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9,074 rows where devstage_curation = "Undetermined" and experiment.library_selection = "cDNA"

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tissue_curation >10

technology >10

devstage_curation_coarse 6

experiment.platform 5

experiment.library_strategy 2

experiment.library_source 2

experiment.library_layout 2

experiment.library_selection 1

  • cDNA · 9,074 ✖

devstage_curation 1

  • Undetermined · 9,074 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
95 95 DRR050167 DRX045209 DRS025834 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing ES1 and EGFP ES1 3 SAMD00044057   sample name:ES1 EGFP rod 003|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044057 DRX045209 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>105</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003043 Ion Torrent PGM sequencing of SAMD00044057       371748120.0 3469843.0 DRR050167 0:107.14 A:107190409;C:79475572;G:83520360;T:101561779;N:0 107       107190409 79475572 83520360 101561779 0 DRX045209 DRS025834 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.81026   0.26715   0.86953   0.52321   51   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
96 96 DRR050166 DRX045208 DRS025833 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing ES1 and EGFP ES1 2 SAMD00044056   sample name:ES1 EGFP rod 002|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044056 DRX045208 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>128</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003043 Ion Torrent PGM sequencing of SAMD00044056       425549011.0 3275261.0 DRR050166 0:129.93 A:126640704;C:86415371;G:90822163;T:121670773;N:0 129       126640704 86415371 90822163 121670773 0 DRX045208 DRS025833 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.80223   0.31429   0.85861   0.5272   57   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
97 97 DRR050165 DRX045207 DRS025832 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing ES1 and EGFP ES1 1 SAMD00044055   sample name:ES1 EGFP rod 001|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044055 DRX045207 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>147</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003043 Ion Torrent PGM sequencing of SAMD00044055       584599765.0 3941083.0 DRR050165 0:148.33 A:164329030;C:129885620;G:136727379;T:153657736;N:0 148       164329030 129885620 136727379 153657736 0 DRX045207 DRS025832 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.83769   0.25395   0.83116   0.52784   185   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
98 98 DRR050164 DRX045206 DRS025831 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing EGFP EGFP 3 SAMD00044054   sample name:EGFP rod 003|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044054 DRX045206 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>88</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003043 Ion Torrent PGM sequencing of SAMD00044054       343014114.0 3827762.0 DRR050164 0:89.61 A:99421434;C:73070267;G:77738821;T:92783592;N:0 89       99421434 73070267 77738821 92783592 0 DRX045206 DRS025831 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.78953   0.25529   0.87367   0.52148   24   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
99 99 DRR050163 DRX045205 DRS025830 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing EGFP EGFP 2 SAMD00044053   sample name:EGFP rod 002|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044053 DRX045205 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>137</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003043 Ion Torrent PGM sequencing of SAMD00044053       533069427.0 3824140.0 DRR050163 0:139.40 A:152608173;C:113928273;G:120051739;T:146481242;N:0 139       152608173 113928273 120051739 146481242 0 DRX045205 DRS025830 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.80412   0.26768   0.85338   0.52255   245   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
100 100 DRR050162 DRX045204 DRS025829 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing EGFP EGFP 1 SAMD00044052   sample name:EGFP rod 001|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044052 DRX045204 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>113</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003043 Ion Torrent PGM sequencing of SAMD00044052       478262965.0 4224064.0 DRR050162 0:113.22 A:136348264;C:104872341;G:113114502;T:123927858;N:0 113       136348264 104872341 113114502 123927858 0 DRX045204 DRS025829 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.86947   0.29839   0.83317   0.51453   80   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
147 147 DRR051067 DRX045959 DRS057267 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.     These cells are from the same fish as h62A GFP plus Tel GFP cells from telencephalon of hspGFF62A;UAS:GFP transgenic zebrafish SAMD00044994   sample name:h62A GFP minus Tel|tissue type:brain|genotype:hspGFF62A;UAS:GFP                 Illumina HiSeq 2500 paired end sequencing of SAMD00044994 DRX045959 h62A GFP minus Tel 1 cDNA synthesis : clontech SMARTer v3 > Library prep : Illumina Nextera XT DNA Library Preparation Kits   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 2500 paired end sequencing of SAMD00044994       17913873600.0 89569368.0 DRR051067 0:100 1:100 A:5009629866;C:3957379257;G:3797879751;T:5144366288;N:4618438 100 100     5009629866 3957379257 3797879751 5144366288 4618438 DRX045959 DRS057267 DRA004277 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 2 0.89075 0.89087 0.23044 0.23295 0.69493 0.69769 0.5366 0.54852 100 100 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified nextera bulk unknown unknown   Japan 2018-01-06 Undetermined Undetermined Brain Nervous System
151 151 DRR051063 DRX045955 DRS057266 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.     These cells are from the same fish as 120A GFP plus Tel GFP cells from telencephalon of SAGFFLF120A;UAS:GFP transgenic zebrafish SAMD00044987   sample name:120A GFP minus Tel|tissue type:brain|genotype:SAGFFLF120A;UAS:GFP                 Illumina HiSeq 2500 paired end sequencing of SAMD00044987 DRX045955 120A GFP minus Tel 1 cDNA synthesis : clontech SMARTer v2 > Library prep : Illumina TrunSeq DNA Sample Preparation Kits   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 2500 paired end sequencing of SAMD00044987       15411400120.0 76294060.0 DRR051063 0:101 1:101 A:4583085286;C:3082552426;G:3134669086;T:4606055524;N:5037798 101 101     4583085286 3082552426 3134669086 4606055524 5037798 DRX045955 DRS057266 DRA004273 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 2 0.89184 0.8842 0.30246 0.30334 0.69232 0.705 0.52824 0.51492 101 101 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   Japan 2018-01-06 Undetermined Undetermined Brain Nervous System
2319 2319 ERR1289947 ERX1361553 ERS954843 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647694 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:23:00Z|External Id:SAMEA3647694|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:23:00Z|INSDC status:public|Submitter Id:ATH5 2 sc 2454965|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:ATH5 2 sc 2454965|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 2#12 15249493 Illumina sequencing of library 15249493 constructed from sample accession ERS954843 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 2. This submission includes reads tagged with the sequence TAGGCATGAGAGTAGA. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_2#12.cram cram 2492206600.0 12461033.0 SC RUN 18222 2#12 0:100 1:100 A:661236051;C:588399772;G:571478215;T:671080581;N:11981 100 100     661236051 588399772 571478215 671080581 11981 ERX1361553 ERS954843 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.94054 0.94077 0.10025 0.10255 0.75779 0.76019 0.4807 0.47966 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2320 2320 ERR1289946 ERX1361552 ERS954842 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647693 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:23:00Z|External Id:SAMEA3647693|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:23:00Z|INSDC status:public|Submitter Id:WT ctrl sc 2454964|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:WT ctrl sc 2454964|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 2#11 15249492 Illumina sequencing of library 15249492 constructed from sample accession ERS954842 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 2. This submission includes reads tagged with the sequence TAGGCATGTATCCTCT. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_2#11.cram cram 2748114600.0 13740573.0 SC RUN 18222 2#11 0:100 1:100 A:747132237;C:630918171;G:613637334;T:756413030;N:13828 100 100     747132237 630918171 613637334 756413030 13828 ERX1361552 ERS954842 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.91201 0.911 0.09071 0.09156 0.88994 0.88988 0.47118 0.49948 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2321 2321 ERR1289945 ERX1361551 ERS954841 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647692 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:59Z|External Id:SAMEA3647692|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:59Z|INSDC status:public|Submitter Id:RX2 ATH5 GFP3 sc 2454963|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ATH5 GFP3 sc 2454963|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 2#10 15249491 Illumina sequencing of library 15249491 constructed from sample accession ERS954841 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 2. This submission includes reads tagged with the sequence TAGGCATGCTCTCTAT. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_2#10.cram cram 3366968000.0 16834840.0 SC RUN 18222 2#10 0:100 1:100 A:881918684;C:806052916;G:790157920;T:888821188;N:17292 100 100     881918684 806052916 790157920 888821188 17292 ERX1361551 ERS954841 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.94171 0.94098 0.0849 0.08607 0.74862 0.75024 0.50963 0.50955 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2322 2322 ERR1289944 ERX1361550 ERS954840 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647691 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647691|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:RX2 ATH5 GFP2 sc 2454962|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ATH5 GFP2 sc 2454962|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 2#9 15249490 Illumina sequencing of library 15249490 constructed from sample accession ERS954840 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 2. This submission includes reads tagged with the sequence TAGGCATGTAGATCGC. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_2#9.cram cram 3222261000.0 16111305.0 SC RUN 18222 2#9 0:100 1:100 A:819997366;C:795302699;G:777099203;T:829845734;N:15998 100 100     819997366 795302699 777099203 829845734 15998 ERX1361550 ERS954840 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.94529 0.94495 0.0603 0.06143 0.76157 0.76238 0.48847 0.4882 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2323 2323 ERR1289943 ERX1361549 ERS954839 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647690 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647690|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 GFP2 high sc 2454961|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 GFP2 high sc 2454961|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 2#8 15249489 Illumina sequencing of library 15249489 constructed from sample accession ERS954839 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 2. This submission includes reads tagged with the sequence GGACTCCTCTAAGCCT. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_2#8.cram cram 3834749800.0 19173749.0 SC RUN 18222 2#8 0:100 1:100 A:992673645;C:929008642;G:906766397;T:1006281701;N:19415 100 100     992673645 929008642 906766397 1006281701 19415 ERX1361549 ERS954839 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.94351 0.94297 0.08055 0.08157 0.72853 0.73095 0.52148 0.51755 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2324 2324 ERR1289942 ERX1361548 ERS954838 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647689 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647689|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 GFP2 low sc 2454960|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 GFP2 low sc 2454960|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 2#7 15249488 Illumina sequencing of library 15249488 constructed from sample accession ERS954838 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 2. This submission includes reads tagged with the sequence GGACTCCTAAGGAGTA. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_2#7.cram cram 1076581000.0 5382905.0 SC RUN 18222 2#7 0:100 1:100 A:285946062;C:254142940;G:242866633;T:293619980;N:5385 100 100     285946062 254142940 242866633 293619980 5385 ERX1361548 ERS954838 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.89818 0.89819 0.1022 0.10292 0.89919 0.89852 0.51448 0.51223 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2325 2325 ERR1289941 ERX1361547 ERS954837 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647688 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647688|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:GFAP ATH5 GFP2 sc 2454959|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:GFAP ATH5 GFP2 sc 2454959|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 2#6 15249487 Illumina sequencing of library 15249487 constructed from sample accession ERS954837 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 2. This submission includes reads tagged with the sequence GGACTCCTACTGCATA. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_2#6.cram cram 3172834800.0 15864174.0 SC RUN 18222 2#6 0:100 1:100 A:841262183;C:748974758;G:730474017;T:852107947;N:15895 100 100     841262183 748974758 730474017 852107947 15895 ERX1361547 ERS954837 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.93515 0.93517 0.10079 0.10267 0.73403 0.73511 0.49831 0.47169 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2326 2326 ERR1289940 ERX1361546 ERS954836 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647687 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647687|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:ATH5 1 sc 2454958|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:ATH5 1 sc 2454958|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 2#5 15249486 Illumina sequencing of library 15249486 constructed from sample accession ERS954836 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 2. This submission includes reads tagged with the sequence GGACTCCTGTAAGGAG. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_2#5.cram cram 1188728400.0 5943642.0 SC RUN 18222 2#5 0:100 1:100 A:322290258;C:273659598;G:266021599;T:326751009;N:5936 100 100     322290258 273659598 266021599 326751009 5936 ERX1361546 ERS954836 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.92438 0.92391 0.12338 0.1251 0.76288 0.76479 0.48734 0.47777 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2327 2327 ERR1289939 ERX1361545 ERS954835 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647686 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647686|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:GFAP ATH5 GFP1 sc 2454957|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:GFAP ATH5 GFP1 sc 2454957|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 2#4 15249485 Illumina sequencing of library 15249485 constructed from sample accession ERS954835 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 2. This submission includes reads tagged with the sequence GGACTCCTAGAGTAGA. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_2#4.cram cram 2335470400.0 11677352.0 SC RUN 18222 2#4 0:100 1:100 A:611730664;C:560095252;G:541373953;T:622259122;N:11409 100 100     611730664 560095252 541373953 622259122 11409 ERX1361545 ERS954835 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.93481 0.93465 0.10573 0.10811 0.77135 0.77303 0.50016 0.50137 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2328 2328 ERR1289938 ERX1361544 ERS954834 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647685 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647685|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 ATH5 GFP1 sc 2454956|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ATH5 GFP1 sc 2454956|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 2#3 15249484 Illumina sequencing of library 15249484 constructed from sample accession ERS954834 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 2. This submission includes reads tagged with the sequence GGACTCCTTATCCTCT. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_2#3.cram cram 2932765000.0 14663825.0 SC RUN 18222 2#3 0:100 1:100 A:762543647;C:708033363;G:692599413;T:769573475;N:15102 100 100     762543647 708033363 692599413 769573475 15102 ERX1361544 ERS954834 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.94442 0.94374 0.07322 0.07439 0.74383 0.74531 0.50604 0.51608 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2329 2329 ERR1289937 ERX1361543 ERS954833 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647684 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:15Z|External Id:SAMEA3647684|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:15Z|INSDC status:public|Submitter Id:RX2 GFP1 sc 2454955|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 GFP1 sc 2454955|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 2#2 15249483 Illumina sequencing of library 15249483 constructed from sample accession ERS954833 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 2. This submission includes reads tagged with the sequence GGACTCCTCTCTCTAT. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_2#2.cram cram 2432398000.0 12161990.0 SC RUN 18222 2#2 0:100 1:100 A:624543123;C:594774023;G:581130641;T:631937939;N:12274 100 100     624543123 594774023 581130641 631937939 12274 ERX1361543 ERS954833 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.94225 0.94103 0.08221 0.0823 0.79289 0.79383 0.51106 0.5129 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2330 2330 ERR1289936 ERX1361542 ERS954832 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647683 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647683|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 ctrl noGFP sc 2454954|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ctrl noGFP sc 2454954|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 2#1 15249482 Illumina sequencing of library 15249482 constructed from sample accession ERS954832 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 2. This submission includes reads tagged with the sequence GGACTCCTTAGATCGC. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_2#1.cram cram 361900800.0 1809504.0 SC RUN 18222 2#1 0:100 1:100 A:84553945;C:97259075;G:92615955;T:87470072;N:1753 100 100     84553945 97259075 92615955 87470072 1753 ERX1361542 ERS954832 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.94897 0.95014 0.07743 0.07772 0.71969 0.72058 0.43784 0.44067 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2331 2331 ERR1289935 ERX1361541 ERS954843 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647694 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:23:00Z|External Id:SAMEA3647694|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:23:00Z|INSDC status:public|Submitter Id:ATH5 2 sc 2454965|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:ATH5 2 sc 2454965|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 1#12 15249493 Illumina sequencing of library 15249493 constructed from sample accession ERS954843 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 1. This submission includes reads tagged with the sequence TAGGCATGAGAGTAGA. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_1#12.cram cram 2487554200.0 12437771.0 SC RUN 18222 1#12 0:100 1:100 A:660028585;C:587257902;G:570415230;T:669842822;N:9661 100 100     660028585 587257902 570415230 669842822 9661 ERX1361541 ERS954843 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.94059 0.9397 0.09914 0.1011 0.75597 0.75862 0.48558 0.48548 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2332 2332 ERR1289934 ERX1361540 ERS954842 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647693 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:23:00Z|External Id:SAMEA3647693|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:23:00Z|INSDC status:public|Submitter Id:WT ctrl sc 2454964|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:WT ctrl sc 2454964|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 1#11 15249492 Illumina sequencing of library 15249492 constructed from sample accession ERS954842 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 1. This submission includes reads tagged with the sequence TAGGCATGTATCCTCT. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_1#11.cram cram 2740851200.0 13704256.0 SC RUN 18222 1#11 0:100 1:100 A:745054545;C:629082779;G:612051041;T:754652050;N:10785 100 100     745054545 629082779 612051041 754652050 10785 ERX1361540 ERS954842 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.91349 0.91229 0.09216 0.09351 0.88962 0.89043 0.48978 0.5028 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2333 2333 ERR1289933 ERX1361539 ERS954841 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647692 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:59Z|External Id:SAMEA3647692|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:59Z|INSDC status:public|Submitter Id:RX2 ATH5 GFP3 sc 2454963|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ATH5 GFP3 sc 2454963|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 1#10 15249491 Illumina sequencing of library 15249491 constructed from sample accession ERS954841 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 1. This submission includes reads tagged with the sequence TAGGCATGCTCTCTAT. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_1#10.cram cram 3357950400.0 16789752.0 SC RUN 18222 1#10 0:100 1:100 A:879637755;C:803810252;G:787961249;T:886528291;N:12853 100 100     879637755 803810252 787961249 886528291 12853 ERX1361539 ERS954841 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.94064 0.94017 0.08377 0.08517 0.74909 0.75136 0.50723 0.50903 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2334 2334 ERR1289932 ERX1361538 ERS954840 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647691 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647691|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:RX2 ATH5 GFP2 sc 2454962|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ATH5 GFP2 sc 2454962|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 1#9 15249490 Illumina sequencing of library 15249490 constructed from sample accession ERS954840 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 1. This submission includes reads tagged with the sequence TAGGCATGTAGATCGC. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_1#9.cram cram 3206581200.0 16032906.0 SC RUN 18222 1#9 0:100 1:100 A:816111545;C:791236086;G:773298814;T:825922398;N:12357 100 100     816111545 791236086 773298814 825922398 12357 ERX1361538 ERS954840 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.94549 0.94564 0.06037 0.06105 0.76043 0.76171 0.48313 0.49555 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2335 2335 ERR1289931 ERX1361537 ERS954839 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647690 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647690|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 GFP2 high sc 2454961|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 GFP2 high sc 2454961|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 1#8 15249489 Illumina sequencing of library 15249489 constructed from sample accession ERS954839 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 1. This submission includes reads tagged with the sequence GGACTCCTCTAAGCCT. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_1#8.cram cram 3822332200.0 19111661.0 SC RUN 18222 1#8 0:100 1:100 A:989542225;C:925823012;G:903835738;T:1003115980;N:15245 100 100     989542225 925823012 903835738 1003115980 15245 ERX1361537 ERS954839 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.94289 0.94174 0.07966 0.08004 0.72764 0.72906 0.51976 0.52464 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2336 2336 ERR1289930 ERX1361536 ERS954838 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647689 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647689|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 GFP2 low sc 2454960|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 GFP2 low sc 2454960|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 1#7 15249488 Illumina sequencing of library 15249488 constructed from sample accession ERS954838 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 1. This submission includes reads tagged with the sequence GGACTCCTAAGGAGTA. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_1#7.cram cram 1072510200.0 5362551.0 SC RUN 18222 1#7 0:100 1:100 A:284863902;C:253046005;G:241968135;T:292627849;N:4309 100 100     284863902 253046005 241968135 292627849 4309 ERX1361536 ERS954838 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.89703 0.89873 0.10191 0.10317 0.89921 0.8984 0.50884 0.51319 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2337 2337 ERR1289929 ERX1361535 ERS954837 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647688 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647688|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:GFAP ATH5 GFP2 sc 2454959|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:GFAP ATH5 GFP2 sc 2454959|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 1#6 15249487 Illumina sequencing of library 15249487 constructed from sample accession ERS954837 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 1. This submission includes reads tagged with the sequence GGACTCCTACTGCATA. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_1#6.cram cram 3159715800.0 15798579.0 SC RUN 18222 1#6 0:100 1:100 A:837700548;C:745877706;G:727508293;T:848616717;N:12536 100 100     837700548 745877706 727508293 848616717 12536 ERX1361535 ERS954837 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.93397 0.93362 0.10011 0.10205 0.73474 0.73612 0.49003 0.49085 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2338 2338 ERR1289928 ERX1361534 ERS954836 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647687 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647687|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:ATH5 1 sc 2454958|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:ATH5 1 sc 2454958|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 1#5 15249486 Illumina sequencing of library 15249486 constructed from sample accession ERS954836 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 1. This submission includes reads tagged with the sequence GGACTCCTGTAAGGAG. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_1#5.cram cram 1184332600.0 5921663.0 SC RUN 18222 1#5 0:100 1:100 A:321129432;C:272595945;G:264945795;T:325656767;N:4661 100 100     321129432 272595945 264945795 325656767 4661 ERX1361534 ERS954836 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.92372 0.92353 0.12445 0.12616 0.76339 0.76495 0.48995 0.48259 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2339 2339 ERR1289927 ERX1361533 ERS954835 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647686 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:54Z|External Id:SAMEA3647686|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:54Z|INSDC status:public|Submitter Id:GFAP ATH5 GFP1 sc 2454957|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:GFAP ATH5 GFP1 sc 2454957|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 1#4 15249485 Illumina sequencing of library 15249485 constructed from sample accession ERS954835 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 1. This submission includes reads tagged with the sequence GGACTCCTAGAGTAGA. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_1#4.cram cram 2331489600.0 11657448.0 SC RUN 18222 1#4 0:100 1:100 A:610715735;C:559128165;G:540406653;T:621229940;N:9107 100 100     610715735 559128165 540406653 621229940 9107 ERX1361533 ERS954835 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.9338 0.93348 0.10518 0.10783 0.77155 0.77374 0.49506 0.49808 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2340 2340 ERR1289926 ERX1361532 ERS954834 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647685 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647685|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 ATH5 GFP1 sc 2454956|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ATH5 GFP1 sc 2454956|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 1#3 15249484 Illumina sequencing of library 15249484 constructed from sample accession ERS954834 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 1. This submission includes reads tagged with the sequence GGACTCCTTATCCTCT. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_1#3.cram cram 2923134800.0 14615674.0 SC RUN 18222 1#3 0:100 1:100 A:760057089;C:705694497;G:690249046;T:767122385;N:11783 100 100     760057089 705694497 690249046 767122385 11783 ERX1361532 ERS954834 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.94509 0.94377 0.07431 0.07512 0.74367 0.74525 0.50981 0.51595 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2341 2341 ERR1289925 ERX1361531 ERS954833 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647684 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:25:15Z|External Id:SAMEA3647684|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:25:15Z|INSDC status:public|Submitter Id:RX2 GFP1 sc 2454955|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 GFP1 sc 2454955|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 1#2 15249483 Illumina sequencing of library 15249483 constructed from sample accession ERS954833 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 1. This submission includes reads tagged with the sequence GGACTCCTCTCTCTAT. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_1#2.cram cram 2423614200.0 12118071.0 SC RUN 18222 1#2 0:100 1:100 A:622254096;C:592596967;G:579007199;T:629746522;N:9416 100 100     622254096 592596967 579007199 629746522 9416 ERX1361531 ERS954833 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.94151 0.94151 0.08127 0.08228 0.79091 0.79235 0.51421 0.50953 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2342 2342 ERR1289924 ERX1361530 ERS954832 ERP012920 PRJEB11523 Zebrafish eye populations transcriptomics Zebrafish_eye_populations_transcriptomics-sc-3967 Transcriptome Analysis To characterise the transcriptome of the stem cells and the proliferative progenitors in the retina of 5 dpf zebrafish Danio rerio eyes were prepared as follows: 20 30 eyes per condition were collected dissociated and FACS sorted. The samples were collected to RLT buffer and RNA extraction was immediately performed. cDNA and Nextera XT libraries were generated and subsequent sequencing was carried out using the Illumina HiSeq 2500 platform. ArrayExpress:E ERAD 441       SAMEA3647683 SC ArrayExpress OrganismPart:eye cell populations|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2016 02 23T15:26:28Z|ENA LAST UPDATE:2018 03 09T09:22:57Z|External Id:SAMEA3647683|INSDC center name:SC|INSDC first public:2016 02 23T15:26:28Z|INSDC last update:2018 03 09T09:22:57Z|INSDC status:public|Submitter Id:RX2 ctrl noGFP sc 2454954|common name:zebrafish|sample description:eye cell populations from zebrafish embryo|sample name:RX2 ctrl noGFP sc 2454954|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing SC EXP 18222 1#1 15249482 Illumina sequencing of library 15249482 constructed from sample accession ERS954832 for study accession ERP012920. This is part of an Illumina multiplexed sequencing run 18222 1. This submission includes reads tagged with the sequence GGACTCCTTAGATCGC. Nextera dual index qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP012920 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 02 23|ENA LAST UPDATE:2018 11 16 18222_1#1.cram cram 359779800.0 1798899.0 SC RUN 18222 1#1 0:100 1:100 A:84065568;C:96668644;G:92071125;T:86973168;N:1295 100 100     84065568 96668644 92071125 86973168 1295 ERX1361530 ERS954832 ERA565862 European Nucleotide Archive Wellcome Sanger Institute 2 0.9502 0.9506 0.07759 0.07791 0.71772 0.71827 0.44568 0.45005 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United Kingdom 2016-02-23 Undetermined Embryo Eye Sensory System
2343 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

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