GSM3070136 r4,0:75.42 1:75.44,A:1631791302;C:834536884;G:988788873;T:2110815191;N:245077,75,75,,,1631791302,834536884,988788873,2110815191,245077,SRX3856798,SRS3100390,SRA675960,GEO,Hubrecht Institute,2,0.07494,0.61393,0.04705,0.14806,0.99032,0.87178,0.49704,0.51802,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47913,SRR6908697,SRX3856797,SRS3100389,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM4 unenriched,GSM3070135,,tissue:WKM4 unenriched|FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM4 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM4 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070135,GSM3070135: WKM4 unenriched; Danio rerio; RNA Seq,GSM3070135,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070135,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM4_unenriched_L001_R2_001.fastq.gz WKM4_unenriched_L001_R1_001.fastq.gz,fastq fastq,1000182622.0,6625590.0,GSM3070135 r1,0:75.50 1:75.46,A:281062086;C:163533727;G:177503446;T:378045390;N:37973,75,75,,,281062086,163533727,177503446,378045390,37973,SRX3856797,SRS3100389,SRA675960,GEO,Hubrecht Institute,2,0.32578,0.64735,0.27911,0.49563,0.94596,0.8396,0.51648,0.52037,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47914,SRR6908698,SRX3856797,SRS3100389,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM4 unenriched,GSM3070135,,tissue:WKM4 unenriched|FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM4 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM4 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070135,GSM3070135: WKM4 unenriched; Danio rerio; RNA Seq,GSM3070135,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070135,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM4_unenriched_L002_R2_001.fastq.gz WKM4_unenriched_L002_R1_001.fastq.gz,fastq fastq,1024598143.0,6787724.0,GSM3070135 r2,0:75.49 1:75.46,A:287879816;C:166711858;G:184760618;T:385194933;N:50918,75,75,,,287879816,166711858,184760618,385194933,50918,SRX3856797,SRS3100389,SRA675960,GEO,Hubrecht Institute,2,0.30906,0.63868,0.26505,0.49323,0.9498,0.84977,0.508,0.53041,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47915,SRR6908699,SRX3856797,SRS3100389,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM4 unenriched,GSM3070135,,tissue:WKM4 unenriched|FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM4 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM4 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070135,GSM3070135: WKM4 unenriched; Danio rerio; RNA Seq,GSM3070135,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070135,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM4_unenriched_L003_R2_001.fastq.gz WKM4_unenriched_L003_R1_001.fastq.gz,fastq fastq,987354885.0,6540694.0,GSM3070135 r3,0:75.50 1:75.46,A:277978811;C:161185677;G:175345183;T:372839184;N:6030,75,75,,,277978811,161185677,175345183,372839184,6030,SRX3856797,SRS3100389,SRA675960,GEO,Hubrecht Institute,2,0.32206,0.64379,0.27584,0.49734,0.94608,0.84764,0.51258,0.52761,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47916,SRR6908700,SRX3856797,SRS3100389,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM4 unenriched,GSM3070135,,tissue:WKM4 unenriched|FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM4 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM4 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070135,GSM3070135: WKM4 unenriched; Danio rerio; RNA Seq,GSM3070135,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070135,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM4_unenriched_L004_R1_001.fastq.gz WKM4_unenriched_L004_R2_001.fastq.gz,fastq fastq,1001846281.0,6636299.0,GSM3070135 r4,0:75.50 1:75.46,A:280586899;C:163214034;G:180353077;T:377687027;N:5244,75,75,,,280586899,163214034,180353077,377687027,5244,SRX3856797,SRS3100389,SRA675960,GEO,Hubrecht Institute,2,0.32088,0.64536,0.27364,0.4929,0.94663,0.84822,0.51406,0.53384,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47921,SRR6908689,SRX3856795,SRS3100387,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM3 unenriched,GSM3070133,,tissue:WKM3 unenriched|FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM3 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM3 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070133,GSM3070133: WKM3 unenriched; Danio rerio; RNA Seq,GSM3070133,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070133,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM3_unenriched_L001_R1_001.fastq.gz WKM3_unenriched_L001_R2_001.fastq.gz,fastq fastq,1418323523.0,9398733.0,GSM3070133 r1,0:75.43 1:75.47,A:422643558;C:211337836;G:207870633;T:576229967;N:241529,75,75,,,422643558,211337836,207870633,576229967,241529,SRX3856795,SRS3100387,SRA675960,GEO,Hubrecht Institute,2,0.38916,0.82774,0.31564,0.36709,0.96169,0.9177,0.50178,0.54487,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47922,SRR6908690,SRX3856795,SRS3100387,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM3 unenriched,GSM3070133,,tissue:WKM3 unenriched|FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM3 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM3 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070133,GSM3070133: WKM3 unenriched; Danio rerio; RNA Seq,GSM3070133,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070133,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM3_unenriched_L002_R1_001.fastq.gz WKM3_unenriched_L002_R2_001.fastq.gz,fastq fastq,1297380885.0,8597567.0,GSM3070133 r2,0:75.43 1:75.47,A:384413707;C:192495936;G:194053875;T:526229304;N:188063,75,75,,,384413707,192495936,194053875,526229304,188063,SRX3856795,SRS3100387,SRA675960,GEO,Hubrecht Institute,2,0.38661,0.82306,0.31693,0.35768,0.96171,0.92468,0.48342,0.54858,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47923,SRR6908691,SRX3856795,SRS3100387,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM3 unenriched,GSM3070133,,tissue:WKM3 unenriched|FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM3 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM3 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070133,GSM3070133: WKM3 unenriched; Danio rerio; RNA Seq,GSM3070133,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070133,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM3_unenriched_L003_R1_001.fastq.gz WKM3_unenriched_L003_R2_001.fastq.gz,fastq fastq,1470091205.0,9741084.0,GSM3070133 r3,0:75.44 1:75.48,A:432738050;C:218429286;G:217928653;T:600846627;N:148589,75,75,,,432738050,218429286,217928653,600846627,148589,SRX3856795,SRS3100387,SRA675960,GEO,Hubrecht Institute,2,0.39516,0.83773,0.32452,0.36027,0.96834,0.91662,0.49614,0.5268,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47924,SRR6908692,SRX3856795,SRS3100387,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM3 unenriched,GSM3070133,,tissue:WKM3 unenriched|FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM3 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM3 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070133,GSM3070133: WKM3 unenriched; Danio rerio; RNA Seq,GSM3070133,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070133,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM3_unenriched_L004_R1_001.fastq.gz WKM3_unenriched_L004_R2_001.fastq.gz,fastq fastq,1400378972.0,9280367.0,GSM3070133 r4,0:75.43 1:75.46,A:412590948;C:206892406;G:210433218;T:570347127;N:115273,75,75,,,412590948,206892406,210433218,570347127,115273,SRX3856795,SRS3100387,SRA675960,GEO,Hubrecht Institute,2,0.3812,0.82835,0.31027,0.35634,0.96889,0.93608,0.50533,0.53883,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47933,SRR6908677,SRX3856791,SRS3100383,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM2 unenriched,GSM3070130,,tissue:WKM2 unenriched|FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM2 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070130,GSM3070130: WKM2 unenriched; Danio rerio; RNA Seq,GSM3070130,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070130,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM2_unenriched_L001_R2_001.fastq.gz WKM2_unenriched_L001_R1_001.fastq.gz,fastq fastq,1050338787.0,6957998.0,GSM3070130 r1,0:75.46 1:75.50,A:307962198;C:162998859;G:159301612;T:419897804;N:178314,75,75,,,307962198,162998859,159301612,419897804,178314,SRX3856791,SRS3100383,SRA675960,GEO,Hubrecht Institute,2,0.40419,0.79829,0.34944,0.46358,0.95463,0.92715,0.5107,0.52123,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47934,SRR6908678,SRX3856791,SRS3100383,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM2 unenriched,GSM3070130,,tissue:WKM2 unenriched|FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM2 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070130,GSM3070130: WKM2 unenriched; Danio rerio; RNA Seq,GSM3070130,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070130,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM2_unenriched_L002_R1_001.fastq.gz WKM2_unenriched_L002_R2_001.fastq.gz,fastq fastq,954172584.0,6321045.0,GSM3070130 r2,0:75.45 1:75.50,A:277724691;C:147647025;G:148192193;T:380472896;N:135779,75,75,,,277724691,147647025,148192193,380472896,135779,SRX3856791,SRS3100383,SRA675960,GEO,Hubrecht Institute,2,0.40099,0.79668,0.34548,0.45475,0.95491,0.93168,0.512,0.51844,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47935,SRR6908679,SRX3856791,SRS3100383,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM2 unenriched,GSM3070130,,tissue:WKM2 unenriched|FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM2 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070130,GSM3070130: WKM2 unenriched; Danio rerio; RNA Seq,GSM3070130,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070130,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM2_unenriched_L003_R1_001.fastq.gz WKM2_unenriched_L003_R2_001.fastq.gz,fastq fastq,1095988368.0,7259975.0,GSM3070130 r3,0:75.47 1:75.50,A:318145632;C:169141931;G:167581935;T:441001916;N:116954,75,75,,,318145632,169141931,167581935,441001916,116954,SRX3856791,SRS3100383,SRA675960,GEO,Hubrecht Institute,2,0.4016,0.81167,0.34543,0.45854,0.96193,0.92427,0.51235,0.51464,76,74,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47936,SRR6908680,SRX3856791,SRS3100383,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM2 unenriched,GSM3070130,,tissue:WKM2 unenriched|FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM2 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070130,GSM3070130: WKM2 unenriched; Danio rerio; RNA Seq,GSM3070130,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070130,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM2_unenriched_L004_R1_001.fastq.gz WKM2_unenriched_L004_R2_001.fastq.gz,fastq fastq,1028881429.0,6816251.0,GSM3070130 r4,0:75.46 1:75.49,A:298430122;C:158105868;G:160593676;T:411666228;N:85535,75,75,,,298430122,158105868,160593676,411666228,85535,SRX3856791,SRS3100383,SRA675960,GEO,Hubrecht Institute,2,0.3924,0.79036,0.33854,0.45285,0.96386,0.94568,0.5146,0.50952,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47945,SRR6908665,SRX3856788,SRS3100380,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM1 unenriched and eosinphils,GSM3070127,,tissue:WKM1 unenriched|FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM1 unenriched and eosinphils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM1 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070127,GSM3070127: WKM1 unenriched and eosinphils; Danio rerio; RNA Seq,GSM3070127,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070127,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM1_unenriched_and_eosinphils_L001_R1_001.fastq.gz WKM1_unenriched_and_eosinphils_L001_R2_001.fastq.gz,fastq fastq,1068305818.0,7080529.0,GSM3070127 r1,0:75.40 1:75.48,A:320413848;C:151660462;G:160069867;T:435805461;N:356180,75,75,,,320413848,151660462,160069867,435805461,356180,SRX3856788,SRS3100380,SRA675960,GEO,Hubrecht Institute,2,0.27598,0.80871,0.19091,0.22599,0.96861,0.84488,0.4721,0.52448,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47946,SRR6908666,SRX3856788,SRS3100380,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM1 unenriched and eosinphils,GSM3070127,,tissue:WKM1 unenriched|FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM1 unenriched and eosinphils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM1 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070127,GSM3070127: WKM1 unenriched and eosinphils; Danio rerio; RNA Seq,GSM3070127,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070127,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM1_unenriched_and_eosinphils_L002_R1_001.fastq.gz WKM1_unenriched_and_eosinphils_L002_R2_001.fastq.gz,fastq fastq,1016514463.0,6737139.0,GSM3070127 r2,0:75.40 1:75.49,A:302565774;C:144096988;G:155267617;T:414283021;N:301063,75,75,,,302565774,144096988,155267617,414283021,301063,SRX3856788,SRS3100380,SRA675960,GEO,Hubrecht Institute,2,0.27295,0.81917,0.18669,0.22848,0.9668,0.84587,0.46708,0.53709,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47947,SRR6908667,SRX3856788,SRS3100380,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM1 unenriched and eosinphils,GSM3070127,,tissue:WKM1 unenriched|FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM1 unenriched and eosinphils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM1 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070127,GSM3070127: WKM1 unenriched and eosinphils; Danio rerio; RNA Seq,GSM3070127,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070127,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM1_unenriched_and_eosinphils_L003_R1_001.fastq.gz WKM1_unenriched_and_eosinphils_L003_R2_001.fastq.gz,fastq fastq,1086053144.0,7197705.0,GSM3070127 r3,0:75.40 1:75.48,A:318255993;C:154002465;G:165796480;T:447901015;N:97191,75,75,,,318255993,154002465,165796480,447901015,97191,SRX3856788,SRS3100380,SRA675960,GEO,Hubrecht Institute,2,0.28052,0.80997,0.19564,0.22597,0.96765,0.84254,0.4696,0.52611,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47948,SRR6908668,SRX3856788,SRS3100380,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM1 unenriched and eosinphils,GSM3070127,,tissue:WKM1 unenriched|FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM1 unenriched and eosinphils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM1 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM1|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070127,GSM3070127: WKM1 unenriched and eosinphils; Danio rerio; RNA Seq,GSM3070127,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070127,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM1_unenriched_and_eosinphils_L004_R1_001.fastq.gz WKM1_unenriched_and_eosinphils_L004_R2_001.fastq.gz,fastq fastq,1085163813.0,7191653.0,GSM3070127 r4,0:75.40 1:75.49,A:312948861;C:153665711;G:169799718;T:448671627;N:77896,75,75,,,312948861,153665711,169799718,448671627,77896,SRX3856788,SRS3100380,SRA675960,GEO,Hubrecht Institute,2,0.26916,0.8114,0.18523,0.22636,0.96627,0.84354,0.47209,0.51851,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47949,SRR6908659,SRX3856787,SRS3100379,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM10 unenriched,GSM3070126,,tissue:WKM10 unenriched|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM10 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM10 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070126,GSM3070126: WKM10 unenriched; Danio rerio; RNA Seq,GSM3070126,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070126,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM10_unenriched_L001_R1_001.fastq.gz WKM10_unenriched_L001_R2_001.fastq.gz,fastq fastq,1891142652.0,12537041.0,GSM3070126 r1,0:75.42 1:75.42,A:557482402;C:271919044;G:315036968;T:746296246;N:407992,75,75,,,557482402,271919044,315036968,746296246,407992,SRX3856787,SRS3100379,SRA675960,GEO,Hubrecht Institute,2,0.16858,0.70113,0.12017,0.25789,0.98484,0.84463,0.51282,0.51143,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47950,SRR6908660,SRX3856787,SRS3100379,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM10 unenriched,GSM3070126,,tissue:WKM10 unenriched|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM10 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM10 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070126,GSM3070126: WKM10 unenriched; Danio rerio; RNA Seq,GSM3070126,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070126,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM10_unenriched_L002_R1_001.fastq.gz WKM10_unenriched_L002_R2_001.fastq.gz,fastq fastq,1846289680.0,12239657.0,GSM3070126 r2,0:75.41 1:75.43,A:544608247;C:262931581;G:312624132;T:725748545;N:377175,75,75,,,544608247,262931581,312624132,725748545,377175,SRX3856787,SRS3100379,SRA675960,GEO,Hubrecht Institute,2,0.17135,0.69505,0.12425,0.25051,0.98466,0.85401,0.548,0.50623,76,74,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47951,SRR6908662,SRX3856787,SRS3100379,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM10 unenriched,GSM3070126,,tissue:WKM10 unenriched|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM10 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM10 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070126,GSM3070126: WKM10 unenriched; Danio rerio; RNA Seq,GSM3070126,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070126,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM10_unenriched_L003_R1_001.fastq.gz WKM10_unenriched_L003_R2_001.fastq.gz,fastq fastq,1832938497.0,12149490.0,GSM3070126 r3,0:75.43 1:75.43,A:535224222;C:265875558;G:305945153;T:725790414;N:103150,75,75,,,535224222,265875558,305945153,725790414,103150,SRX3856787,SRS3100379,SRA675960,GEO,Hubrecht Institute,2,0.14834,0.7084,0.1064,0.2628,0.98884,0.83997,0.47131,0.50686,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47952,SRR6908663,SRX3856787,SRS3100379,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM10 unenriched,GSM3070126,,tissue:WKM10 unenriched|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched,WKM10 unenriched,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM10 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070126,GSM3070126: WKM10 unenriched; Danio rerio; RNA Seq,GSM3070126,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070126,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM10_unenriched_L004_R1_001.fastq.gz WKM10_unenriched_L004_R2_001.fastq.gz,fastq fastq,1728520288.0,11457514.0,GSM3070126 r4,0:75.42 1:75.44,A:506773176;C:249233970;G:290907978;T:681531010;N:74154,75,75,,,506773176,249233970,290907978,681531010,74154,SRX3856787,SRS3100379,SRA675960,GEO,Hubrecht Institute,2,0.15928,0.69759,0.11494,0.25416,0.98748,0.85257,0.49753,0.48714,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47957,SRR6908651,SRX3856785,SRS3100378,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM10 hspcs,GSM3070124,,tissue:WKM10 hspcs|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs,WKM10 hspcs,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM10 hspcs,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs,GSM3070124,GSM3070124: WKM10 hspcs; Danio rerio; RNA Seq,GSM3070124,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070124,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM10_hspcs_L001_R2_001.fastq.gz WKM10_hspcs_L001_R1_001.fastq.gz,fastq fastq,1590301844.0,10544259.0,GSM3070124 r1,0:75.41 1:75.41,A:475941511;C:228957206;G:273207488;T:611864346;N:331293,75,75,,,475941511,228957206,273207488,611864346,331293,SRX3856785,SRS3100378,SRA675960,GEO,Hubrecht Institute,2,0.1094,0.64845,0.07241,0.20022,0.99003,0.86858,0.47375,0.52521,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47958,SRR6908652,SRX3856785,SRS3100378,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM10 hspcs,GSM3070124,,tissue:WKM10 hspcs|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs,WKM10 hspcs,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM10 hspcs,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs,GSM3070124,GSM3070124: WKM10 hspcs; Danio rerio; RNA Seq,GSM3070124,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070124,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM10_hspcs_L002_R1_001.fastq.gz WKM10_hspcs_L002_R2_001.fastq.gz,fastq fastq,1541424200.0,10220291.0,GSM3070124 r2,0:75.40 1:75.42,A:461686116;C:219412558;G:269584176;T:590440374;N:300976,75,75,,,461686116,219412558,269584176,590440374,300976,SRX3856785,SRS3100378,SRA675960,GEO,Hubrecht Institute,2,0.10207,0.63661,0.06952,0.19781,0.9906,0.88067,0.49271,0.52658,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47959,SRR6908653,SRX3856785,SRS3100378,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM10 hspcs,GSM3070124,,tissue:WKM10 hspcs|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs,WKM10 hspcs,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM10 hspcs,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs,GSM3070124,GSM3070124: WKM10 hspcs; Danio rerio; RNA Seq,GSM3070124,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070124,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM10_hspcs_L003_R1_001.fastq.gz WKM10_hspcs_L003_R2_001.fastq.gz,fastq fastq,1522328486.0,10091828.0,GSM3070124 r3,0:75.42 1:75.42,A:451216714;C:220917351;G:262800832;T:587312728;N:80861,75,75,,,451216714,220917351,262800832,587312728,80861,SRX3856785,SRS3100378,SRA675960,GEO,Hubrecht Institute,2,0.13574,0.65823,0.09073,0.20336,0.99275,0.86434,0.43289,0.52956,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47960,SRR6908654,SRX3856785,SRS3100378,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM10 hspcs,GSM3070124,,tissue:WKM10 hspcs|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs,WKM10 hspcs,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM10 hspcs,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:hspcs,GSM3070124,GSM3070124: WKM10 hspcs; Danio rerio; RNA Seq,GSM3070124,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070124,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM10_hspcs_L004_R1_001.fastq.gz WKM10_hspcs_L004_R2_001.fastq.gz,fastq fastq,1411385405.0,9356766.0,GSM3070124 r4,0:75.41 1:75.43,A:420850958;C:203157222;G:246195731;T:541125854;N:55640,75,75,,,420850958,203157222,246195731,541125854,55640,SRX3856785,SRS3100378,SRA675960,GEO,Hubrecht Institute,2,0.1075,0.63447,0.07148,0.19425,0.99168,0.87858,0.46045,0.52468,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47961,SRR6908647,SRX3856784,SRS3100376,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched6,GSM3070123,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched6,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070123,GSM3070123: TD2 unenriched6; Danio rerio; RNA Seq,GSM3070123,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070123,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched6_L001_R1_001.fastq.gz TD2_unenriched6_L001_R2_001.fastq.gz,fastq fastq,545810961.0,3618641.0,GSM3070123 r1,0:75.34 1:75.49,A:168172042;C:76647486;G:75443312;T:225350562;N:197559,75,75,,,168172042,76647486,75443312,225350562,197559,SRX3856784,SRS3100376,SRA675960,GEO,Hubrecht Institute,2,0.21696,0.7915,0.16188,0.2193,0.99671,0.95925,0.45419,0.56183,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47962,SRR6908648,SRX3856784,SRS3100376,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched6,GSM3070123,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched6,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070123,GSM3070123: TD2 unenriched6; Danio rerio; RNA Seq,GSM3070123,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070123,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched6_L002_R1_001.fastq.gz TD2_unenriched6_L002_R2_001.fastq.gz,fastq fastq,551469212.0,3655214.0,GSM3070123 r2,0:75.36 1:75.52,A:164774688;C:77140941;G:80606976;T:228739873;N:206734,75,75,,,164774688,77140941,80606976,228739873,206734,SRX3856784,SRS3100376,SRA675960,GEO,Hubrecht Institute,2,0.19654,0.81842,0.14863,0.22131,0.99734,0.94988,0.44495,0.52385,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47963,SRR6908649,SRX3856784,SRS3100376,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched6,GSM3070123,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched6,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070123,GSM3070123: TD2 unenriched6; Danio rerio; RNA Seq,GSM3070123,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070123,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched6_L003_R2_001.fastq.gz TD2_unenriched6_L003_R1_001.fastq.gz,fastq fastq,450161969.0,2984169.0,GSM3070123 r3,0:75.35 1:75.50,A:138199135;C:62817422;G:62600807;T:186468898;N:75707,75,75,,,138199135,62817422,62600807,186468898,75707,SRX3856784,SRS3100376,SRA675960,GEO,Hubrecht Institute,2,0.21607,0.79287,0.16404,0.21905,0.99703,0.95676,0.48017,0.55646,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47964,SRR6908650,SRX3856784,SRS3100376,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched6,GSM3070123,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched6,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070123,GSM3070123: TD2 unenriched6; Danio rerio; RNA Seq,GSM3070123,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070123,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched6_L004_R1_001.fastq.gz TD2_unenriched6_L004_R2_001.fastq.gz,fastq fastq,442656356.0,2934612.0,GSM3070123 r4,0:75.33 1:75.51,A:135781084;C:61366386;G:62664738;T:182773713;N:70435,75,75,,,135781084,61366386,62664738,182773713,70435,SRX3856784,SRS3100376,SRA675960,GEO,Hubrecht Institute,2,0.18178,0.75305,0.13685,0.21602,0.99776,0.9779,0.4152,0.56284,76,74,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47965,SRR6908643,SRX3856783,SRS3100375,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched5,GSM3070122,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched5,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070122,GSM3070122: TD2 unenriched5; Danio rerio; RNA Seq,GSM3070122,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070122,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched5_L001_R1_001.fastq.gz TD2_unenriched5_L001_R2_001.fastq.gz,fastq fastq,693452896.0,4598401.0,GSM3070122 r1,0:75.33 1:75.48,A:213825079;C:97881059;G:95953069;T:285544984;N:248705,75,75,,,213825079,97881059,95953069,285544984,248705,SRX3856783,SRS3100375,SRA675960,GEO,Hubrecht Institute,2,0.16673,0.76013,0.12371,0.17909,0.99671,0.95943,0.51028,0.50627,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47966,SRR6908644,SRX3856783,SRS3100375,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched5,GSM3070122,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched5,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070122,GSM3070122: TD2 unenriched5; Danio rerio; RNA Seq,GSM3070122,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070122,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched5_L002_R1_001.fastq.gz TD2_unenriched5_L002_R2_001.fastq.gz,fastq fastq,699177190.0,4635107.0,GSM3070122 r2,0:75.34 1:75.50,A:208880260;C:98335526;G:102541505;T:289154313;N:265586,75,75,,,208880260,98335526,102541505,289154313,265586,SRX3856783,SRS3100375,SRA675960,GEO,Hubrecht Institute,2,0.16993,0.79459,0.12771,0.18893,0.99693,0.94675,0.4163,0.53497,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47967,SRR6908645,SRX3856783,SRS3100375,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched5,GSM3070122,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched5,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070122,GSM3070122: TD2 unenriched5; Danio rerio; RNA Seq,GSM3070122,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070122,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched5_L003_R1_001.fastq.gz TD2_unenriched5_L003_R2_001.fastq.gz,fastq fastq,576884372.0,3824943.0,GSM3070122 r3,0:75.33 1:75.49,A:177240215;C:80846391;G:80350870;T:238347702;N:99194,75,75,,,177240215,80846391,80350870,238347702,99194,SRX3856783,SRS3100375,SRA675960,GEO,Hubrecht Institute,2,0.16558,0.7756,0.12819,0.17822,0.99709,0.95432,0.42857,0.53851,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47968,SRR6908646,SRX3856783,SRS3100375,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched5,GSM3070122,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched5,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070122,GSM3070122: TD2 unenriched5; Danio rerio; RNA Seq,GSM3070122,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070122,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched5_L004_R1_001.fastq.gz TD2_unenriched5_L004_R2_001.fastq.gz,fastq fastq,576258135.0,3821008.0,GSM3070122 r4,0:75.32 1:75.49,A:176675655;C:80188796;G:82006998;T:237292671;N:94015,75,75,,,176675655,80188796,82006998,237292671,94015,SRX3856783,SRS3100375,SRA675960,GEO,Hubrecht Institute,2,0.14911,0.72985,0.12068,0.18331,0.99831,0.97735,0.4031,0.53561,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47969,SRR6908639,SRX3856782,SRS3100374,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched4,GSM3070121,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched4,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070121,GSM3070121: TD2 unenriched4; Danio rerio; RNA Seq,GSM3070121,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070121,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched4_L001_R1_001.fastq.gz TD2_unenriched4_L001_R2_001.fastq.gz,fastq fastq,698012656.0,4628160.0,GSM3070121 r1,0:75.33 1:75.49,A:215875472;C:99834912;G:97411477;T:284642018;N:248777,75,75,,,215875472,99834912,97411477,284642018,248777,SRX3856782,SRS3100374,SRA675960,GEO,Hubrecht Institute,2,0.13242,0.78521,0.09514,0.21281,0.99695,0.96187,0.55958,0.54425,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47970,SRR6908640,SRX3856782,SRS3100374,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched4,GSM3070121,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched4,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070121,GSM3070121: TD2 unenriched4; Danio rerio; RNA Seq,GSM3070121,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070121,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched4_L002_R1_001.fastq.gz TD2_unenriched4_L002_R2_001.fastq.gz,fastq fastq,700004319.0,4640053.0,GSM3070121 r2,0:75.35 1:75.52,A:209624561;C:99781032;G:103500007;T:286831762;N:266957,75,75,,,209624561,99781032,103500007,286831762,266957,SRX3856782,SRS3100374,SRA675960,GEO,Hubrecht Institute,2,0.13829,0.81458,0.10266,0.21216,0.99687,0.94913,0.54395,0.53632,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47971,SRR6908641,SRX3856782,SRS3100374,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched4,GSM3070121,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched4,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070121,GSM3070121: TD2 unenriched4; Danio rerio; RNA Seq,GSM3070121,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070121,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched4_L003_R1_001.fastq.gz TD2_unenriched4_L003_R2_001.fastq.gz,fastq fastq,574436722.0,3808300.0,GSM3070121 r3,0:75.34 1:75.50,A:177021417;C:81616991;G:80653244;T:235045589;N:99481,75,75,,,177021417,81616991,80653244,235045589,99481,SRX3856782,SRS3100374,SRA675960,GEO,Hubrecht Institute,2,0.12255,0.79777,0.09509,0.21314,0.99772,0.95735,0.44927,0.54033,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47972,SRR6908642,SRX3856782,SRS3100374,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched4,GSM3070121,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched4,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070121,GSM3070121: TD2 unenriched4; Danio rerio; RNA Seq,GSM3070121,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070121,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched4_L004_R1_001.fastq.gz TD2_unenriched4_L004_R2_001.fastq.gz,fastq fastq,569447738.0,3775476.0,GSM3070121 r4,0:75.32 1:75.51,A:175211390;C:80267913;G:81642398;T:232235494;N:90543,75,75,,,175211390,80267913,81642398,232235494,90543,SRX3856782,SRS3100374,SRA675960,GEO,Hubrecht Institute,2,0.12315,0.75952,0.09398,0.20424,0.99784,0.97788,0.46825,0.56598,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47973,SRR6908635,SRX3856781,SRS3100373,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched3,GSM3070120,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched3,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070120,GSM3070120: TD2 unenriched3; Danio rerio; RNA Seq,GSM3070120,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070120,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched3_L001_R1_001.fastq.gz TD2_unenriched3_L001_R2_001.fastq.gz,fastq fastq,1064615599.0,7058899.0,GSM3070120 r1,0:75.33 1:75.49,A:331155753;C:152195592;G:149457994;T:431416903;N:389357,75,75,,,331155753,152195592,149457994,431416903,389357,SRX3856781,SRS3100373,SRA675960,GEO,Hubrecht Institute,2,0.12965,0.76924,0.09102,0.22546,0.99693,0.95895,0.46568,0.56174,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47974,SRR6908636,SRX3856781,SRS3100373,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched3,GSM3070120,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched3,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070120,GSM3070120: TD2 unenriched3; Danio rerio; RNA Seq,GSM3070120,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070120,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched3_L002_R1_001.fastq.gz TD2_unenriched3_L002_R2_001.fastq.gz,fastq fastq,1070747888.0,7097567.0,GSM3070120 r2,0:75.35 1:75.51,A:322612282;C:152497154;G:159486633;T:435752070;N:399749,75,75,,,322612282,152497154,159486633,435752070,399749,SRX3856781,SRS3100373,SRA675960,GEO,Hubrecht Institute,2,0.11805,0.79563,0.08703,0.22302,0.99738,0.94838,0.49404,0.53615,75,74,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47975,SRR6908637,SRX3856781,SRS3100373,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched3,GSM3070120,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched3,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070120,GSM3070120: TD2 unenriched3; Danio rerio; RNA Seq,GSM3070120,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070120,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched3_L003_R1_001.fastq.gz TD2_unenriched3_L003_R2_001.fastq.gz,fastq fastq,886095506.0,5874463.0,GSM3070120 r3,0:75.34 1:75.50,A:274560800;C:125930642;G:125194660;T:360267888;N:141516,75,75,,,274560800,125930642,125194660,360267888,141516,SRX3856781,SRS3100373,SRA675960,GEO,Hubrecht Institute,2,0.11795,0.77243,0.08536,0.2207,0.99752,0.95554,0.48447,0.53023,74,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47976,SRR6908638,SRX3856781,SRS3100373,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched3,GSM3070120,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched3,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070120,GSM3070120: TD2 unenriched3; Danio rerio; RNA Seq,GSM3070120,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070120,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched3_L004_R1_001.fastq.gz TD2_unenriched3_L004_R2_001.fastq.gz,fastq fastq,886839338.0,5879735.0,GSM3070120 r4,0:75.33 1:75.50,A:274032562;C:125082235;G:128147333;T:359436665;N:140543,75,75,,,274032562,125082235,128147333,359436665,140543,SRX3856781,SRS3100373,SRA675960,GEO,Hubrecht Institute,2,0.10406,0.73196,0.07637,0.22039,0.99805,0.97806,0.57024,0.5327,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47977,SRR6908631,SRX3856780,SRS3100372,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched2,GSM3070119,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched2,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070119,GSM3070119: TD2 unenriched2; Danio rerio; RNA Seq,GSM3070119,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070119,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched2_L001_R2_001.fastq.gz TD2_unenriched2_L001_R1_001.fastq.gz,fastq fastq,704234076.0,4666720.0,GSM3070119 r1,0:75.40 1:75.51,A:214197936;C:98747742;G:99261324;T:291802858;N:224216,75,75,,,214197936,98747742,99261324,291802858,224216,SRX3856780,SRS3100372,SRA675960,GEO,Hubrecht Institute,2,0.35492,0.86117,0.25299,0.26523,0.97461,0.90398,0.48193,0.51578,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47978,SRR6908632,SRX3856780,SRS3100372,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched2,GSM3070119,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched2,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070119,GSM3070119: TD2 unenriched2; Danio rerio; RNA Seq,GSM3070119,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070119,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched2_L002_R1_001.fastq.gz TD2_unenriched2_L002_R2_001.fastq.gz,fastq fastq,765278281.0,5071250.0,GSM3070119 r2,0:75.39 1:75.51,A:229620635;C:106485326;G:110950848;T:318002131;N:219341,75,75,,,229620635,106485326,110950848,318002131,219341,SRX3856780,SRS3100372,SRA675960,GEO,Hubrecht Institute,2,0.34672,0.85932,0.24701,0.26154,0.97309,0.90404,0.44868,0.53509,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47979,SRR6908633,SRX3856780,SRS3100372,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched2,GSM3070119,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched2,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070119,GSM3070119: TD2 unenriched2; Danio rerio; RNA Seq,GSM3070119,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070119,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched2_L003_R2_001.fastq.gz TD2_unenriched2_L003_R1_001.fastq.gz,fastq fastq,687934305.0,4558488.0,GSM3070119 r3,0:75.41 1:75.51,A:206475938;C:96511863;G:97660355;T:287209767;N:76382,75,75,,,206475938,96511863,97660355,287209767,76382,SRX3856780,SRS3100372,SRA675960,GEO,Hubrecht Institute,2,0.36436,0.861,0.2595,0.26448,0.97699,0.90772,0.47159,0.5237,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47980,SRR6908634,SRX3856780,SRS3100372,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched2,GSM3070119,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched2,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070119,GSM3070119: TD2 unenriched2; Danio rerio; RNA Seq,GSM3070119,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070119,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched2_L004_R2_001.fastq.gz TD2_unenriched2_L004_R1_001.fastq.gz,fastq fastq,726529569.0,4814235.0,GSM3070119 r4,0:75.40 1:75.51,A:216493809;C:101292463;G:105024164;T:303652778;N:66355,75,75,,,216493809,101292463,105024164,303652778,66355,SRX3856780,SRS3100372,SRA675960,GEO,Hubrecht Institute,2,0.35832,0.85478,0.25668,0.26566,0.97786,0.9232,0.43793,0.51027,75,74,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47981,SRR6908627,SRX3856779,SRS3100371,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched1,GSM3070118,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched1,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070118,GSM3070118: TD2 unenriched1; Danio rerio; RNA Seq,GSM3070118,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070118,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched1_L001_R1_001.fastq.gz TD2_unenriched1_L001_R2_001.fastq.gz,fastq fastq,854990718.0,5665060.0,GSM3070118 r1,0:75.41 1:75.52,A:254734570;C:122614765;G:124439336;T:352929607;N:272440,75,75,,,254734570,122614765,124439336,352929607,272440,SRX3856779,SRS3100371,SRA675960,GEO,Hubrecht Institute,2,0.36338,0.86281,0.26887,0.24825,0.97011,0.88966,0.52127,0.54178,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47982,SRR6908628,SRX3856779,SRS3100371,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched1,GSM3070118,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched1,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070118,GSM3070118: TD2 unenriched1; Danio rerio; RNA Seq,GSM3070118,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070118,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched1_L002_R1_001.fastq.gz TD2_unenriched1_L002_R2_001.fastq.gz,fastq fastq,930416984.0,6164856.0,GSM3070118 r2,0:75.40 1:75.52,A:273371770;C:132477140;G:139134453;T:385153908;N:279713,75,75,,,273371770,132477140,139134453,385153908,279713,SRX3856779,SRS3100371,SRA675960,GEO,Hubrecht Institute,2,0.35067,0.86515,0.25837,0.24485,0.97041,0.88838,0.50653,0.5351,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47983,SRR6908629,SRX3856779,SRS3100371,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched1,GSM3070118,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched1,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070118,GSM3070118: TD2 unenriched1; Danio rerio; RNA Seq,GSM3070118,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070118,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched1_L003_R1_001.fastq.gz TD2_unenriched1_L003_R2_001.fastq.gz,fastq fastq,854585314.0,5662042.0,GSM3070118 r3,0:75.42 1:75.52,A:251015969;C:122655652;G:125410058;T:355402307;N:101328,75,75,,,251015969,122655652,125410058,355402307,101328,SRX3856779,SRS3100371,SRA675960,GEO,Hubrecht Institute,2,0.37061,0.86557,0.27852,0.24591,0.97498,0.89335,0.49141,0.48962,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System
47984,SRR6908630,SRX3856779,SRS3100371,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,TD2 unenriched1,GSM3070118,,tissue:TD2 unenriched|FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,TD2 unenriched1,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,TD2 unenriched,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:TD2|cell type:whole kidney marrow single cells|cell subtype:unenriched,GSM3070118,GSM3070118: TD2 unenriched1; Danio rerio; RNA Seq,GSM3070118,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070118,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,TD2_unenriched1_L004_R1_001.fastq.gz TD2_unenriched1_L004_R2_001.fastq.gz,fastq fastq,886769985.0,5875288.0,GSM3070118 r4,0:75.41 1:75.52,A:258347255;C:126714596;G:132415950;T:369203307;N:88877,75,75,,,258347255,126714596,132415950,369203307,88877,SRX3856779,SRS3100371,SRA675960,GEO,Hubrecht Institute,2,0.36759,0.86048,0.27631,0.23985,0.97526,0.90682,0.49809,0.53286,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Kidney,Renal System