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
38,DRR408248,DRX393854,DRS407179,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line  TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs  and isolated GFP+ ENs and dsRed+ ENCDCs.  Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 3,zebrafish ENCDC replicate 3,SAMD00529468,,sample name:zebrafish ENCDC replicate 3|biological replicate:enteric neural crest derived cells 3|strain:Tgsox10:cre; EF3alpha:loxP gfp loxP dsred,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529468,DRX393854,190326ENvsNC N706 5day;NeuralCrestDerivedCell;rep3,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP012042,NextSeq 550 paired end sequencing of SAMD00529468,,,,3803721121.0,24526633.0,DRR408248,0:77.54 1:77.54,A:999106107;C:897663781;G:921501114;T:979486853;N:5963266,77,77,,,999106107,897663781,921501114,979486853,5963266,DRX393854,DRS407179,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Brain,Nervous System
39,DRR408247,DRX393853,DRS407178,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line  TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs  and isolated GFP+ ENs and dsRed+ ENCDCs.  Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 2,zebrafish ENCDC replicate 2,SAMD00529467,,sample name:zebrafish ENCDC replicate 2|biological replicate:enteric neural crest derived cells 2|strain:Tgsox10:cre; EF2alpha:loxP gfp loxP dsred,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529467,DRX393853,190326ENvsNC N705 5day;NeuralCrestDerivedCell;rep2,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP012042,NextSeq 550 paired end sequencing of SAMD00529467,,,,3436798274.0,22156202.0,DRR408247,0:77.56 1:77.56,A:900848174;C:812031426;G:832960423;T:885671203;N:5287048,77,77,,,900848174,812031426,832960423,885671203,5287048,DRX393853,DRS407178,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Brain,Nervous System
40,DRR408246,DRX393852,DRS407177,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line  TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs  and isolated GFP+ ENs and dsRed+ ENCDCs.  Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 1,zebrafish ENCDC replicate 1,SAMD00529466,,sample name:zebrafish ENCDC replicate 1|biological replicate:enteric neural crest derived cells 1|strain:Tgsox10:cre; EF1alpha:loxP gfp loxP dsred,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529466,DRX393852,190326ENvsNC N704 5day;NeuralCrestDerivedCell;rep1,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP012042,NextSeq 550 paired end sequencing of SAMD00529466,,,,3582073512.0,23135170.0,DRR408246,0:77.41 1:77.42,A:943152815;C:841972211;G:863627245;T:927361159;N:5960082,77,77,,,943152815,841972211,863627245,927361159,5960082,DRX393852,DRS407177,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Brain,Nervous System
41,DRR408245,DRX393851,DRS407176,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line  TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs  and isolated GFP+ ENs and dsRed+ ENCDCs.  Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day GFP positive enteric neurons replicate 3,zebrafish EN replicate 3,SAMD00529465,,sample name:zebrafish EN replicate 3|biological replicate:eneteric neurons 3|strain:TgSAGFFLF219B; uas:gfp,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529465,DRX393851,190326ENvsNC N703 5day;EntericNeuron;rep3,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP012042,NextSeq 550 paired end sequencing of SAMD00529465,,,,3729799291.0,23985772.0,DRR408245,0:77.75 1:77.75,A:978752781;C:879988139;G:903976580;T:962122970;N:4958821,77,77,,,978752781,879988139,903976580,962122970,4958821,DRX393851,DRS407176,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Undetermined,Undetermined
42,DRR408244,DRX393850,DRS407175,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line  TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs  and isolated GFP+ ENs and dsRed+ ENCDCs.  Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day GFP positive enteric neurons replicate 2,zebrafish EN replicate 2,SAMD00529464,,sample name:zebrafish EN replicate 2|biological replicate:eneteric neurons 2|strain:TgSAGFFLF218B; uas:gfp,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529464,DRX393850,190326ENvsNC N702 5day;EntericNeuron;rep2,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP012042,NextSeq 550 paired end sequencing of SAMD00529464,,,,3315994810.0,21477755.0,DRR408244,0:77.19 1:77.20,A:873970427;C:778042505;G:798459853;T:859611841;N:5910184,77,77,,,873970427,778042505,798459853,859611841,5910184,DRX393850,DRS407175,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Undetermined,Undetermined
43,DRR408243,DRX393849,DRS407174,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line  TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs  and isolated GFP+ ENs and dsRed+ ENCDCs.  Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day GFP positive enteric neurons replicate 1,zebrafish EN replicate 1,SAMD00529463,,sample name:zebrafish EN replicate 1|biological replicate:eneteric neurons 1|strain:TgSAGFFLF217B; uas:gfp,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529463,DRX393849,190326ENvsNC N701 5day;EntericNeuron;rep1,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP012042,NextSeq 550 paired end sequencing of SAMD00529463,,,,2999501518.0,19455440.0,DRR408243,0:77.08 1:77.09,A:788053541;C:705895776;G:724185148;T:775760738;N:5606315,77,77,,,788053541,705895776,724185148,775760738,5606315,DRX393849,DRS407174,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Undetermined,Undetermined
147,DRR051067,DRX045959,DRS057267,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,These cells are from the same fish as h62A GFP plus Tel,GFP  cells from telencephalon of hspGFF62A;UAS:GFP transgenic zebrafish,SAMD00044994,,sample name:h62A GFP minus Tel|tissue type:brain|genotype:hspGFF62A;UAS:GFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00044994,DRX045959,h62A GFP minus Tel,1,cDNA synthesis : clontech SMARTer v3  > Library prep : Illumina Nextera XT DNA Library Preparation Kits,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00044994,,,,17913873600.0,89569368.0,DRR051067,0:100 1:100,A:5009629866;C:3957379257;G:3797879751;T:5144366288;N:4618438,100,100,,,5009629866,3957379257,3797879751,5144366288,4618438,DRX045959,DRS057267,DRA004277,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.89075,0.89087,0.23044,0.23295,0.69493,0.69769,0.5366,0.54852,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,unknown,unknown,,Japan,2018-01-06,Undetermined,Undetermined,Brain,Nervous System
151,DRR051063,DRX045955,DRS057266,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,These cells are from the same fish as 120A GFP plus Tel,GFP  cells from telencephalon of SAGFFLF120A;UAS:GFP transgenic zebrafish,SAMD00044987,,sample name:120A GFP minus Tel|tissue type:brain|genotype:SAGFFLF120A;UAS:GFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing of SAMD00044987,DRX045955,120A GFP minus Tel,1,cDNA synthesis : clontech SMARTer v2  > Library prep : Illumina TrunSeq DNA Sample Preparation Kits,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 2500 paired end sequencing of SAMD00044987,,,,15411400120.0,76294060.0,DRR051063,0:101 1:101,A:4583085286;C:3082552426;G:3134669086;T:4606055524;N:5037798,101,101,,,4583085286,3082552426,3134669086,4606055524,5037798,DRX045955,DRS057266,DRA004273,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),2,0.89184,0.8842,0.30246,0.30334,0.69232,0.705,0.52824,0.51492,101,101,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Japan,2018-01-06,Undetermined,Undetermined,Brain,Nervous System
280,DRR161311,DRX151936,DRS095335,DRP005084,PRJDB7735,Gene expression profile in adult zebrafish liver,DRP005084,Transcriptome Analysis,Increasing use of zebrafish in toxicological researches requires knowledge on gene expression profile in liver that play a major role in xenobiotic metabolism. Our research provide a basal gene expression profile in adult zebrafish liver.,,,,Transcriptome of female Danio rerio liver,SAMD00153247,,sample name:transcriptome zebrafish female|sex:female|strain:RIKEN WT|tissue:liver,,,,,,,,,NextSeq 500 paired end sequencing of SAMD00153247,DRX151936,f,1,1,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP005084,NextSeq 500 paired end sequencing of SAMD00153247,,,,2338564937.0,15498367.0,DRR161311,0:75.45 1:75.44,A:613899755;C:541756858;G:548366901;T:633083422;N:1458001,75,75,,,613899755,541756858,548366901,633083422,1458001,DRX151936,DRS095335,DRA007652,"OBICHIKU|Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine","Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine",2,0.95814,0.96362,0.05394,0.04517,0.77932,0.7834,0.37385,0.37264,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-05-20,Undetermined,Adult,Liver,Liver and Biliary System
281,DRR161310,DRX151935,DRS095334,DRP005084,PRJDB7735,Gene expression profile in adult zebrafish liver,DRP005084,Transcriptome Analysis,Increasing use of zebrafish in toxicological researches requires knowledge on gene expression profile in liver that play a major role in xenobiotic metabolism. Our research provide a basal gene expression profile in adult zebrafish liver.,,,,Transcriptome of male Danio rerio liver,SAMD00153246,,sample name:transcriptome zebrafish male|sex:male|strain:RIKEN WT|tissue:liver,,,,,,,,,NextSeq 500 paired end sequencing of SAMD00153246,DRX151935,m,1,1,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP005084,NextSeq 500 paired end sequencing of SAMD00153246,,,,2506978527.0,16611154.0,DRR161310,0:75.48 1:75.44,A:672321355;C:568289588;G:569411670;T:695545626;N:1410288,75,75,,,672321355,568289588,569411670,695545626,1410288,DRX151935,DRS095334,DRA007652,"OBICHIKU|Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine","Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine",2,0.94746,0.95115,0.07899,0.06363,0.80837,0.8115,0.52008,0.58743,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-05-20,Undetermined,Adult,Liver,Liver and Biliary System
2319,ERR1289947,ERX1361553,ERS954843,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647694,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:23:00Z|External Id:SAMEA3647694|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:23:00Z|INSDC status:public|Submitter Id:ATH5 2 sc 2454965|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:ATH5 2 sc 2454965|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#12,15249493,Illumina sequencing of library 15249493  constructed from sample accession ERS954843 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence TAGGCATGAGAGTAGA.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#12.cram,cram,2492206600.0,12461033.0,SC RUN 18222 2#12,0:100 1:100,A:661236051;C:588399772;G:571478215;T:671080581;N:11981,100,100,,,661236051,588399772,571478215,671080581,11981,ERX1361553,ERS954843,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94054,0.94077,0.10025,0.10255,0.75779,0.76019,0.4807,0.47966,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2320,ERR1289946,ERX1361552,ERS954842,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647693,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:23:00Z|External Id:SAMEA3647693|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:23:00Z|INSDC status:public|Submitter Id:WT ctrl sc 2454964|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:WT ctrl sc 2454964|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#11,15249492,Illumina sequencing of library 15249492  constructed from sample accession ERS954842 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence TAGGCATGTATCCTCT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#11.cram,cram,2748114600.0,13740573.0,SC RUN 18222 2#11,0:100 1:100,A:747132237;C:630918171;G:613637334;T:756413030;N:13828,100,100,,,747132237,630918171,613637334,756413030,13828,ERX1361552,ERS954842,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.91201,0.911,0.09071,0.09156,0.88994,0.88988,0.47118,0.49948,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2321,ERR1289945,ERX1361551,ERS954841,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647692,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:59Z|External Id:SAMEA3647692|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:59Z|INSDC status:public|Submitter Id:RX2 ATH5 GFP3 sc 2454963|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ATH5 GFP3 sc 2454963|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#10,15249491,Illumina sequencing of library 15249491  constructed from sample accession ERS954841 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence TAGGCATGCTCTCTAT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#10.cram,cram,3366968000.0,16834840.0,SC RUN 18222 2#10,0:100 1:100,A:881918684;C:806052916;G:790157920;T:888821188;N:17292,100,100,,,881918684,806052916,790157920,888821188,17292,ERX1361551,ERS954841,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94171,0.94098,0.0849,0.08607,0.74862,0.75024,0.50963,0.50955,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2322,ERR1289944,ERX1361550,ERS954840,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647691,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647691|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:RX2 ATH5 GFP2 sc 2454962|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ATH5 GFP2 sc 2454962|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#9,15249490,Illumina sequencing of library 15249490  constructed from sample accession ERS954840 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence TAGGCATGTAGATCGC.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#9.cram,cram,3222261000.0,16111305.0,SC RUN 18222 2#9,0:100 1:100,A:819997366;C:795302699;G:777099203;T:829845734;N:15998,100,100,,,819997366,795302699,777099203,829845734,15998,ERX1361550,ERS954840,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94529,0.94495,0.0603,0.06143,0.76157,0.76238,0.48847,0.4882,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2323,ERR1289943,ERX1361549,ERS954839,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647690,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647690|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 GFP2 high sc 2454961|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 GFP2 high sc 2454961|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#8,15249489,Illumina sequencing of library 15249489  constructed from sample accession ERS954839 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence GGACTCCTCTAAGCCT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#8.cram,cram,3834749800.0,19173749.0,SC RUN 18222 2#8,0:100 1:100,A:992673645;C:929008642;G:906766397;T:1006281701;N:19415,100,100,,,992673645,929008642,906766397,1006281701,19415,ERX1361549,ERS954839,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94351,0.94297,0.08055,0.08157,0.72853,0.73095,0.52148,0.51755,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2324,ERR1289942,ERX1361548,ERS954838,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647689,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647689|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 GFP2 low sc 2454960|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 GFP2 low sc 2454960|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#7,15249488,Illumina sequencing of library 15249488  constructed from sample accession ERS954838 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence GGACTCCTAAGGAGTA.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#7.cram,cram,1076581000.0,5382905.0,SC RUN 18222 2#7,0:100 1:100,A:285946062;C:254142940;G:242866633;T:293619980;N:5385,100,100,,,285946062,254142940,242866633,293619980,5385,ERX1361548,ERS954838,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.89818,0.89819,0.1022,0.10292,0.89919,0.89852,0.51448,0.51223,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2325,ERR1289941,ERX1361547,ERS954837,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647688,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647688|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:GFAP ATH5 GFP2 sc 2454959|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:GFAP ATH5 GFP2 sc 2454959|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#6,15249487,Illumina sequencing of library 15249487  constructed from sample accession ERS954837 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence GGACTCCTACTGCATA.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#6.cram,cram,3172834800.0,15864174.0,SC RUN 18222 2#6,0:100 1:100,A:841262183;C:748974758;G:730474017;T:852107947;N:15895,100,100,,,841262183,748974758,730474017,852107947,15895,ERX1361547,ERS954837,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.93515,0.93517,0.10079,0.10267,0.73403,0.73511,0.49831,0.47169,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2326,ERR1289940,ERX1361546,ERS954836,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647687,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647687|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:ATH5 1 sc 2454958|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:ATH5 1 sc 2454958|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#5,15249486,Illumina sequencing of library 15249486  constructed from sample accession ERS954836 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence GGACTCCTGTAAGGAG.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#5.cram,cram,1188728400.0,5943642.0,SC RUN 18222 2#5,0:100 1:100,A:322290258;C:273659598;G:266021599;T:326751009;N:5936,100,100,,,322290258,273659598,266021599,326751009,5936,ERX1361546,ERS954836,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.92438,0.92391,0.12338,0.1251,0.76288,0.76479,0.48734,0.47777,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2327,ERR1289939,ERX1361545,ERS954835,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647686,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647686|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:GFAP ATH5 GFP1 sc 2454957|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:GFAP ATH5 GFP1 sc 2454957|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#4,15249485,Illumina sequencing of library 15249485  constructed from sample accession ERS954835 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence GGACTCCTAGAGTAGA.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#4.cram,cram,2335470400.0,11677352.0,SC RUN 18222 2#4,0:100 1:100,A:611730664;C:560095252;G:541373953;T:622259122;N:11409,100,100,,,611730664,560095252,541373953,622259122,11409,ERX1361545,ERS954835,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.93481,0.93465,0.10573,0.10811,0.77135,0.77303,0.50016,0.50137,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2328,ERR1289938,ERX1361544,ERS954834,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647685,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647685|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 ATH5 GFP1 sc 2454956|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ATH5 GFP1 sc 2454956|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#3,15249484,Illumina sequencing of library 15249484  constructed from sample accession ERS954834 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence GGACTCCTTATCCTCT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#3.cram,cram,2932765000.0,14663825.0,SC RUN 18222 2#3,0:100 1:100,A:762543647;C:708033363;G:692599413;T:769573475;N:15102,100,100,,,762543647,708033363,692599413,769573475,15102,ERX1361544,ERS954834,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94442,0.94374,0.07322,0.07439,0.74383,0.74531,0.50604,0.51608,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2329,ERR1289937,ERX1361543,ERS954833,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647684,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:15Z|External Id:SAMEA3647684|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:15Z|INSDC status:public|Submitter Id:RX2 GFP1 sc 2454955|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 GFP1 sc 2454955|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#2,15249483,Illumina sequencing of library 15249483  constructed from sample accession ERS954833 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence GGACTCCTCTCTCTAT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#2.cram,cram,2432398000.0,12161990.0,SC RUN 18222 2#2,0:100 1:100,A:624543123;C:594774023;G:581130641;T:631937939;N:12274,100,100,,,624543123,594774023,581130641,631937939,12274,ERX1361543,ERS954833,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94225,0.94103,0.08221,0.0823,0.79289,0.79383,0.51106,0.5129,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2330,ERR1289936,ERX1361542,ERS954832,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647683,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647683|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 ctrl noGFP sc 2454954|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ctrl noGFP sc 2454954|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 2#1,15249482,Illumina sequencing of library 15249482  constructed from sample accession ERS954832 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 2.  This submission includes reads tagged with the sequence GGACTCCTTAGATCGC.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_2#1.cram,cram,361900800.0,1809504.0,SC RUN 18222 2#1,0:100 1:100,A:84553945;C:97259075;G:92615955;T:87470072;N:1753,100,100,,,84553945,97259075,92615955,87470072,1753,ERX1361542,ERS954832,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94897,0.95014,0.07743,0.07772,0.71969,0.72058,0.43784,0.44067,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2331,ERR1289935,ERX1361541,ERS954843,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647694,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:23:00Z|External Id:SAMEA3647694|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:23:00Z|INSDC status:public|Submitter Id:ATH5 2 sc 2454965|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:ATH5 2 sc 2454965|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#12,15249493,Illumina sequencing of library 15249493  constructed from sample accession ERS954843 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence TAGGCATGAGAGTAGA.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#12.cram,cram,2487554200.0,12437771.0,SC RUN 18222 1#12,0:100 1:100,A:660028585;C:587257902;G:570415230;T:669842822;N:9661,100,100,,,660028585,587257902,570415230,669842822,9661,ERX1361541,ERS954843,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94059,0.9397,0.09914,0.1011,0.75597,0.75862,0.48558,0.48548,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2332,ERR1289934,ERX1361540,ERS954842,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647693,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:23:00Z|External Id:SAMEA3647693|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:23:00Z|INSDC status:public|Submitter Id:WT ctrl sc 2454964|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:WT ctrl sc 2454964|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#11,15249492,Illumina sequencing of library 15249492  constructed from sample accession ERS954842 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence TAGGCATGTATCCTCT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#11.cram,cram,2740851200.0,13704256.0,SC RUN 18222 1#11,0:100 1:100,A:745054545;C:629082779;G:612051041;T:754652050;N:10785,100,100,,,745054545,629082779,612051041,754652050,10785,ERX1361540,ERS954842,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.91349,0.91229,0.09216,0.09351,0.88962,0.89043,0.48978,0.5028,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2333,ERR1289933,ERX1361539,ERS954841,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647692,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:59Z|External Id:SAMEA3647692|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:59Z|INSDC status:public|Submitter Id:RX2 ATH5 GFP3 sc 2454963|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ATH5 GFP3 sc 2454963|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#10,15249491,Illumina sequencing of library 15249491  constructed from sample accession ERS954841 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence TAGGCATGCTCTCTAT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#10.cram,cram,3357950400.0,16789752.0,SC RUN 18222 1#10,0:100 1:100,A:879637755;C:803810252;G:787961249;T:886528291;N:12853,100,100,,,879637755,803810252,787961249,886528291,12853,ERX1361539,ERS954841,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94064,0.94017,0.08377,0.08517,0.74909,0.75136,0.50723,0.50903,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2334,ERR1289932,ERX1361538,ERS954840,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647691,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647691|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:RX2 ATH5 GFP2 sc 2454962|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ATH5 GFP2 sc 2454962|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#9,15249490,Illumina sequencing of library 15249490  constructed from sample accession ERS954840 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence TAGGCATGTAGATCGC.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#9.cram,cram,3206581200.0,16032906.0,SC RUN 18222 1#9,0:100 1:100,A:816111545;C:791236086;G:773298814;T:825922398;N:12357,100,100,,,816111545,791236086,773298814,825922398,12357,ERX1361538,ERS954840,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94549,0.94564,0.06037,0.06105,0.76043,0.76171,0.48313,0.49555,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2335,ERR1289931,ERX1361537,ERS954839,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647690,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647690|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 GFP2 high sc 2454961|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 GFP2 high sc 2454961|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#8,15249489,Illumina sequencing of library 15249489  constructed from sample accession ERS954839 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence GGACTCCTCTAAGCCT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#8.cram,cram,3822332200.0,19111661.0,SC RUN 18222 1#8,0:100 1:100,A:989542225;C:925823012;G:903835738;T:1003115980;N:15245,100,100,,,989542225,925823012,903835738,1003115980,15245,ERX1361537,ERS954839,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94289,0.94174,0.07966,0.08004,0.72764,0.72906,0.51976,0.52464,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2336,ERR1289930,ERX1361536,ERS954838,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647689,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647689|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 GFP2 low sc 2454960|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 GFP2 low sc 2454960|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#7,15249488,Illumina sequencing of library 15249488  constructed from sample accession ERS954838 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence GGACTCCTAAGGAGTA.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#7.cram,cram,1072510200.0,5362551.0,SC RUN 18222 1#7,0:100 1:100,A:284863902;C:253046005;G:241968135;T:292627849;N:4309,100,100,,,284863902,253046005,241968135,292627849,4309,ERX1361536,ERS954838,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.89703,0.89873,0.10191,0.10317,0.89921,0.8984,0.50884,0.51319,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2337,ERR1289929,ERX1361535,ERS954837,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647688,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647688|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:GFAP ATH5 GFP2 sc 2454959|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:GFAP ATH5 GFP2 sc 2454959|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#6,15249487,Illumina sequencing of library 15249487  constructed from sample accession ERS954837 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence GGACTCCTACTGCATA.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#6.cram,cram,3159715800.0,15798579.0,SC RUN 18222 1#6,0:100 1:100,A:837700548;C:745877706;G:727508293;T:848616717;N:12536,100,100,,,837700548,745877706,727508293,848616717,12536,ERX1361535,ERS954837,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.93397,0.93362,0.10011,0.10205,0.73474,0.73612,0.49003,0.49085,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2338,ERR1289928,ERX1361534,ERS954836,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647687,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647687|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:ATH5 1 sc 2454958|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:ATH5 1 sc 2454958|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#5,15249486,Illumina sequencing of library 15249486  constructed from sample accession ERS954836 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence GGACTCCTGTAAGGAG.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#5.cram,cram,1184332600.0,5921663.0,SC RUN 18222 1#5,0:100 1:100,A:321129432;C:272595945;G:264945795;T:325656767;N:4661,100,100,,,321129432,272595945,264945795,325656767,4661,ERX1361534,ERS954836,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.92372,0.92353,0.12445,0.12616,0.76339,0.76495,0.48995,0.48259,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2339,ERR1289927,ERX1361533,ERS954835,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647686,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647686|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:GFAP ATH5 GFP1 sc 2454957|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:GFAP ATH5 GFP1 sc 2454957|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#4,15249485,Illumina sequencing of library 15249485  constructed from sample accession ERS954835 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence GGACTCCTAGAGTAGA.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#4.cram,cram,2331489600.0,11657448.0,SC RUN 18222 1#4,0:100 1:100,A:610715735;C:559128165;G:540406653;T:621229940;N:9107,100,100,,,610715735,559128165,540406653,621229940,9107,ERX1361533,ERS954835,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.9338,0.93348,0.10518,0.10783,0.77155,0.77374,0.49506,0.49808,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2340,ERR1289926,ERX1361532,ERS954834,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647685,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647685|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 ATH5 GFP1 sc 2454956|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ATH5 GFP1 sc 2454956|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#3,15249484,Illumina sequencing of library 15249484  constructed from sample accession ERS954834 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence GGACTCCTTATCCTCT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#3.cram,cram,2923134800.0,14615674.0,SC RUN 18222 1#3,0:100 1:100,A:760057089;C:705694497;G:690249046;T:767122385;N:11783,100,100,,,760057089,705694497,690249046,767122385,11783,ERX1361532,ERS954834,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94509,0.94377,0.07431,0.07512,0.74367,0.74525,0.50981,0.51595,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2341,ERR1289925,ERX1361531,ERS954833,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647684,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:15Z|External Id:SAMEA3647684|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:15Z|INSDC status:public|Submitter Id:RX2 GFP1 sc 2454955|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 GFP1 sc 2454955|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#2,15249483,Illumina sequencing of library 15249483  constructed from sample accession ERS954833 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence GGACTCCTCTCTCTAT.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#2.cram,cram,2423614200.0,12118071.0,SC RUN 18222 1#2,0:100 1:100,A:622254096;C:592596967;G:579007199;T:629746522;N:9416,100,100,,,622254096,592596967,579007199,629746522,9416,ERX1361531,ERS954833,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.94151,0.94151,0.08127,0.08228,0.79091,0.79235,0.51421,0.50953,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2342,ERR1289924,ERX1361530,ERS954832,ERP012920,PRJEB11523,Zebrafish eye populations transcriptomics,Zebrafish_eye_populations_transcriptomics-sc-3967,Transcriptome Analysis,To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio  eyes were prepared as follows: 20 30 eyes per condition were collected  dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated  and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform.,ArrayExpress:E ERAD 441,,,,SAMEA3647683,SC,ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647683|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 ctrl noGFP sc 2454954|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ctrl noGFP sc 2454954|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 18222 1#1,15249482,Illumina sequencing of library 15249482  constructed from sample accession ERS954832 for study accession ERP012920.  This is part of an Illumina multiplexed sequencing run 18222 1.  This submission includes reads tagged with the sequence GGACTCCTTAGATCGC.,Nextera dual index qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP012920,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16,18222_1#1.cram,cram,359779800.0,1798899.0,SC RUN 18222 1#1,0:100 1:100,A:84065568;C:96668644;G:92071125;T:86973168;N:1295,100,100,,,84065568,96668644,92071125,86973168,1295,ERX1361530,ERS954832,ERA565862,European Nucleotide Archive,Wellcome Sanger Institute,2,0.9502,0.9506,0.07759,0.07791,0.71772,0.71827,0.44568,0.45005,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United Kingdom,2016-02-23,Undetermined,Embryo,Eye,Sensory System
2343,ERR1125090,ERX1204289,ERS959300,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 H9,SAMEA3652151,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:46Z|External Id:SAMEA3652151|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:46Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 H9|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:913.0|experiment:Original|fsc:30951.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 H9|scientific name:Danio rerio|ssc:120.0|well:H9,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 H9,HIGH 2 H9,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 913.0:egfp fluorescence|Experimental Factor: 30951.0:fsc|Experimental Factor: 120.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_H9_1.fq.gz HIGH_2_H9_2.fq.gz,fastq fastq,512023000.0,2048092.0,E MTAB 3947:HIGH 2 H9 ,0:125 1:125,A:140308299;C:119943911;G:107010121;T:144702244;N:58425,125,125,,,140308299,119943911,107010121,144702244,58425,ERX1204289,ERS959300,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.69292,0.58147,0.39048,0.32294,0.95422,0.95773,0.56684,0.55802,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2344,ERR1125089,ERX1204288,ERS959299,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 H8,SAMEA3652150,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:46Z|External Id:SAMEA3652150|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:46Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 H8|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:998.0|experiment:Original|fsc:20186.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 H8|scientific name:Danio rerio|ssc:119.0|well:H8,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 H8,HIGH 2 H8,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 998.0:egfp fluorescence|Experimental Factor: 20186.0:fsc|Experimental Factor: 119.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_H8_1.fq.gz HIGH_2_H8_2.fq.gz,fastq fastq,748858750.0,2995435.0,E MTAB 3947:HIGH 2 H8 ,0:125 1:125,A:202958013;C:177925445;G:163584543;T:204300253;N:90496,125,125,,,202958013,177925445,163584543,204300253,90496,ERX1204288,ERS959299,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.65867,0.54592,0.42603,0.34824,0.9441,0.94957,0.594,0.58243,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2345,ERR1125088,ERX1204287,ERS959298,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 H7,SAMEA3652149,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:46Z|External Id:SAMEA3652149|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:46Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 H7|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:2221.0|experiment:Original|fsc:33199.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 H7|scientific name:Danio rerio|ssc:116.0|well:H7,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 H7,HIGH 2 H7,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 2221.0:egfp fluorescence|Experimental Factor: 33199.0:fsc|Experimental Factor: 116.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_H7_1.fq.gz HIGH_2_H7_2.fq.gz,fastq fastq,285237750.0,1140951.0,E MTAB 3947:HIGH 2 H7 ,0:125 1:125,A:80046402;C:65911990;G:56070317;T:83174302;N:34739,125,125,,,80046402,65911990,56070317,83174302,34739,ERX1204287,ERS959298,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.61645,0.50639,0.391,0.31746,0.94769,0.95341,0.54299,0.5457,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2346,ERR1125087,ERX1204286,ERS959297,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 H6,SAMEA3652148,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:52Z|External Id:SAMEA3652148|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:52Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 H6|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:465.0|experiment:Original|fsc:29094.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 H6|scientific name:Danio rerio|ssc:89.0|well:H6,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 H6,HIGH 2 H6,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 465.0:egfp fluorescence|Experimental Factor: 29094.0:fsc|Experimental Factor: 89.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_H6_1.fq.gz HIGH_2_H6_2.fq.gz,fastq fastq,638624000.0,2554496.0,E MTAB 3947:HIGH 2 H6 ,0:125 1:125,A:175532916;C:147934323;G:135438512;T:179644376;N:73873,125,125,,,175532916,147934323,135438512,179644376,73873,ERX1204286,ERS959297,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.76122,0.64398,0.31116,0.25959,0.94192,0.94621,0.56148,0.56441,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2347,ERR1125086,ERX1204285,ERS959296,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 H5,SAMEA3652147,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:46Z|External Id:SAMEA3652147|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:46Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 H5|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:889.0|experiment:Original|fsc:22845.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 H5|scientific name:Danio rerio|ssc:110.0|well:H5,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 H5,HIGH 2 H5,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 889.0:egfp fluorescence|Experimental Factor: 22845.0:fsc|Experimental Factor: 110.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_H5_1.fq.gz HIGH_2_H5_2.fq.gz,fastq fastq,503866750.0,2015467.0,E MTAB 3947:HIGH 2 H5 ,0:125 1:125,A:141839569;C:113778792;G:100790228;T:147398469;N:59692,125,125,,,141839569,113778792,100790228,147398469,59692,ERX1204285,ERS959296,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.69291,0.56946,0.50139,0.40831,0.93531,0.94087,0.54026,0.52906,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2348,ERR1125085,ERX1204284,ERS959295,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 H4,SAMEA3652146,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:52Z|External Id:SAMEA3652146|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:52Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 H4|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:705.0|experiment:Original|fsc:28750.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 H4|scientific name:Danio rerio|ssc:130.0|well:H4,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 H4,HIGH 2 H4,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 705.0:egfp fluorescence|Experimental Factor: 28750.0:fsc|Experimental Factor: 130.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_H4_1.fq.gz HIGH_2_H4_2.fq.gz,fastq fastq,559149250.0,2236597.0,E MTAB 3947:HIGH 2 H4 ,0:125 1:125,A:155538823;C:128853235;G:113767154;T:160924124;N:65914,125,125,,,155538823,128853235,113767154,160924124,65914,ERX1204284,ERS959295,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.67927,0.5685,0.39459,0.32681,0.9539,0.95791,0.55659,0.56782,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2349,ERR1125084,ERX1204283,ERS959294,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 H3,SAMEA3652145,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:20Z|External Id:SAMEA3652145|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:25:20Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 H3|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1001.0|experiment:Original|fsc:29702.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 H3|scientific name:Danio rerio|ssc:111.0|well:H3,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 H3,HIGH 2 H3,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1001.0:egfp fluorescence|Experimental Factor: 29702.0:fsc|Experimental Factor: 111.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_H3_1.fq.gz HIGH_2_H3_2.fq.gz,fastq fastq,318391750.0,1273567.0,E MTAB 3947:HIGH 2 H3 ,0:125 1:125,A:92362404;C:70641903;G:63273746;T:92076705;N:36992,125,125,,,92362404,70641903,63273746,92076705,36992,ERX1204283,ERS959294,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.66681,0.55179,0.37708,0.30712,0.95057,0.95517,0.56608,0.56086,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2350,ERR1125083,ERX1204282,ERS959293,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 H2,SAMEA3652144,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:41Z|External Id:SAMEA3652144|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:41Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 H2|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:3681.0|experiment:Original|fsc:24503.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 H2|scientific name:Danio rerio|ssc:120.0|well:H2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 H2,HIGH 2 H2,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 3681.0:egfp fluorescence|Experimental Factor: 24503.0:fsc|Experimental Factor: 120.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_H2_1.fq.gz HIGH_2_H2_2.fq.gz,fastq fastq,1817650750.0,7270603.0,E MTAB 3947:HIGH 2 H2 ,0:125 1:125,A:488811409;C:431331917;G:395349978;T:501936461;N:220985,125,125,,,488811409,431331917,395349978,501936461,220985,ERX1204282,ERS959293,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.61268,0.53203,0.29604,0.25901,0.98506,0.98555,0.48851,0.47275,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2351,ERR1125082,ERX1204281,ERS959292,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 H12,SAMEA3652143,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:20Z|External Id:SAMEA3652143|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:25:20Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 H12|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:381.0|experiment:Original|fsc:35415.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 H12|scientific name:Danio rerio|ssc:70.0|well:H12,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 H12,HIGH 2 H12,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 381.0:egfp fluorescence|Experimental Factor: 35415.0:fsc|Experimental Factor: 70.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_H12_1.fq.gz HIGH_2_H12_2.fq.gz,fastq fastq,547785000.0,2191140.0,E MTAB 3947:HIGH 2 H12 ,0:125 1:125,A:152103377;C:124659105;G:116512220;T:154445053;N:65245,125,125,,,152103377,124659105,116512220,154445053,65245,ERX1204281,ERS959292,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.83057,0.71086,0.22657,0.18894,0.9287,0.93275,0.60907,0.63864,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2352,ERR1125081,ERX1204280,ERS959291,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 H11,SAMEA3652142,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:41Z|External Id:SAMEA3652142|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:41Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 H11|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1377.0|experiment:Original|fsc:34116.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 H11|scientific name:Danio rerio|ssc:126.0|well:H11,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 H11,HIGH 2 H11,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1377.0:egfp fluorescence|Experimental Factor: 34116.0:fsc|Experimental Factor: 126.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_H11_1.fq.gz HIGH_2_H11_2.fq.gz,fastq fastq,564139250.0,2256557.0,E MTAB 3947:HIGH 2 H11 ,0:125 1:125,A:162185525;C:126637668;G:113969658;T:161280891;N:65508,125,125,,,162185525,126637668,113969658,161280891,65508,ERX1204280,ERS959291,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.69685,0.58593,0.39239,0.32847,0.95931,0.96262,0.54396,0.55248,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2353,ERR1125080,ERX1204279,ERS959290,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 H10,SAMEA3652141,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:52Z|External Id:SAMEA3652141|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:52Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 H10|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:2138.0|experiment:Original|fsc:24294.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 H10|scientific name:Danio rerio|ssc:256.0|well:H10,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 H10,HIGH 2 H10,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 2138.0:egfp fluorescence|Experimental Factor: 24294.0:fsc|Experimental Factor: 256.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_H10_1.fq.gz HIGH_2_H10_2.fq.gz,fastq fastq,444255000.0,1777020.0,E MTAB 3947:HIGH 2 H10 ,0:125 1:125,A:123690892;C:101773143;G:92417709;T:126320727;N:52529,125,125,,,123690892,101773143,92417709,126320727,52529,ERX1204279,ERS959290,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.69249,0.57925,0.39113,0.32374,0.95599,0.95962,0.5265,0.49492,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2354,ERR1125079,ERX1204278,ERS959289,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 H1,SAMEA3652140,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:52Z|External Id:SAMEA3652140|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:52Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 H1|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1274.0|experiment:Original|fsc:25937.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 H1|scientific name:Danio rerio|ssc:80.0|well:H1,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 H1,HIGH 2 H1,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1274.0:egfp fluorescence|Experimental Factor: 25937.0:fsc|Experimental Factor: 80.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_H1_1.fq.gz HIGH_2_H1_2.fq.gz,fastq fastq,439078750.0,1756315.0,E MTAB 3947:HIGH 2 H1 ,0:125 1:125,A:124340384;C:99221881;G:89989919;T:125475523;N:51043,125,125,,,124340384,99221881,89989919,125475523,51043,ERX1204278,ERS959289,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.6883,0.57301,0.40963,0.3371,0.95814,0.96258,0.5723,0.57772,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2355,ERR1125078,ERX1204277,ERS959288,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 G9,SAMEA3652139,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:20Z|External Id:SAMEA3652139|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:25:20Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 G9|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:458.0|experiment:Original|fsc:32057.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 G9|scientific name:Danio rerio|ssc:106.0|well:G9,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 G9,HIGH 2 G9,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 458.0:egfp fluorescence|Experimental Factor: 32057.0:fsc|Experimental Factor: 106.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_G9_1.fq.gz HIGH_2_G9_2.fq.gz,fastq fastq,459419750.0,1837679.0,E MTAB 3947:HIGH 2 G9 ,0:125 1:125,A:124965253;C:109515316;G:94767411;T:130118835;N:52935,125,125,,,124965253,109515316,94767411,130118835,52935,ERX1204277,ERS959288,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.78681,0.6729,0.28283,0.23694,0.94966,0.95235,0.45373,0.63151,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2356,ERR1125077,ERX1204276,ERS959287,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 G8,SAMEA3652138,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:49Z|External Id:SAMEA3652138|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:49Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 G8|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:971.0|experiment:Original|fsc:23872.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 G8|scientific name:Danio rerio|ssc:78.0|well:G8,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 G8,HIGH 2 G8,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 971.0:egfp fluorescence|Experimental Factor: 23872.0:fsc|Experimental Factor: 78.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_G8_1.fq.gz HIGH_2_G8_2.fq.gz,fastq fastq,575080750.0,2300323.0,E MTAB 3947:HIGH 2 G8 ,0:125 1:125,A:158832969;C:136424495;G:117844174;T:161912153;N:66959,125,125,,,158832969,136424495,117844174,161912153,66959,ERX1204276,ERS959287,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.67294,0.56042,0.36371,0.29887,0.94199,0.94815,0.52948,0.48976,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2357,ERR1125076,ERX1204275,ERS959286,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 G7,SAMEA3652137,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:41Z|External Id:SAMEA3652137|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:41Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 G7|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:732.0|experiment:Original|fsc:20684.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 G7|scientific name:Danio rerio|ssc:118.0|well:G7,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 G7,HIGH 2 G7,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 732.0:egfp fluorescence|Experimental Factor: 20684.0:fsc|Experimental Factor: 118.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_G7_1.fq.gz HIGH_2_G7_2.fq.gz,fastq fastq,1047728000.0,4190912.0,E MTAB 3947:HIGH 2 G7 ,0:125 1:125,A:278741929;C:255515134;G:223466753;T:289885657;N:118527,125,125,,,278741929,255515134,223466753,289885657,118527,ERX1204275,ERS959286,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.88624,0.77051,0.17524,0.151,0.92585,0.92906,0.57938,0.48524,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2358,ERR1125075,ERX1204274,ERS959285,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 G6,SAMEA3652136,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:49Z|External Id:SAMEA3652136|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:49Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 G6|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:513.0|experiment:Original|fsc:55609.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 G6|scientific name:Danio rerio|ssc:289.0|well:G6,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 G6,HIGH 2 G6,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 513.0:egfp fluorescence|Experimental Factor: 55609.0:fsc|Experimental Factor: 289.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_G6_1.fq.gz HIGH_2_G6_2.fq.gz,fastq fastq,827454750.0,3309819.0,E MTAB 3947:HIGH 2 G6 ,0:125 1:125,A:227586441;C:192249391;G:170692002;T:236829325;N:97591,125,125,,,227586441,192249391,170692002,236829325,97591,ERX1204274,ERS959285,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.79015,0.6601,0.39392,0.32355,0.92346,0.92936,0.46424,0.60593,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2359,ERR1125074,ERX1204273,ERS959284,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 G5,SAMEA3652135,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:49Z|External Id:SAMEA3652135|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:49Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 G5|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:2309.0|experiment:Original|fsc:28317.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 G5|scientific name:Danio rerio|ssc:119.0|well:G5,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 G5,HIGH 2 G5,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 2309.0:egfp fluorescence|Experimental Factor: 28317.0:fsc|Experimental Factor: 119.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_G5_1.fq.gz HIGH_2_G5_2.fq.gz,fastq fastq,710441250.0,2841765.0,E MTAB 3947:HIGH 2 G5 ,0:125 1:125,A:193023736;C:169567853;G:145782205;T:201982364;N:85092,125,125,,,193023736,169567853,145782205,201982364,85092,ERX1204273,ERS959284,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.71466,0.59939,0.38234,0.3158,0.95428,0.95765,0.55915,0.52948,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2360,ERR1125073,ERX1204272,ERS959283,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 G4,SAMEA3652134,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:49Z|External Id:SAMEA3652134|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:49Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 G4|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:3232.0|experiment:Original|fsc:27085.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 G4|scientific name:Danio rerio|ssc:153.0|well:G4,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 G4,HIGH 2 G4,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 3232.0:egfp fluorescence|Experimental Factor: 27085.0:fsc|Experimental Factor: 153.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_G4_1.fq.gz HIGH_2_G4_2.fq.gz,fastq fastq,481548750.0,1926195.0,E MTAB 3947:HIGH 2 G4 ,0:125 1:125,A:134258673;C:112027431;G:94702679;T:140510643;N:49324,125,125,,,134258673,112027431,94702679,140510643,49324,ERX1204272,ERS959283,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.693,0.57366,0.44712,0.36776,0.95207,0.95643,0.55781,0.55513,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2361,ERR1125072,ERX1204271,ERS959282,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 G3,SAMEA3652133,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:41Z|External Id:SAMEA3652133|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:41Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 G3|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1147.0|experiment:Original|fsc:21062.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 G3|scientific name:Danio rerio|ssc:163.0|well:G3,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 G3,HIGH 2 G3,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1147.0:egfp fluorescence|Experimental Factor: 21062.0:fsc|Experimental Factor: 163.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_G3_1.fq.gz HIGH_2_G3_2.fq.gz,fastq fastq,580950500.0,2323802.0,E MTAB 3947:HIGH 2 G3 ,0:125 1:125,A:166020999;C:131541373;G:114686700;T:168631560;N:69868,125,125,,,166020999,131541373,114686700,168631560,69868,ERX1204271,ERS959282,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.74429,0.62191,0.4281,0.35388,0.9489,0.95302,0.57486,0.57113,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2362,ERR1125071,ERX1204270,ERS959281,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 G2,SAMEA3652132,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:41Z|External Id:SAMEA3652132|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:41Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 G2|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1260.0|experiment:Original|fsc:19085.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 G2|scientific name:Danio rerio|ssc:258.0|well:G2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 G2,HIGH 2 G2,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1260.0:egfp fluorescence|Experimental Factor: 19085.0:fsc|Experimental Factor: 258.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_G2_1.fq.gz HIGH_2_G2_2.fq.gz,fastq fastq,981968750.0,3927875.0,E MTAB 3947:HIGH 2 G2 ,0:125 1:125,A:269236295;C:232331615;G:201687129;T:278600621;N:113090,125,125,,,269236295,232331615,201687129,278600621,113090,ERX1204270,ERS959281,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.76104,0.64535,0.39808,0.33408,0.95962,0.96347,0.58431,0.58783,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2363,ERR1125070,ERX1204269,ERS959280,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 G12,SAMEA3652131,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:41Z|External Id:SAMEA3652131|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:41Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 G12|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:496.0|experiment:Original|fsc:30728.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 G12|scientific name:Danio rerio|ssc:74.0|well:G12,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 G12,HIGH 2 G12,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 496.0:egfp fluorescence|Experimental Factor: 30728.0:fsc|Experimental Factor: 74.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_G12_1.fq.gz HIGH_2_G12_2.fq.gz,fastq fastq,1018091000.0,4072364.0,E MTAB 3947:HIGH 2 G12 ,0:125 1:125,A:282601299;C:235501274;G:209565850;T:290299755;N:122822,125,125,,,282601299,235501274,209565850,290299755,122822,ERX1204269,ERS959280,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.74885,0.63685,0.40559,0.34365,0.95946,0.96305,0.57059,0.57898,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2364,ERR1125069,ERX1204268,ERS959279,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 G11,SAMEA3652130,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:41Z|External Id:SAMEA3652130|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:41Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 G11|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1223.0|experiment:Original|fsc:29091.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 G11|scientific name:Danio rerio|ssc:107.0|well:G11,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 G11,HIGH 2 G11,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1223.0:egfp fluorescence|Experimental Factor: 29091.0:fsc|Experimental Factor: 107.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_G11_1.fq.gz HIGH_2_G11_2.fq.gz,fastq fastq,538346500.0,2153386.0,E MTAB 3947:HIGH 2 G11 ,0:125 1:125,A:153448853;C:123870390;G:106224297;T:154741718;N:61242,125,125,,,153448853,123870390,106224297,154741718,61242,ERX1204268,ERS959279,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.69048,0.59053,0.29294,0.25224,0.96944,0.97143,0.53644,0.53596,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2365,ERR1125068,ERX1204267,ERS959278,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 G10,SAMEA3652129,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:41Z|External Id:SAMEA3652129|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:41Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 G10|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:2387.0|experiment:Original|fsc:25703.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 G10|scientific name:Danio rerio|ssc:105.0|well:G10,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 G10,HIGH 2 G10,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 2387.0:egfp fluorescence|Experimental Factor: 25703.0:fsc|Experimental Factor: 105.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_G10_1.fq.gz HIGH_2_G10_2.fq.gz,fastq fastq,515389500.0,2061558.0,E MTAB 3947:HIGH 2 G10 ,0:125 1:125,A:142747105;C:120191159;G:104738517;T:147652040;N:60679,125,125,,,142747105,120191159,104738517,147652040,60679,ERX1204267,ERS959278,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.7361,0.6268,0.32462,0.27366,0.95897,0.9624,0.60978,0.45744,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2366,ERR1125067,ERX1204266,ERS959277,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 G1,SAMEA3652128,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:49Z|External Id:SAMEA3652128|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:49Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 G1|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:433.0|experiment:Original|fsc:30363.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 G1|scientific name:Danio rerio|ssc:160.0|well:G1,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 G1,HIGH 2 G1,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 433.0:egfp fluorescence|Experimental Factor: 30363.0:fsc|Experimental Factor: 160.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_G1_1.fq.gz HIGH_2_G1_2.fq.gz,fastq fastq,1038747250.0,4154989.0,E MTAB 3947:HIGH 2 G1 ,0:125 1:125,A:288549918;C:239664221;G:218176409;T:292239189;N:117513,125,125,,,288549918,239664221,218176409,292239189,117513,ERX1204266,ERS959277,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.91376,0.8013,0.14576,0.12583,0.90532,0.91015,0.58217,0.58053,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2367,ERR1125066,ERX1204265,ERS959276,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 F9,SAMEA3652127,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:20Z|External Id:SAMEA3652127|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:25:20Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 F9|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1159.0|experiment:Original|fsc:33914.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 F9|scientific name:Danio rerio|ssc:86.0|well:F9,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 F9,HIGH 2 F9,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1159.0:egfp fluorescence|Experimental Factor: 33914.0:fsc|Experimental Factor: 86.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_F9_1.fq.gz HIGH_2_F9_2.fq.gz,fastq fastq,375664250.0,1502657.0,E MTAB 3947:HIGH 2 F9 ,0:125 1:125,A:104160254;C:87140047;G:76475791;T:107842008;N:46150,125,125,,,104160254,87140047,76475791,107842008,46150,ERX1204265,ERS959276,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.67321,0.55971,0.39094,0.3217,0.95576,0.96008,0.55917,0.55154,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2368,ERR1125065,ERX1204264,ERS959275,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 F8,SAMEA3652126,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:20Z|External Id:SAMEA3652126|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:25:20Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 F8|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:2626.0|experiment:Original|fsc:31408.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 F8|scientific name:Danio rerio|ssc:123.0|well:F8,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 F8,HIGH 2 F8,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 2626.0:egfp fluorescence|Experimental Factor: 31408.0:fsc|Experimental Factor: 123.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_F8_1.fq.gz HIGH_2_F8_2.fq.gz,fastq fastq,627584250.0,2510337.0,E MTAB 3947:HIGH 2 F8 ,0:125 1:125,A:171232891;C:149087394;G:134913860;T:172276861;N:73244,125,125,,,171232891,149087394,134913860,172276861,73244,ERX1204264,ERS959275,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.65263,0.54254,0.40577,0.33392,0.95716,0.96106,0.51257,0.51973,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2369,ERR1125064,ERX1204263,ERS959274,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 F7,SAMEA3652125,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:49Z|External Id:SAMEA3652125|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:49Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 F7|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:2187.0|experiment:Original|fsc:24219.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 F7|scientific name:Danio rerio|ssc:110.0|well:F7,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 F7,HIGH 2 F7,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 2187.0:egfp fluorescence|Experimental Factor: 24219.0:fsc|Experimental Factor: 110.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_F7_1.fq.gz HIGH_2_F7_2.fq.gz,fastq fastq,479393250.0,1917573.0,E MTAB 3947:HIGH 2 F7 ,0:125 1:125,A:130417494;C:114686632;G:98752118;T:135482075;N:54931,125,125,,,130417494,114686632,98752118,135482075,54931,ERX1204263,ERS959274,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.6207,0.51096,0.40173,0.32857,0.9567,0.96209,0.55385,0.54813,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2370,ERR1125063,ERX1204262,ERS959273,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 F6,SAMEA3652124,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:35Z|External Id:SAMEA3652124|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:35Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 F6|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1050.0|experiment:Original|fsc:22592.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 F6|scientific name:Danio rerio|ssc:79.0|well:F6,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 F6,HIGH 2 F6,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1050.0:egfp fluorescence|Experimental Factor: 22592.0:fsc|Experimental Factor: 79.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_F6_1.fq.gz HIGH_2_F6_2.fq.gz,fastq fastq,1044289250.0,4177157.0,E MTAB 3947:HIGH 2 F6 ,0:125 1:125,A:287995598;C:239955378;G:219257648;T:296959565;N:121061,125,125,,,287995598,239955378,219257648,296959565,121061,ERX1204262,ERS959273,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.76336,0.63064,0.59117,0.48599,0.93618,0.94186,0.55558,0.54831,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2371,ERR1125062,ERX1204261,ERS959272,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 F5,SAMEA3652123,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:49Z|External Id:SAMEA3652123|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:49Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 F5|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:3369.0|experiment:Original|fsc:41743.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 F5|scientific name:Danio rerio|ssc:152.0|well:F5,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 F5,HIGH 2 F5,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 3369.0:egfp fluorescence|Experimental Factor: 41743.0:fsc|Experimental Factor: 152.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_F5_1.fq.gz HIGH_2_F5_2.fq.gz,fastq fastq,808296750.0,3233187.0,E MTAB 3947:HIGH 2 F5 ,0:125 1:125,A:217965654;C:192224466;G:173071476;T:224941585;N:93569,125,125,,,217965654,192224466,173071476,224941585,93569,ERX1204261,ERS959272,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.73306,0.62033,0.4006,0.33584,0.95909,0.9625,0.53447,0.5403,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2372,ERR1125061,ERX1204260,ERS959271,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 F4,SAMEA3652122,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:49Z|External Id:SAMEA3652122|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:49Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 F4|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1040.0|experiment:Original|fsc:23136.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 F4|scientific name:Danio rerio|ssc:176.0|well:F4,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 F4,HIGH 2 F4,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1040.0:egfp fluorescence|Experimental Factor: 23136.0:fsc|Experimental Factor: 176.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_F4_1.fq.gz HIGH_2_F4_2.fq.gz,fastq fastq,684758500.0,2739034.0,E MTAB 3947:HIGH 2 F4 ,0:125 1:125,A:191204926;C:156704038;G:137681431;T:199089228;N:78877,125,125,,,191204926,156704038,137681431,199089228,78877,ERX1204260,ERS959271,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.73464,0.6009,0.56069,0.45592,0.92874,0.936,0.56652,0.56984,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2373,ERR1125060,ERX1204259,ERS959270,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 F3,SAMEA3652121,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:34Z|External Id:SAMEA3652121|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:34Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 F3|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:466.0|experiment:Original|fsc:29321.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 F3|scientific name:Danio rerio|ssc:105.0|well:F3,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 F3,HIGH 2 F3,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 466.0:egfp fluorescence|Experimental Factor: 29321.0:fsc|Experimental Factor: 105.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_F3_1.fq.gz HIGH_2_F3_2.fq.gz,fastq fastq,631831750.0,2527327.0,E MTAB 3947:HIGH 2 F3 ,0:125 1:125,A:176511026;C:145144478;G:132625105;T:177477974;N:73167,125,125,,,176511026,145144478,132625105,177477974,73167,ERX1204259,ERS959270,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.7961,0.67398,0.31039,0.25659,0.93545,0.93955,0.55903,0.57192,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2374,ERR1125059,ERX1204258,ERS959269,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 F2,SAMEA3652120,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:45Z|External Id:SAMEA3652120|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:45Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 F2|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1762.0|experiment:Original|fsc:32483.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 F2|scientific name:Danio rerio|ssc:160.0|well:F2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 F2,HIGH 2 F2,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1762.0:egfp fluorescence|Experimental Factor: 32483.0:fsc|Experimental Factor: 160.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_F2_1.fq.gz HIGH_2_F2_2.fq.gz,fastq fastq,792024500.0,3168098.0,E MTAB 3947:HIGH 2 F2 ,0:125 1:125,A:216898622;C:185945515;G:166158006;T:222930188;N:92169,125,125,,,216898622,185945515,166158006,222930188,92169,ERX1204258,ERS959269,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.67742,0.56577,0.36086,0.29693,0.96015,0.96325,0.46955,0.50053,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2375,ERR1125058,ERX1204257,ERS959268,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 F12,SAMEA3652119,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:45Z|External Id:SAMEA3652119|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:45Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 F12|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:947.0|experiment:Original|fsc:65535.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 F12|scientific name:Danio rerio|ssc:1166.0|well:F12,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 F12,HIGH 2 F12,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 947.0:egfp fluorescence|Experimental Factor: 65535.0:fsc|Experimental Factor: 1166.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_F12_1.fq.gz HIGH_2_F12_2.fq.gz,fastq fastq,687760000.0,2751040.0,E MTAB 3947:HIGH 2 F12 ,0:125 1:125,A:190873427;C:157656613;G:144460249;T:194688401;N:81310,125,125,,,190873427,157656613,144460249,194688401,81310,ERX1204257,ERS959268,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.73646,0.61046,0.32015,0.26493,0.94592,0.95055,0.63296,0.63645,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2376,ERR1125057,ERX1204256,ERS959267,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 F11,SAMEA3652118,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:20Z|External Id:SAMEA3652118|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:25:20Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 F11|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1347.0|experiment:Original|fsc:20073.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 F11|scientific name:Danio rerio|ssc:92.0|well:F11,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 F11,HIGH 2 F11,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1347.0:egfp fluorescence|Experimental Factor: 20073.0:fsc|Experimental Factor: 92.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_F11_1.fq.gz HIGH_2_F11_2.fq.gz,fastq fastq,626744500.0,2506978.0,E MTAB 3947:HIGH 2 F11 ,0:125 1:125,A:175730345;C:144656405;G:130504517;T:175782178;N:71055,125,125,,,175730345,144656405,130504517,175782178,71055,ERX1204256,ERS959267,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.66424,0.55168,0.35564,0.29132,0.95996,0.96439,0.51242,0.53231,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2377,ERR1125056,ERX1204255,ERS959266,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 F10,SAMEA3652117,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:20Z|External Id:SAMEA3652117|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:25:20Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 F10|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:862.0|experiment:Original|fsc:35214.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 F10|scientific name:Danio rerio|ssc:109.0|well:F10,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 F10,HIGH 2 F10,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 862.0:egfp fluorescence|Experimental Factor: 35214.0:fsc|Experimental Factor: 109.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_F10_1.fq.gz HIGH_2_F10_2.fq.gz,fastq fastq,519439750.0,2077759.0,E MTAB 3947:HIGH 2 F10 ,0:125 1:125,A:143192126;C:120188838;G:109094271;T:146904293;N:60222,125,125,,,143192126,120188838,109094271,146904293,60222,ERX1204255,ERS959266,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.72897,0.60737,0.41624,0.34359,0.95398,0.95777,0.53614,0.53515,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2378,ERR1125055,ERX1204254,ERS959265,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 F1,SAMEA3652116,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:34Z|External Id:SAMEA3652116|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:34Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 F1|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1855.0|experiment:Original|fsc:31068.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 F1|scientific name:Danio rerio|ssc:76.0|well:F1,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 F1,HIGH 2 F1,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1855.0:egfp fluorescence|Experimental Factor: 31068.0:fsc|Experimental Factor: 76.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_F1_1.fq.gz HIGH_2_F1_2.fq.gz,fastq fastq,600950250.0,2403801.0,E MTAB 3947:HIGH 2 F1 ,0:125 1:125,A:166807507;C:139033939;G:126409681;T:168629741;N:69382,125,125,,,166807507,139033939,126409681,168629741,69382,ERX1204254,ERS959265,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.74055,0.63081,0.36303,0.30846,0.96662,0.96942,0.55632,0.56237,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2379,ERR1125054,ERX1204253,ERS959264,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 E9,SAMEA3652115,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:45Z|External Id:SAMEA3652115|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:45Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 E9|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:532.0|experiment:Original|fsc:27121.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 E9|scientific name:Danio rerio|ssc:72.0|well:E9,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 E9,HIGH 2 E9,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 532.0:egfp fluorescence|Experimental Factor: 27121.0:fsc|Experimental Factor: 72.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_E9_1.fq.gz HIGH_2_E9_2.fq.gz,fastq fastq,187484500.0,749938.0,E MTAB 3947:HIGH 2 E9 ,0:125 1:125,A:51434671;C:44934503;G:37255767;T:53838087;N:21472,125,125,,,51434671,44934503,37255767,53838087,21472,ERX1204253,ERS959264,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.66473,0.554,0.43891,0.36489,0.95789,0.96084,0.53896,0.54575,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2380,ERR1125053,ERX1204252,ERS959263,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 E8,SAMEA3652114,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:45Z|External Id:SAMEA3652114|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:45Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 E8|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1875.0|experiment:Original|fsc:25042.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 E8|scientific name:Danio rerio|ssc:134.0|well:E8,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 E8,HIGH 2 E8,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1875.0:egfp fluorescence|Experimental Factor: 25042.0:fsc|Experimental Factor: 134.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_E8_1.fq.gz HIGH_2_E8_2.fq.gz,fastq fastq,876355250.0,3505421.0,E MTAB 3947:HIGH 2 E8 ,0:125 1:125,A:237393091;C:210793475;G:186228956;T:241839031;N:100697,125,125,,,237393091,210793475,186228956,241839031,100697,ERX1204252,ERS959263,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.73851,0.61987,0.46723,0.38952,0.9568,0.96136,0.54404,0.54092,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2381,ERR1125052,ERX1204251,ERS959262,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 E7,SAMEA3652113,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:45Z|External Id:SAMEA3652113|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:45Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 E7|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1059.0|experiment:Original|fsc:14223.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 E7|scientific name:Danio rerio|ssc:117.0|well:E7,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 E7,HIGH 2 E7,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1059.0:egfp fluorescence|Experimental Factor: 14223.0:fsc|Experimental Factor: 117.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_E7_1.fq.gz HIGH_2_E7_2.fq.gz,fastq fastq,501706250.0,2006825.0,E MTAB 3947:HIGH 2 E7 ,0:125 1:125,A:135325209;C:121579138;G:102670085;T:142073920;N:57898,125,125,,,135325209,121579138,102670085,142073920,57898,ERX1204251,ERS959262,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.71512,0.60628,0.42465,0.35806,0.95777,0.96226,0.56261,0.55962,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2382,ERR1125051,ERX1204250,ERS959261,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 E6,SAMEA3652112,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:34Z|External Id:SAMEA3652112|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:34Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 E6|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1130.0|experiment:Original|fsc:13402.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 E6|scientific name:Danio rerio|ssc:136.0|well:E6,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 E6,HIGH 2 E6,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1130.0:egfp fluorescence|Experimental Factor: 13402.0:fsc|Experimental Factor: 136.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_E6_1.fq.gz HIGH_2_E6_2.fq.gz,fastq fastq,390029250.0,1560117.0,E MTAB 3947:HIGH 2 E6 ,0:125 1:125,A:104987389;C:93901036;G:81049566;T:110046887;N:44372,125,125,,,104987389,93901036,81049566,110046887,44372,ERX1204250,ERS959261,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.6907,0.58093,0.61893,0.52232,0.96203,0.96802,0.64719,0.65774,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2383,ERR1125050,ERX1204249,ERS959260,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 E5,SAMEA3652111,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:34Z|External Id:SAMEA3652111|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:34Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 E5|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:747.0|experiment:Original|fsc:15709.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 E5|scientific name:Danio rerio|ssc:61.0|well:E5,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 E5,HIGH 2 E5,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 747.0:egfp fluorescence|Experimental Factor: 15709.0:fsc|Experimental Factor: 61.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_E5_1.fq.gz HIGH_2_E5_2.fq.gz,fastq fastq,560963000.0,2243852.0,E MTAB 3947:HIGH 2 E5 ,0:125 1:125,A:147718067;C:139609684;G:118562561;T:155008803;N:63885,125,125,,,147718067,139609684,118562561,155008803,63885,ERX1204249,ERS959260,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.63449,0.5312,0.49742,0.41545,0.96964,0.97258,0.68819,0.69503,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2384,ERR1125049,ERX1204248,ERS959259,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 E4,SAMEA3652110,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:34Z|External Id:SAMEA3652110|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:34Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 E4|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1631.0|experiment:Original|fsc:26215.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 E4|scientific name:Danio rerio|ssc:83.0|well:E4,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 E4,HIGH 2 E4,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1631.0:egfp fluorescence|Experimental Factor: 26215.0:fsc|Experimental Factor: 83.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_E4_1.fq.gz HIGH_2_E4_2.fq.gz,fastq fastq,525117250.0,2100469.0,E MTAB 3947:HIGH 2 E4 ,0:125 1:125,A:142914307;C:126324808;G:106185175;T:149634797;N:58163,125,125,,,142914307,126324808,106185175,149634797,58163,ERX1204248,ERS959259,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.71092,0.59914,0.41274,0.34488,0.95696,0.9601,0.54284,0.5638,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2385,ERR1125048,ERX1204247,ERS959258,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 E3,SAMEA3652109,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:45Z|External Id:SAMEA3652109|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:45Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 E3|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:849.0|experiment:Original|fsc:28706.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 E3|scientific name:Danio rerio|ssc:105.0|well:E3,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 E3,HIGH 2 E3,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 849.0:egfp fluorescence|Experimental Factor: 28706.0:fsc|Experimental Factor: 105.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_E3_1.fq.gz HIGH_2_E3_2.fq.gz,fastq fastq,627639500.0,2510558.0,E MTAB 3947:HIGH 2 E3 ,0:125 1:125,A:173942067;C:147827595;G:129015836;T:176783406;N:70596,125,125,,,173942067,147827595,129015836,176783406,70596,ERX1204247,ERS959258,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.70206,0.58547,0.40534,0.3338,0.95599,0.95948,0.54209,0.46412,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2386,ERR1125047,ERX1204246,ERS959257,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 E2,SAMEA3652108,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:20Z|External Id:SAMEA3652108|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:25:20Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 E2|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:959.0|experiment:Original|fsc:29913.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 E2|scientific name:Danio rerio|ssc:65.0|well:E2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 E2,HIGH 2 E2,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 959.0:egfp fluorescence|Experimental Factor: 29913.0:fsc|Experimental Factor: 65.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_E2_1.fq.gz HIGH_2_E2_2.fq.gz,fastq fastq,792161250.0,3168645.0,E MTAB 3947:HIGH 2 E2 ,0:125 1:125,A:215870277;C:188878534;G:163314847;T:224007577;N:90015,125,125,,,215870277,188878534,163314847,224007577,90015,ERX1204246,ERS959257,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.73698,0.61661,0.42238,0.34998,0.95755,0.96118,0.56067,0.57279,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2387,ERR1125046,ERX1204245,ERS959256,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 E12,SAMEA3652107,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:18Z|External Id:SAMEA3652107|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:25:18Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 E12|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1247.0|experiment:Original|fsc:37953.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 E12|scientific name:Danio rerio|ssc:79.0|well:E12,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 E12,HIGH 2 E12,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1247.0:egfp fluorescence|Experimental Factor: 37953.0:fsc|Experimental Factor: 79.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_E12_1.fq.gz HIGH_2_E12_2.fq.gz,fastq fastq,788729750.0,3154919.0,E MTAB 3947:HIGH 2 E12 ,0:125 1:125,A:218153507;C:183757145;G:162306106;T:224424051;N:88941,125,125,,,218153507,183757145,162306106,224424051,88941,ERX1204245,ERS959256,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.73027,0.61432,0.38289,0.31853,0.95584,0.95868,0.55225,0.49473,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2388,ERR1125045,ERX1204244,ERS959255,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 E11,SAMEA3652106,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:45Z|External Id:SAMEA3652106|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:45Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 E11|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1177.0|experiment:Original|fsc:34414.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 E11|scientific name:Danio rerio|ssc:127.0|well:E11,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 E11,HIGH 2 E11,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1177.0:egfp fluorescence|Experimental Factor: 34414.0:fsc|Experimental Factor: 127.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_E11_1.fq.gz HIGH_2_E11_2.fq.gz,fastq fastq,511486250.0,2045945.0,E MTAB 3947:HIGH 2 E11 ,0:125 1:125,A:144668385;C:117705552;G:101783406;T:147271313;N:57594,125,125,,,144668385,117705552,101783406,147271313,57594,ERX1204244,ERS959255,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.7158,0.59048,0.45882,0.37406,0.93839,0.94371,0.54766,0.54436,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2389,ERR1125044,ERX1204243,ERS959254,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 E10,SAMEA3652105,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:18Z|External Id:SAMEA3652105|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:25:18Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 E10|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:849.0|experiment:Original|fsc:36542.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 E10|scientific name:Danio rerio|ssc:119.0|well:E10,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 E10,HIGH 2 E10,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 849.0:egfp fluorescence|Experimental Factor: 36542.0:fsc|Experimental Factor: 119.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_E10_1.fq.gz HIGH_2_E10_2.fq.gz,fastq fastq,411904750.0,1647619.0,E MTAB 3947:HIGH 2 E10 ,0:125 1:125,A:113115595;C:97711878;G:83747481;T:117282071;N:47725,125,125,,,113115595,97711878,83747481,117282071,47725,ERX1204243,ERS959254,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.70307,0.59003,0.43501,0.36371,0.95891,0.96288,0.57044,0.57958,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2390,ERR1125043,ERX1204242,ERS959253,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 E1,SAMEA3652104,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:45Z|External Id:SAMEA3652104|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:45Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 E1|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:962.0|experiment:Original|fsc:21930.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 E1|scientific name:Danio rerio|ssc:184.0|well:E1,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 E1,HIGH 2 E1,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 962.0:egfp fluorescence|Experimental Factor: 21930.0:fsc|Experimental Factor: 184.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_E1_1.fq.gz HIGH_2_E1_2.fq.gz,fastq fastq,610366500.0,2441466.0,E MTAB 3947:HIGH 2 E1 ,0:125 1:125,A:169301384;C:142276900;G:124701466;T:174014261;N:72489,125,125,,,169301384,142276900,124701466,174014261,72489,ERX1204242,ERS959253,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.76142,0.64488,0.35538,0.29968,0.95158,0.95465,0.59421,0.5893,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2391,ERR1125042,ERX1204241,ERS959252,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 D9,SAMEA3652103,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:34Z|External Id:SAMEA3652103|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:34Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 D9|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:389.0|experiment:Original|fsc:33044.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 D9|scientific name:Danio rerio|ssc:90.0|well:D9,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 D9,HIGH 2 D9,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 389.0:egfp fluorescence|Experimental Factor: 33044.0:fsc|Experimental Factor: 90.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_D9_1.fq.gz HIGH_2_D9_2.fq.gz,fastq fastq,773947000.0,3095788.0,E MTAB 3947:HIGH 2 D9 ,0:125 1:125,A:207149087;C:187591047;G:163006079;T:216107138;N:93649,125,125,,,207149087,187591047,163006079,216107138,93649,ERX1204241,ERS959252,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.77315,0.64743,0.43084,0.3564,0.94231,0.94852,0.56204,0.55905,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2392,ERR1125041,ERX1204240,ERS959251,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 D8,SAMEA3652102,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:34Z|External Id:SAMEA3652102|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:34Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 D8|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1738.0|experiment:Original|fsc:14264.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 D8|scientific name:Danio rerio|ssc:186.0|well:D8,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 D8,HIGH 2 D8,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1738.0:egfp fluorescence|Experimental Factor: 14264.0:fsc|Experimental Factor: 186.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_D8_1.fq.gz HIGH_2_D8_2.fq.gz,fastq fastq,772715000.0,3090860.0,E MTAB 3947:HIGH 2 D8 ,0:125 1:125,A:208112215;C:186695249;G:165717839;T:212096791;N:92906,125,125,,,208112215,186695249,165717839,212096791,92906,ERX1204240,ERS959251,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.72445,0.61392,0.49615,0.42224,0.9586,0.96311,0.53308,0.537,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2393,ERR1125040,ERX1204239,ERS959250,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 D7,SAMEA3652101,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:29Z|External Id:SAMEA3652101|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:29Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 D7|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:2231.0|experiment:Original|fsc:39432.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 D7|scientific name:Danio rerio|ssc:118.0|well:D7,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 D7,HIGH 2 D7,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 2231.0:egfp fluorescence|Experimental Factor: 39432.0:fsc|Experimental Factor: 118.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_D7_1.fq.gz HIGH_2_D7_2.fq.gz,fastq fastq,638914250.0,2555657.0,E MTAB 3947:HIGH 2 D7 ,0:125 1:125,A:173591457;C:153344648;G:131413605;T:180487805;N:76735,125,125,,,173591457,153344648,131413605,180487805,76735,ERX1204239,ERS959250,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.74423,0.64152,0.31699,0.27653,0.96899,0.97177,0.51422,0.53472,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2394,ERR1125039,ERX1204238,ERS959249,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 D6,SAMEA3652100,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:18Z|External Id:SAMEA3652100|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:25:18Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 D6|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1396.0|experiment:Original|fsc:26170.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 D6|scientific name:Danio rerio|ssc:155.0|well:D6,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 D6,HIGH 2 D6,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1396.0:egfp fluorescence|Experimental Factor: 26170.0:fsc|Experimental Factor: 155.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_D6_1.fq.gz HIGH_2_D6_2.fq.gz,fastq fastq,750059000.0,3000236.0,E MTAB 3947:HIGH 2 D6 ,0:125 1:125,A:202887309;C:178977639;G:157262690;T:210842722;N:88640,125,125,,,202887309,178977639,157262690,210842722,88640,ERX1204238,ERS959249,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.70502,0.59278,0.39558,0.33132,0.95418,0.95958,0.55404,0.54722,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2395,ERR1125038,ERX1204237,ERS959248,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 D5,SAMEA3652099,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:29Z|External Id:SAMEA3652099|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:29Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 D5|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:964.0|experiment:Original|fsc:15292.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 D5|scientific name:Danio rerio|ssc:130.0|well:D5,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 D5,HIGH 2 D5,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 964.0:egfp fluorescence|Experimental Factor: 15292.0:fsc|Experimental Factor: 130.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_D5_1.fq.gz HIGH_2_D5_2.fq.gz,fastq fastq,543768500.0,2175074.0,E MTAB 3947:HIGH 2 D5 ,0:125 1:125,A:148137359;C:129956618;G:110971408;T:154637980;N:65135,125,125,,,148137359,129956618,110971408,154637980,65135,ERX1204237,ERS959248,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.71658,0.60321,0.38889,0.32735,0.96063,0.96493,0.51871,0.5223,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2396,ERR1125037,ERX1204236,ERS959247,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 D4,SAMEA3652098,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:29Z|External Id:SAMEA3652098|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:29Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 D4|broker name:ArrayExpress|cells:0.0|common name:zebrafish|condition:EGFP high|experiment:Original|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 D4|scientific name:Danio rerio|well:D4,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 D4,HIGH 2 D4,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_D4_1.fq.gz HIGH_2_D4_2.fq.gz,fastq fastq,312928750.0,1251715.0,E MTAB 3947:HIGH 2 D4 ,0:125 1:125,A:85281040;C:76897881;G:61603254;T:89108903;N:37672,125,125,,,85281040,76897881,61603254,89108903,37672,ERX1204236,ERS959247,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.35115,0.31089,0.35025,0.3107,0.99776,0.99957,0.61718,0.54545,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2397,ERR1125036,ERX1204235,ERS959246,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 D3,SAMEA3652097,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:18Z|External Id:SAMEA3652097|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:25:18Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 D3|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:803.0|experiment:Original|fsc:31420.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 D3|scientific name:Danio rerio|ssc:140.0|well:D3,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 D3,HIGH 2 D3,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 803.0:egfp fluorescence|Experimental Factor: 31420.0:fsc|Experimental Factor: 140.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_D3_1.fq.gz HIGH_2_D3_2.fq.gz,fastq fastq,723847000.0,2895388.0,E MTAB 3947:HIGH 2 D3 ,0:125 1:125,A:200458575;C:169877197;G:150167810;T:203256930;N:86488,125,125,,,200458575,169877197,150167810,203256930,86488,ERX1204235,ERS959246,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.75419,0.64034,0.36984,0.3151,0.95708,0.96039,0.53095,0.50284,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2398,ERR1125035,ERX1204234,ERS959245,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 D2,SAMEA3652096,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:29Z|External Id:SAMEA3652096|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:29Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 D2|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:662.0|experiment:Original|fsc:32552.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 D2|scientific name:Danio rerio|ssc:95.0|well:D2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 D2,HIGH 2 D2,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 662.0:egfp fluorescence|Experimental Factor: 32552.0:fsc|Experimental Factor: 95.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_D2_1.fq.gz HIGH_2_D2_2.fq.gz,fastq fastq,694990250.0,2779961.0,E MTAB 3947:HIGH 2 D2 ,0:125 1:125,A:189494688;C:165653500;G:143769621;T:195989087;N:83354,125,125,,,189494688,165653500,143769621,195989087,83354,ERX1204234,ERS959245,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.72644,0.61252,0.34721,0.29373,0.95793,0.96286,0.55784,0.55774,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2399,ERR1125034,ERX1204233,ERS959244,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 D12,SAMEA3652095,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:42Z|External Id:SAMEA3652095|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:42Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 D12|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:881.0|experiment:Original|fsc:24648.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 D12|scientific name:Danio rerio|ssc:112.0|well:D12,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 D12,HIGH 2 D12,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 881.0:egfp fluorescence|Experimental Factor: 24648.0:fsc|Experimental Factor: 112.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_D12_1.fq.gz HIGH_2_D12_2.fq.gz,fastq fastq,536311000.0,2145244.0,E MTAB 3947:HIGH 2 D12 ,0:125 1:125,A:148855015;C:124341852;G:110168969;T:152881254;N:63910,125,125,,,148855015,124341852,110168969,152881254,63910,ERX1204233,ERS959244,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.6808,0.56959,0.35128,0.29335,0.95797,0.96297,0.51258,0.53501,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2400,ERR1125033,ERX1204232,ERS959243,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 D11,SAMEA3652094,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:42Z|External Id:SAMEA3652094|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:42Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 D11|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1138.0|experiment:Original|fsc:32961.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 D11|scientific name:Danio rerio|ssc:94.0|well:D11,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 D11,HIGH 2 D11,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1138.0:egfp fluorescence|Experimental Factor: 32961.0:fsc|Experimental Factor: 94.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_D11_1.fq.gz HIGH_2_D11_2.fq.gz,fastq fastq,785209000.0,3140836.0,E MTAB 3947:HIGH 2 D11 ,0:125 1:125,A:218915810;C:183612565;G:162058033;T:220524632;N:97960,125,125,,,218915810,183612565,162058033,220524632,97960,ERX1204232,ERS959243,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.75119,0.6416,0.35343,0.30303,0.9651,0.96775,0.52168,0.49655,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2401,ERR1125032,ERX1204231,ERS959242,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 D10,SAMEA3652093,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:42Z|External Id:SAMEA3652093|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:42Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 D10|broker name:ArrayExpress|cells:0.0|common name:zebrafish|condition:EGFP high|experiment:Original|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 D10|scientific name:Danio rerio|well:D10,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 D10,HIGH 2 D10,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_D10_1.fq.gz HIGH_2_D10_2.fq.gz,fastq fastq,341083750.0,1364335.0,E MTAB 3947:HIGH 2 D10 ,0:125 1:125,A:92845013;C:83124811;G:69465399;T:95608900;N:39627,125,125,,,92845013,83124811,69465399,95608900,39627,ERX1204231,ERS959242,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.42413,0.3739,0.42374,0.37379,0.99898,0.99975,0.52727,0.58333,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2402,ERR1125031,ERX1204230,ERS959241,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 D1,SAMEA3652092,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:42Z|External Id:SAMEA3652092|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:42Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 D1|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:854.0|experiment:Original|fsc:24493.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 D1|scientific name:Danio rerio|ssc:70.0|well:D1,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 D1,HIGH 2 D1,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 854.0:egfp fluorescence|Experimental Factor: 24493.0:fsc|Experimental Factor: 70.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_D1_1.fq.gz HIGH_2_D1_2.fq.gz,fastq fastq,703674500.0,2814698.0,E MTAB 3947:HIGH 2 D1 ,0:125 1:125,A:192729540;C:165871361;G:147990040;T:197001546;N:82013,125,125,,,192729540,165871361,147990040,197001546,82013,ERX1204230,ERS959241,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.76596,0.65254,0.33452,0.2849,0.95609,0.96065,0.52949,0.51289,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2403,ERR1125030,ERX1204229,ERS959240,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 C9,SAMEA3652091,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:29Z|External Id:SAMEA3652091|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:29Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 C9|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:681.0|experiment:Original|fsc:32999.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 C9|scientific name:Danio rerio|ssc:88.0|well:C9,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 C9,HIGH 2 C9,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 681.0:egfp fluorescence|Experimental Factor: 32999.0:fsc|Experimental Factor: 88.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_C9_1.fq.gz HIGH_2_C9_2.fq.gz,fastq fastq,324213000.0,1296852.0,E MTAB 3947:HIGH 2 C9 ,0:125 1:125,A:89823850;C:75398434;G:68056324;T:90896536;N:37856,125,125,,,89823850,75398434,68056324,90896536,37856,ERX1204229,ERS959240,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.70874,0.59092,0.49105,0.4067,0.94714,0.9511,0.48605,0.50381,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2404,ERR1125029,ERX1204228,ERS959239,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 C8,SAMEA3652090,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:29Z|External Id:SAMEA3652090|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:29Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 C8|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1528.0|experiment:Original|fsc:30264.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 C8|scientific name:Danio rerio|ssc:107.0|well:C8,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 C8,HIGH 2 C8,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1528.0:egfp fluorescence|Experimental Factor: 30264.0:fsc|Experimental Factor: 107.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_C8_1.fq.gz HIGH_2_C8_2.fq.gz,fastq fastq,688682500.0,2754730.0,E MTAB 3947:HIGH 2 C8 ,0:125 1:125,A:193110334;C:157931387;G:146467846;T:191091131;N:81802,125,125,,,193110334,157931387,146467846,191091131,81802,ERX1204228,ERS959239,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.7339,0.60975,0.44186,0.36143,0.94274,0.94821,0.55287,0.55823,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2405,ERR1125028,ERX1204227,ERS959238,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 C7,SAMEA3652089,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:42Z|External Id:SAMEA3652089|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:42Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 C7|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:913.0|experiment:Original|fsc:29661.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 C7|scientific name:Danio rerio|ssc:63.0|well:C7,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 C7,HIGH 2 C7,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 913.0:egfp fluorescence|Experimental Factor: 29661.0:fsc|Experimental Factor: 63.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_C7_1.fq.gz HIGH_2_C7_2.fq.gz,fastq fastq,792417750.0,3169671.0,E MTAB 3947:HIGH 2 C7 ,0:125 1:125,A:219415176;C:185644798;G:165135543;T:222129339;N:92894,125,125,,,219415176,185644798,165135543,222129339,92894,ERX1204227,ERS959238,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.73766,0.63147,0.33446,0.28572,0.96065,0.96284,0.54318,0.54753,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2406,ERR1125027,ERX1204226,ERS959237,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 C6,SAMEA3652088,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:29Z|External Id:SAMEA3652088|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:29Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 C6|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1738.0|experiment:Original|fsc:13568.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 C6|scientific name:Danio rerio|ssc:164.0|well:C6,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 C6,HIGH 2 C6,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1738.0:egfp fluorescence|Experimental Factor: 13568.0:fsc|Experimental Factor: 164.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_C6_1.fq.gz HIGH_2_C6_2.fq.gz,fastq fastq,728036250.0,2912145.0,E MTAB 3947:HIGH 2 C6 ,0:125 1:125,A:204037509;C:165727645;G:152568040;T:205614870;N:88186,125,125,,,204037509,165727645,152568040,205614870,88186,ERX1204226,ERS959237,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.72442,0.60735,0.43746,0.3648,0.95057,0.95383,0.53184,0.55502,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2407,ERR1125026,ERX1204225,ERS959236,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 C5,SAMEA3652087,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:29Z|External Id:SAMEA3652087|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:29Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 C5|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:2724.0|experiment:Original|fsc:14570.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 C5|scientific name:Danio rerio|ssc:106.0|well:C5,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 C5,HIGH 2 C5,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 2724.0:egfp fluorescence|Experimental Factor: 14570.0:fsc|Experimental Factor: 106.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_C5_1.fq.gz HIGH_2_C5_2.fq.gz,fastq fastq,598501500.0,2394006.0,E MTAB 3947:HIGH 2 C5 ,0:125 1:125,A:166754428;C:138610770;G:124906293;T:168161078;N:68931,125,125,,,166754428,138610770,124906293,168161078,68931,ERX1204225,ERS959236,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.70493,0.59542,0.36454,0.30514,0.96088,0.96366,0.48714,0.48943,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system
2408,ERR1125025,ERX1204224,ERS959235,ERP013160,PRJEB11748,Analysis of single CD41 cell transcriptomes from Zebrafish,E-MTAB-3947,Transcriptome Analysis,Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes  and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.,ArrayExpress:E MTAB 3947,,Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,HIGH 2 C4,SAMEA3652086,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:23Z|External Id:SAMEA3652086|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:23Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 C4|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1245.0|experiment:Original|fsc:27370.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 C4|scientific name:Danio rerio|ssc:143.0|well:C4,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 C4,HIGH 2 C4,Analysis of single CD41 cell transcriptomes from Zebrafish,A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment  circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers 26  and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time  information about cell size and granularity  as well as the level of the fluorescence  were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27  28  with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.,Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 1245.0:egfp fluorescence|Experimental Factor: 27370.0:fsc|Experimental Factor: 143.0:ssc,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP013160,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16,HIGH_2_C4_1.fq.gz HIGH_2_C4_2.fq.gz,fastq fastq,531855500.0,2127422.0,E MTAB 3947:HIGH 2 C4 ,0:125 1:125,A:148952396;C:122496758;G:109850705;T:150491572;N:64069,125,125,,,148952396,122496758,109850705,150491572,64069,ERX1204224,ERS959235,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.72288,0.60428,0.4123,0.34106,0.95446,0.95799,0.57377,0.57075,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2016-01-08,Undetermined,Undetermined,Multi-tissue,Multi-system