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
95,DRR050167,DRX045209,DRS025834,DRP003043,PRJDB4416,Transcriptome analysis in ES1 expressing rods of zebrafish,DRP003043,Transcriptome Analysis,Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.,,,Zebrafish rods expressing ES1 and EGFP,ES1 3,SAMD00044057,,sample name:ES1 EGFP rod 003|strain:Tubingen long fin|cell type:rod,,,,,,,,,Ion Torrent PGM sequencing of SAMD00044057,DRX045209,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>105</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003043,Ion Torrent PGM sequencing of SAMD00044057,,,,371748120.0,3469843.0,DRR050167,0:107.14,A:107190409;C:79475572;G:83520360;T:101561779;N:0,107,,,,107190409,79475572,83520360,101561779,0,DRX045209,DRS025834,DRA004229,"OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.",Osaka university,1,0.81026,,0.26715,,0.86953,,0.52321,,51,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2016-03-09,Undetermined,Undetermined,Fin,Surface Structure
96,DRR050166,DRX045208,DRS025833,DRP003043,PRJDB4416,Transcriptome analysis in ES1 expressing rods of zebrafish,DRP003043,Transcriptome Analysis,Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.,,,Zebrafish rods expressing ES1 and EGFP,ES1 2,SAMD00044056,,sample name:ES1 EGFP rod 002|strain:Tubingen long fin|cell type:rod,,,,,,,,,Ion Torrent PGM sequencing of SAMD00044056,DRX045208,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>128</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003043,Ion Torrent PGM sequencing of SAMD00044056,,,,425549011.0,3275261.0,DRR050166,0:129.93,A:126640704;C:86415371;G:90822163;T:121670773;N:0,129,,,,126640704,86415371,90822163,121670773,0,DRX045208,DRS025833,DRA004229,"OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.",Osaka university,1,0.80223,,0.31429,,0.85861,,0.5272,,57,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2016-03-09,Undetermined,Undetermined,Fin,Surface Structure
97,DRR050165,DRX045207,DRS025832,DRP003043,PRJDB4416,Transcriptome analysis in ES1 expressing rods of zebrafish,DRP003043,Transcriptome Analysis,Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.,,,Zebrafish rods expressing ES1 and EGFP,ES1 1,SAMD00044055,,sample name:ES1 EGFP rod 001|strain:Tubingen long fin|cell type:rod,,,,,,,,,Ion Torrent PGM sequencing of SAMD00044055,DRX045207,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>147</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003043,Ion Torrent PGM sequencing of SAMD00044055,,,,584599765.0,3941083.0,DRR050165,0:148.33,A:164329030;C:129885620;G:136727379;T:153657736;N:0,148,,,,164329030,129885620,136727379,153657736,0,DRX045207,DRS025832,DRA004229,"OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.",Osaka university,1,0.83769,,0.25395,,0.83116,,0.52784,,185,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2016-03-09,Undetermined,Undetermined,Fin,Surface Structure
98,DRR050164,DRX045206,DRS025831,DRP003043,PRJDB4416,Transcriptome analysis in ES1 expressing rods of zebrafish,DRP003043,Transcriptome Analysis,Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.,,,Zebrafish rods expressing EGFP,EGFP 3,SAMD00044054,,sample name:EGFP rod 003|strain:Tubingen long fin|cell type:rod,,,,,,,,,Ion Torrent PGM sequencing of SAMD00044054,DRX045206,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>88</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003043,Ion Torrent PGM sequencing of SAMD00044054,,,,343014114.0,3827762.0,DRR050164,0:89.61,A:99421434;C:73070267;G:77738821;T:92783592;N:0,89,,,,99421434,73070267,77738821,92783592,0,DRX045206,DRS025831,DRA004229,"OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.",Osaka university,1,0.78953,,0.25529,,0.87367,,0.52148,,24,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2016-03-09,Undetermined,Undetermined,Fin,Surface Structure
99,DRR050163,DRX045205,DRS025830,DRP003043,PRJDB4416,Transcriptome analysis in ES1 expressing rods of zebrafish,DRP003043,Transcriptome Analysis,Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.,,,Zebrafish rods expressing EGFP,EGFP 2,SAMD00044053,,sample name:EGFP rod 002|strain:Tubingen long fin|cell type:rod,,,,,,,,,Ion Torrent PGM sequencing of SAMD00044053,DRX045205,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>137</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003043,Ion Torrent PGM sequencing of SAMD00044053,,,,533069427.0,3824140.0,DRR050163,0:139.40,A:152608173;C:113928273;G:120051739;T:146481242;N:0,139,,,,152608173,113928273,120051739,146481242,0,DRX045205,DRS025830,DRA004229,"OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.",Osaka university,1,0.80412,,0.26768,,0.85338,,0.52255,,245,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2016-03-09,Undetermined,Undetermined,Fin,Surface Structure
100,DRR050162,DRX045204,DRS025829,DRP003043,PRJDB4416,Transcriptome analysis in ES1 expressing rods of zebrafish,DRP003043,Transcriptome Analysis,Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.,,,Zebrafish rods expressing EGFP,EGFP 1,SAMD00044052,,sample name:EGFP rod 001|strain:Tubingen long fin|cell type:rod,,,,,,,,,Ion Torrent PGM sequencing of SAMD00044052,DRX045204,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>113</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003043,Ion Torrent PGM sequencing of SAMD00044052,,,,478262965.0,4224064.0,DRR050162,0:113.22,A:136348264;C:104872341;G:113114502;T:123927858;N:0,113,,,,136348264,104872341,113114502,123927858,0,DRX045204,DRS025829,DRA004229,"OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.",Osaka university,1,0.86947,,0.29839,,0.83317,,0.51453,,80,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2016-03-09,Undetermined,Undetermined,Fin,Surface Structure
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
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
2409,ERR1125024,ERX1204223,ERS959234,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 C3,SAMEA3652085,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:42Z|External Id:SAMEA3652085|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 C3|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:2265.0|experiment:Original|fsc:28458.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 C3|scientific name:Danio rerio|ssc:94.0|well:C3,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 C3,HIGH 2 C3,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: 2265.0:egfp fluorescence|Experimental Factor: 28458.0: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_C3_1.fq.gz HIGH_2_C3_2.fq.gz,fastq fastq,746601000.0,2986404.0,E MTAB 3947:HIGH 2 C3 ,0:125 1:125,A:210779832;C:171187687;G:157927459;T:206618456;N:87566,125,125,,,210779832,171187687,157927459,206618456,87566,ERX1204223,ERS959234,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.74949,0.63858,0.38831,0.32939,0.96386,0.9666,0.57811,0.5769,125,125,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
2410,ERR1125023,ERX1204222,ERS959233,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 C2,SAMEA3652084,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:18Z|External Id:SAMEA3652084|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 C2|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:482.0|experiment:Original|fsc:35551.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 C2|scientific name:Danio rerio|ssc:94.0|well:C2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 C2,HIGH 2 C2,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: 482.0:egfp fluorescence|Experimental Factor: 35551.0: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_C2_1.fq.gz HIGH_2_C2_2.fq.gz,fastq fastq,577151250.0,2308605.0,E MTAB 3947:HIGH 2 C2 ,0:125 1:125,A:163137663;C:131492413;G:117953962;T:164499312;N:67900,125,125,,,163137663,131492413,117953962,164499312,67900,ERX1204222,ERS959233,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.50413,0.41914,0.28497,0.23435,0.95812,0.96203,0.53948,0.53382,125,125,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
2411,ERR1125022,ERX1204221,ERS959232,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 C12,SAMEA3652083,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:18Z|External Id:SAMEA3652083|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 C12|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1548.0|experiment:Original|fsc:37017.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 C12|scientific name:Danio rerio|ssc:144.0|well:C12,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 C12,HIGH 2 C12,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: 1548.0:egfp fluorescence|Experimental Factor: 37017.0:fsc|Experimental Factor: 144.0: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_C12_1.fq.gz HIGH_2_C12_2.fq.gz,fastq fastq,748434250.0,2993737.0,E MTAB 3947:HIGH 2 C12 ,0:125 1:125,A:212500284;C:167516552;G:156580935;T:211748631;N:87848,125,125,,,212500284,167516552,156580935,211748631,87848,ERX1204221,ERS959232,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.71827,0.59991,0.40986,0.33948,0.95434,0.95868,0.55538,0.55577,125,125,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
2412,ERR1125021,ERX1204220,ERS959231,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 C11,SAMEA3652082,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:18Z|External Id:SAMEA3652082|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 C11|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:923.0|experiment:Original|fsc:25404.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 C11|scientific name:Danio rerio|ssc:99.0|well:C11,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 C11,HIGH 2 C11,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: 923.0:egfp fluorescence|Experimental Factor: 25404.0:fsc|Experimental Factor: 99.0: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_C11_1.fq.gz HIGH_2_C11_2.fq.gz,fastq fastq,602712500.0,2410850.0,E MTAB 3947:HIGH 2 C11 ,0:125 1:125,A:171304232;C:137143717;G:126295749;T:167898745;N:70057,125,125,,,171304232,137143717,126295749,167898745,70057,ERX1204220,ERS959231,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.71708,0.60506,0.37132,0.31027,0.95891,0.96284,0.46614,0.57196,125,125,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
2413,ERR1125020,ERX1204219,ERS959230,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 C10,SAMEA3652081,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:18Z|External Id:SAMEA3652081|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 C10|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:448.0|experiment:Original|fsc:18198.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 C10|scientific name:Danio rerio|ssc:71.0|well:C10,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 C10,HIGH 2 C10,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: 448.0:egfp fluorescence|Experimental Factor: 18198.0:fsc|Experimental Factor: 71.0: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_C10_1.fq.gz HIGH_2_C10_2.fq.gz,fastq fastq,858632750.0,3434531.0,E MTAB 3947:HIGH 2 C10 ,0:125 1:125,A:236198102;C:199474873;G:186059198;T:236799346;N:101231,125,125,,,236198102,199474873,186059198,236799346,101231,ERX1204219,ERS959230,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.84557,0.72598,0.22661,0.19085,0.93596,0.93809,0.54847,0.54263,125,125,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
2414,ERR1125019,ERX1204218,ERS959229,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 C1,SAMEA3652080,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:42Z|External Id:SAMEA3652080|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 C1|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1645.0|experiment:Original|fsc:30620.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 C1|scientific name:Danio rerio|ssc:181.0|well:C1,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 C1,HIGH 2 C1,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: 1645.0:egfp fluorescence|Experimental Factor: 30620.0:fsc|Experimental Factor: 181.0: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_C1_1.fq.gz HIGH_2_C1_2.fq.gz,fastq fastq,677411000.0,2709644.0,E MTAB 3947:HIGH 2 C1 ,0:125 1:125,A:190739727;C:153866338;G:142400197;T:190324923;N:79815,125,125,,,190739727,153866338,142400197,190324923,79815,ERX1204218,ERS959229,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.73701,0.61953,0.3984,0.3309,0.95177,0.95487,0.52653,0.50846,125,125,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
2415,ERR1125018,ERX1204217,ERS959228,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 B9,SAMEA3652079,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:16Z|External Id:SAMEA3652079|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:25:16Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 B9|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:2075.0|experiment:Original|fsc:29774.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 B9|scientific name:Danio rerio|ssc:75.0|well:B9,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 B9,HIGH 2 B9,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: 2075.0:egfp fluorescence|Experimental Factor: 29774.0:fsc|Experimental Factor: 75.0: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_B9_1.fq.gz HIGH_2_B9_2.fq.gz,fastq fastq,133472500.0,533890.0,E MTAB 3947:HIGH 2 B9 ,0:125 1:125,A:37586264;C:30785763;G:27455939;T:37628078;N:16456,125,125,,,37586264,30785763,27455939,37628078,16456,ERX1204217,ERS959228,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.68814,0.57566,0.40017,0.33032,0.95329,0.9559,0.56663,0.569,125,125,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
2416,ERR1125017,ERX1204216,ERS959227,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 B8,SAMEA3652078,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:23Z|External Id:SAMEA3652078|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 B8|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1169.0|experiment:Original|fsc:22602.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 B8|scientific name:Danio rerio|ssc:90.0|well:B8,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 B8,HIGH 2 B8,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: 1169.0:egfp fluorescence|Experimental Factor: 22602.0: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_B8_1.fq.gz HIGH_2_B8_2.fq.gz,fastq fastq,746457500.0,2985830.0,E MTAB 3947:HIGH 2 B8 ,0:125 1:125,A:205351546;C:175332828;G:162976941;T:202706544;N:89641,125,125,,,205351546,175332828,162976941,202706544,89641,ERX1204216,ERS959227,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.70597,0.58768,0.41042,0.33777,0.95134,0.95631,0.52988,0.54797,125,125,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
2417,ERR1125016,ERX1204215,ERS959226,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 B7,SAMEA3652077,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:42Z|External Id:SAMEA3652077|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 B7|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:913.0|experiment:Original|fsc:41241.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 B7|scientific name:Danio rerio|ssc:55.0|well:B7,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 B7,HIGH 2 B7,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: 41241.0:fsc|Experimental Factor: 55.0: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_B7_1.fq.gz HIGH_2_B7_2.fq.gz,fastq fastq,688559000.0,2754236.0,E MTAB 3947:HIGH 2 B7 ,0:125 1:125,A:189350327;C:162852633;G:144622699;T:191649792;N:83549,125,125,,,189350327,162852633,144622699,191649792,83549,ERX1204215,ERS959226,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.75396,0.63965,0.26609,0.22087,0.94339,0.94667,0.57972,0.48587,125,125,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
2418,ERR1125015,ERX1204214,ERS959225,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 B6,SAMEA3652076,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:16Z|External Id:SAMEA3652076|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:25:16Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 B6|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1206.0|experiment:Original|fsc:15919.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 B6|scientific name:Danio rerio|ssc:152.0|well:B6,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 B6,HIGH 2 B6,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: 1206.0:egfp fluorescence|Experimental Factor: 15919.0: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_B6_1.fq.gz HIGH_2_B6_2.fq.gz,fastq fastq,567376250.0,2269505.0,E MTAB 3947:HIGH 2 B6 ,0:125 1:125,A:161665583;C:126592766;G:115829607;T:163219915;N:68379,125,125,,,161665583,126592766,115829607,163219915,68379,ERX1204214,ERS959225,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.53901,0.44383,0.33165,0.26966,0.94878,0.95422,0.56193,0.5569,125,125,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
2419,ERR1125014,ERX1204213,ERS959224,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 B5,SAMEA3652075,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:23Z|External Id:SAMEA3652075|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 B5|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:940.0|experiment:Original|fsc:29177.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 B5|scientific name:Danio rerio|ssc:176.0|well:B5,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 B5,HIGH 2 B5,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: 940.0:egfp fluorescence|Experimental Factor: 29177.0: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_B5_1.fq.gz HIGH_2_B5_2.fq.gz,fastq fastq,597814000.0,2391256.0,E MTAB 3947:HIGH 2 B5 ,0:125 1:125,A:166324027;C:138643893;G:124996333;T:167776897;N:72850,125,125,,,166324027,138643893,124996333,167776897,72850,ERX1204213,ERS959224,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.70584,0.5871,0.43466,0.35728,0.95396,0.95791,0.52584,0.53163,125,125,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
2420,ERR1125013,ERX1204212,ERS959223,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 B4,SAMEA3652074,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:23Z|External Id:SAMEA3652074|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 B4|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1665.0|experiment:Original|fsc:29051.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 B4|scientific name:Danio rerio|ssc:98.0|well:B4,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 B4,HIGH 2 B4,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: 1665.0:egfp fluorescence|Experimental Factor: 29051.0:fsc|Experimental Factor: 98.0: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_B4_1.fq.gz HIGH_2_B4_2.fq.gz,fastq fastq,492056000.0,1968224.0,E MTAB 3947:HIGH 2 B4 ,0:125 1:125,A:136121951;C:115110359;G:103436733;T:137328520;N:58437,125,125,,,136121951,115110359,103436733,137328520,58437,ERX1204212,ERS959223,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.70874,0.59035,0.40819,0.33557,0.9515,0.95582,0.52997,0.5225,125,125,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
2421,ERR1125012,ERX1204211,ERS959222,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 B3,SAMEA3652073,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:38Z|External Id:SAMEA3652073|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:38Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 B3|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:810.0|experiment:Original|fsc:33036.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 B3|scientific name:Danio rerio|ssc:124.0|well:B3,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 B3,HIGH 2 B3,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: 810.0:egfp fluorescence|Experimental Factor: 33036.0:fsc|Experimental Factor: 124.0: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_B3_1.fq.gz HIGH_2_B3_2.fq.gz,fastq fastq,702391750.0,2809567.0,E MTAB 3947:HIGH 2 B3 ,0:125 1:125,A:199736058;C:159583440;G:146984666;T:196005402;N:82184,125,125,,,199736058,159583440,146984666,196005402,82184,ERX1204211,ERS959222,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.74355,0.6283,0.38429,0.32192,0.9587,0.96132,0.57614,0.57726,125,125,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
2422,ERR1125011,ERX1204210,ERS959221,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 B2,SAMEA3652072,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:23Z|External Id:SAMEA3652072|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 B2|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1020.0|experiment:Original|fsc:28657.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 B2|scientific name:Danio rerio|ssc:103.0|well:B2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 B2,HIGH 2 B2,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: 1020.0:egfp fluorescence|Experimental Factor: 28657.0:fsc|Experimental Factor: 103.0: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_B2_1.fq.gz HIGH_2_B2_2.fq.gz,fastq fastq,497307750.0,1989231.0,E MTAB 3947:HIGH 2 B2 ,0:125 1:125,A:143025030;C:111720974;G:99552715;T:142948908;N:60123,125,125,,,143025030,111720974,99552715,142948908,60123,ERX1204210,ERS959221,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.69598,0.57901,0.41271,0.33912,0.9554,0.95921,0.57302,0.5561,125,125,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
2423,ERR1125010,ERX1204209,ERS959220,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 B12,SAMEA3652071,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:16Z|External Id:SAMEA3652071|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:25:16Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 B12|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:845.0|experiment:Original|fsc:28871.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 B12|scientific name:Danio rerio|ssc:85.0|well:B12,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 B12,HIGH 2 B12,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: 845.0:egfp fluorescence|Experimental Factor: 28871.0:fsc|Experimental Factor: 85.0: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_B12_1.fq.gz HIGH_2_B12_2.fq.gz,fastq fastq,724324500.0,2897298.0,E MTAB 3947:HIGH 2 B12 ,0:125 1:125,A:206976059;C:161393744;G:150157708;T:205709843;N:87146,125,125,,,206976059,161393744,150157708,205709843,87146,ERX1204209,ERS959220,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.70374,0.5852,0.4239,0.34937,0.9554,0.95946,0.5618,0.55814,125,125,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
2424,ERR1125009,ERX1204208,ERS959219,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 B11,SAMEA3652070,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:38Z|External Id:SAMEA3652070|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:38Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 B11|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:2080.0|experiment:Original|fsc:30888.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 B11|scientific name:Danio rerio|ssc:121.0|well:B11,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 B11,HIGH 2 B11,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: 2080.0:egfp fluorescence|Experimental Factor: 30888.0:fsc|Experimental Factor: 121.0: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_B11_1.fq.gz HIGH_2_B11_2.fq.gz,fastq fastq,686882000.0,2747528.0,E MTAB 3947:HIGH 2 B11 ,0:125 1:125,A:193878282;C:158790264;G:145680246;T:188450276;N:82932,125,125,,,193878282,158790264,145680246,188450276,82932,ERX1204208,ERS959219,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.73609,0.62279,0.39912,0.33433,0.95937,0.9623,0.53785,0.50022,125,125,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
2425,ERR1125008,ERX1204207,ERS959218,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 B10,SAMEA3652069,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:23Z|External Id:SAMEA3652069|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 B10|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1943.0|experiment:Original|fsc:20791.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 B10|scientific name:Danio rerio|ssc:177.0|well:B10,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 B10,HIGH 2 B10,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: 1943.0:egfp fluorescence|Experimental Factor: 20791.0:fsc|Experimental Factor: 177.0: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_B10_1.fq.gz HIGH_2_B10_2.fq.gz,fastq fastq,619664500.0,2478658.0,E MTAB 3947:HIGH 2 B10 ,0:125 1:125,A:171491122;C:143787528;G:132588275;T:171725121;N:72454,125,125,,,171491122,143787528,132588275,171725121,72454,ERX1204207,ERS959218,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.72673,0.61127,0.44346,0.37072,0.96004,0.96408,0.47438,0.51929,125,125,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
2426,ERR1125007,ERX1204206,ERS959217,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 B1,SAMEA3652068,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:23Z|External Id:SAMEA3652068|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 B1|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:683.0|experiment:Original|fsc:37507.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 B1|scientific name:Danio rerio|ssc:81.0|well:B1,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 B1,HIGH 2 B1,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: 683.0:egfp fluorescence|Experimental Factor: 37507.0:fsc|Experimental Factor: 81.0: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_B1_1.fq.gz HIGH_2_B1_2.fq.gz,fastq fastq,598727250.0,2394909.0,E MTAB 3947:HIGH 2 B1 ,0:125 1:125,A:168763713;C:136230060;G:126047079;T:167614630;N:71768,125,125,,,168763713,136230060,126047079,167614630,71768,ERX1204206,ERS959217,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.75198,0.63571,0.35872,0.29818,0.95753,0.96023,0.51035,0.51105,125,125,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
2427,ERR1125006,ERX1204205,ERS959216,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 A9,SAMEA3652067,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:16Z|External Id:SAMEA3652067|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:25:16Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 A9|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1062.0|experiment:Original|fsc:20462.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 A9|scientific name:Danio rerio|ssc:112.0|well:A9,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 A9,HIGH 2 A9,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: 1062.0:egfp fluorescence|Experimental Factor: 20462.0: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_A9_1.fq.gz HIGH_2_A9_2.fq.gz,fastq fastq,235150500.0,940602.0,E MTAB 3947:HIGH 2 A9 ,0:125 1:125,A:64709727;C:55290040;G:48683567;T:66439385;N:27781,125,125,,,64709727,55290040,48683567,66439385,27781,ERX1204205,ERS959216,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.71466,0.60195,0.36862,0.30781,0.95846,0.96221,0.52784,0.52989,125,125,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
2428,ERR1125005,ERX1204204,ERS959215,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 A8,SAMEA3652066,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:38Z|External Id:SAMEA3652066|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:38Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 A8|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1816.0|experiment:Original|fsc:23959.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 A8|scientific name:Danio rerio|ssc:131.0|well:A8,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 A8,HIGH 2 A8,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: 1816.0:egfp fluorescence|Experimental Factor: 23959.0:fsc|Experimental Factor: 131.0: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_A8_1.fq.gz HIGH_2_A8_2.fq.gz,fastq fastq,411990250.0,1647961.0,E MTAB 3947:HIGH 2 A8 ,0:125 1:125,A:115633720;C:95512217;G:84820282;T:115976883;N:47148,125,125,,,115633720,95512217,84820282,115976883,47148,ERX1204204,ERS959215,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.62078,0.51083,0.38526,0.3145,0.95572,0.96128,0.58604,0.59225,125,125,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
2429,ERR1125004,ERX1204203,ERS959214,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 A7,SAMEA3652065,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:23Z|External Id:SAMEA3652065|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 A7|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:415.0|experiment:Original|fsc:33487.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 A7|scientific name:Danio rerio|ssc:74.0|well:A7,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 A7,HIGH 2 A7,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: 415.0:egfp fluorescence|Experimental Factor: 33487.0: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_A7_1.fq.gz HIGH_2_A7_2.fq.gz,fastq fastq,391732000.0,1566928.0,E MTAB 3947:HIGH 2 A7 ,0:125 1:125,A:109169573;C:91581017;G:78073153;T:112865475;N:42782,125,125,,,109169573,91581017,78073153,112865475,42782,ERX1204203,ERS959214,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.71097,0.60098,0.27937,0.23216,0.94763,0.95124,0.54099,0.54521,125,125,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
2430,ERR1125003,ERX1204202,ERS959213,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 A6,SAMEA3652064,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:38Z|External Id:SAMEA3652064|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:38Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 A6|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:2724.0|experiment:Original|fsc:11087.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 A6|scientific name:Danio rerio|ssc:138.0|well:A6,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 A6,HIGH 2 A6,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: 11087.0:fsc|Experimental Factor: 138.0: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_A6_1.fq.gz HIGH_2_A6_2.fq.gz,fastq fastq,469393250.0,1877573.0,E MTAB 3947:HIGH 2 A6 ,0:125 1:125,A:131867414;C:107036944;G:94545740;T:135887751;N:55401,125,125,,,131867414,107036944,94545740,135887751,55401,ERX1204202,ERS959213,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.64527,0.52872,0.44989,0.36587,0.94909,0.95493,0.50356,0.52818,125,125,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
2431,ERR1125002,ERX1204201,ERS959212,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 A5,SAMEA3652063,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:38Z|External Id:SAMEA3652063|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:38Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 A5|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1338.0|experiment:Original|fsc:27554.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 A5|scientific name:Danio rerio|ssc:106.0|well:A5,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 A5,HIGH 2 A5,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: 1338.0:egfp fluorescence|Experimental Factor: 27554.0: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_A5_1.fq.gz HIGH_2_A5_2.fq.gz,fastq fastq,358499750.0,1433999.0,E MTAB 3947:HIGH 2 A5 ,0:125 1:125,A:99967262;C:83245116;G:72063378;T:103182965;N:41029,125,125,,,99967262,83245116,72063378,103182965,41029,ERX1204201,ERS959212,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.68434,0.5683,0.36795,0.30069,0.95041,0.95592,0.54282,0.53689,125,125,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
2432,ERR1125001,ERX1204200,ERS959211,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 A4,SAMEA3652062,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:18Z|External Id:SAMEA3652062|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:18Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 A4|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1030.0|experiment:Original|fsc:28335.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 A4|scientific name:Danio rerio|ssc:78.0|well:A4,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 A4,HIGH 2 A4,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: 1030.0:egfp fluorescence|Experimental Factor: 28335.0: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_A4_1.fq.gz HIGH_2_A4_2.fq.gz,fastq fastq,409690000.0,1638760.0,E MTAB 3947:HIGH 2 A4 ,0:125 1:125,A:113400195;C:95200471;G:83889014;T:117157086;N:43234,125,125,,,113400195,95200471,83889014,117157086,43234,ERX1204200,ERS959211,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.7238,0.61361,0.32938,0.27581,0.95457,0.95785,0.5107,0.52897,125,125,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
2433,ERR1125000,ERX1204199,ERS959210,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 A3,SAMEA3652061,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:25:16Z|External Id:SAMEA3652061|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:25:16Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 A3|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1719.0|experiment:Original|fsc:27281.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 A3|scientific name:Danio rerio|ssc:133.0|well:A3,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 A3,HIGH 2 A3,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: 1719.0:egfp fluorescence|Experimental Factor: 27281.0:fsc|Experimental Factor: 133.0: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_A3_1.fq.gz HIGH_2_A3_2.fq.gz,fastq fastq,491303500.0,1965214.0,E MTAB 3947:HIGH 2 A3 ,0:125 1:125,A:140223481;C:111407934;G:98985396;T:140631370;N:55319,125,125,,,140223481,111407934,98985396,140631370,55319,ERX1204199,ERS959210,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.69552,0.57579,0.4253,0.34973,0.95361,0.95824,0.59743,0.60657,125,125,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
2434,ERR1124999,ERX1204198,ERS959209,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 A2,SAMEA3652060,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:26:18Z|External Id:SAMEA3652060|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:26:18Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 A2|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:1181.0|experiment:Original|fsc:31794.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 A2|scientific name:Danio rerio|ssc:170.0|well:A2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 A2,HIGH 2 A2,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: 1181.0:egfp fluorescence|Experimental Factor: 31794.0:fsc|Experimental Factor: 170.0: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_A2_1.fq.gz HIGH_2_A2_2.fq.gz,fastq fastq,691993250.0,2767973.0,E MTAB 3947:HIGH 2 A2 ,0:125 1:125,A:194386250;C:158850498;G:140892698;T:197783348;N:80456,125,125,,,194386250,158850498,140892698,197783348,80456,ERX1204198,ERS959209,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.76026,0.64643,0.30724,0.25626,0.9599,0.9629,0.67287,0.66786,125,125,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