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
51,DRR029943,DRX026961,DRS086501,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,oocyte maturation duirng natural paring,zebrafish ovary isolated from adult fish at oocyte maturation duirng natural paring. [RNAseq],SAMD00025433,,sample name:5 OM|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025433,DRX026961,5 OM,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025433,,,,573617016.0,15933806.0,DRR029943,0:36,A:130606804;C:141376330;G:145891720;T:155734276;N:7886,36,,,,130606804,141376330,145891720,155734276,7886,DRX026961,DRS086501,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91108,,0.0173,,0.76205,,0.46319,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Multi-tissue,Multi-system
168,DRR075402,DRX069316,DRS075497,DRP004473,PRJDB5226,Effects of local gut tumor on whole organismal gene expressions in zebrafish,DRP004473,Other,How tumors affects whole organismal physiology remains largely unknown. To address this  we established the novel gut tumor model in zebrafish  Danio rerio. This model develops tumor at an early stage of juvenile development  when zebrafish larvae are small <4mm  enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.,,,The liver of tumor fish 7dpf,Tumor liver,SAMD00065416,,sample name:6 Tumor liver 150701 Hiseq3A l3 022|tissue type:Liver,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00065416,DRX069316,Tumor liver,1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>,DRP004473,Illumina HiSeq 2500 sequencing of SAMD00065416,,,,1091167236.0,30310201.0,DRR075402,0:36,A:272216839;C:257523620;G:259746158;T:301642763;N:37856,36,,,,272216839,257523620,259746158,301642763,37856,DRX069316,DRS075497,DRA005199,"ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International","The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International",1,0.90443,,0.08935,,0.71863,,0.51145,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2018-09-19,Larval,Larval,Multi-tissue,Multi-system
169,DRR075401,DRX069315,DRS075496,DRP004473,PRJDB5226,Effects of local gut tumor on whole organismal gene expressions in zebrafish,DRP004473,Other,How tumors affects whole organismal physiology remains largely unknown. To address this  we established the novel gut tumor model in zebrafish  Danio rerio. This model develops tumor at an early stage of juvenile development  when zebrafish larvae are small <4mm  enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.,,,The gut of tumor fish 7dpf,Tumor gut,SAMD00065415,,sample name:5 Tumor gut 150701 Hiseq3A l3 021|tissue type:Gut,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00065415,DRX069315,Tumor gut,1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>,DRP004473,Illumina HiSeq 2500 sequencing of SAMD00065415,,,,1423792872.0,39549802.0,DRR075401,0:36,A:342328685;C:346616167;G:341519547;T:393278536;N:49937,36,,,,342328685,346616167,341519547,393278536,49937,DRX069315,DRS075496,DRA005199,"ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International","The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International",1,0.91303,,0.0869,,0.70494,,0.44332,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2018-09-19,Larval,Larval,Multi-tissue,Multi-system
170,DRR075400,DRX069314,DRS075495,DRP004473,PRJDB5226,Effects of local gut tumor on whole organismal gene expressions in zebrafish,DRP004473,Other,How tumors affects whole organismal physiology remains largely unknown. To address this  we established the novel gut tumor model in zebrafish  Danio rerio. This model develops tumor at an early stage of juvenile development  when zebrafish larvae are small <4mm  enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.,,,The remaining part of body of tumor fish 7dpf,Tumor body,SAMD00065414,,sample name:4 Tumor body 150701 Hiseq3A l3 020|tissue type:Body,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00065414,DRX069314,Tumor body,1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>,DRP004473,Illumina HiSeq 2500 sequencing of SAMD00065414,,,,1168514964.0,32458749.0,DRR075400,0:36,A:286579925;C:275496498;G:278133055;T:328265078;N:40408,36,,,,286579925,275496498,278133055,328265078,40408,DRX069314,DRS075495,DRA005199,"ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International","The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International",1,0.89927,,0.15051,,0.66714,,0.47579,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2018-09-19,Larval,Larval,Multi-tissue,Multi-system
175,DRR084197,DRX078028,DRS086522,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,natural paring early sample,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate2],SAMD00073604,,sample name:M 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073604,DRX078028,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073604,,,,1389837888.0,38606608.0,DRR084197,0:36,A:320671418;C:336948866;G:347550258;T:381720581;N:2946765,36,,,,320671418,336948866,347550258,381720581,2946765,DRX078028,DRS086522,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.89763,,0.02235,,0.76445,,0.46381,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Zygote,Embryo,Multi-tissue,Multi-system
181,DRR084191,DRX078022,DRS086516,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,natural paring early sample,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate1],SAMD00073598,,sample name:M|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073598,DRX078022,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073598,,,,1050981012.0,29193917.0,DRR084191,0:36,A:241048832;C:256186268;G:260277071;T:293299597;N:169244,36,,,,241048832,256186268,260277071,293299597,169244,DRX078022,DRS086516,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.9088,,0.02369,,0.7624,,0.47998,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Zygote,Embryo,Multi-tissue,Multi-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
2435,ERR1124998,ERX1204197,ERS959208,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 A12,SAMEA3652059,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:38Z|External Id:SAMEA3652059|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 A12|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:803.0|experiment:Original|fsc:31770.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 A12|scientific name:Danio rerio|ssc:88.0|well:A12,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 A12,HIGH 2 A12,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: 31770.0: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_A12_1.fq.gz HIGH_2_A12_2.fq.gz,fastq fastq,255037750.0,1020151.0,E MTAB 3947:HIGH 2 A12 ,0:125 1:125,A:74627903;C:55765462;G:49131966;T:75484997;N:27422,125,125,,,74627903,55765462,49131966,75484997,27422,ERX1204197,ERS959208,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.63571,0.54379,0.23048,0.20073,0.97934,0.97991,0.55209,0.55372,125,125,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
2436,ERR1124997,ERX1204196,ERS959207,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 A11,SAMEA3652058,EMBL-EBI,ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:38Z|External Id:SAMEA3652058|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 A11|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:881.0|experiment:Original|fsc:30036.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 A11|scientific name:Danio rerio|ssc:81.0|well:A11,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish,E MTAB 3947:HIGH 2 A11,HIGH 2 A11,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: 30036.0: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_A11_1.fq.gz HIGH_2_A11_2.fq.gz,fastq fastq,695946750.0,2783787.0,E MTAB 3947:HIGH 2 A11 ,0:125 1:125,A:195562723;C:160296142;G:144532913;T:195475645;N:79327,125,125,,,195562723,160296142,144532913,195475645,79327,ERX1204196,ERS959207,ERA533479,EMBL-EBI|European Nucleotide Archive,EMBL-EBI|European Nucleotide Archive,2,0.75254,0.63608,0.35139,0.29487,0.95566,0.95883,0.57191,0.57231,125,125,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