metadata: run_metadata: 4,693 rows where experiment.library_selection = "cDNA", experiment.library_strategy = "RNA-Seq" and tissue_curation

4,693 rows where experiment.library_selection = "cDNA", experiment.library_strategy = "RNA-Seq" and tissue_curation_coarse = "Multi-system"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
51	51	DRR029943	DRX026961	DRS086501	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.		oocyte maturation duirng natural paring	zebrafish ovary isolated from adult fish at oocyte maturation duirng natural paring. [RNAseq]	SAMD00025433		sample name:5 OM\|strain:roy\|tissue type:ovary\|dev stage:adult	Illumina HiSeq 2500 sequencing of SAMD00025433	DRX026961	5 OM	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025433				573617016.0	15933806.0	DRR029943	0:36	A:130606804;C:141376330;G:145891720;T:155734276;N:7886	36		130606804	141376330	145891720	155734276	7886	DRX026961	DRS086501	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91108		0.0173		0.76205		0.46319		36		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Multi-tissue	Multi-system
168	168	DRR075402	DRX069316	DRS075497	DRP004473	PRJDB5226	Effects of local gut tumor on whole organismal gene expressions in zebrafish	DRP004473	Other	How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.		The liver of tumor fish 7dpf	Tumor liver	SAMD00065416		sample name:6 Tumor liver 150701 Hiseq3A l3 022\|tissue type:Liver	Illumina HiSeq 2500 sequencing of SAMD00065416	DRX069316	Tumor liver	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004473	Illumina HiSeq 2500 sequencing of SAMD00065416				1091167236.0	30310201.0	DRR075402	0:36	A:272216839;C:257523620;G:259746158;T:301642763;N:37856	36		272216839	257523620	259746158	301642763	37856	DRX069316	DRS075497	DRA005199	ATR\|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International	The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International	1	0.90443		0.08935		0.71863		0.51145		36		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2018-09-19	Larval	Larval	Multi-tissue	Multi-system
169	169	DRR075401	DRX069315	DRS075496	DRP004473	PRJDB5226	Effects of local gut tumor on whole organismal gene expressions in zebrafish	DRP004473	Other	How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.		The gut of tumor fish 7dpf	Tumor gut	SAMD00065415		sample name:5 Tumor gut 150701 Hiseq3A l3 021\|tissue type:Gut	Illumina HiSeq 2500 sequencing of SAMD00065415	DRX069315	Tumor gut	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004473	Illumina HiSeq 2500 sequencing of SAMD00065415				1423792872.0	39549802.0	DRR075401	0:36	A:342328685;C:346616167;G:341519547;T:393278536;N:49937	36		342328685	346616167	341519547	393278536	49937	DRX069315	DRS075496	DRA005199	ATR\|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International	The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International	1	0.91303		0.0869		0.70494		0.44332		36		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2018-09-19	Larval	Larval	Multi-tissue	Multi-system
170	170	DRR075400	DRX069314	DRS075495	DRP004473	PRJDB5226	Effects of local gut tumor on whole organismal gene expressions in zebrafish	DRP004473	Other	How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.		The remaining part of body of tumor fish 7dpf	Tumor body	SAMD00065414		sample name:4 Tumor body 150701 Hiseq3A l3 020\|tissue type:Body	Illumina HiSeq 2500 sequencing of SAMD00065414	DRX069314	Tumor body	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004473	Illumina HiSeq 2500 sequencing of SAMD00065414				1168514964.0	32458749.0	DRR075400	0:36	A:286579925;C:275496498;G:278133055;T:328265078;N:40408	36		286579925	275496498	278133055	328265078	40408	DRX069314	DRS075495	DRA005199	ATR\|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International	The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International	1	0.89927		0.15051		0.66714		0.47579		36		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2018-09-19	Larval	Larval	Multi-tissue	Multi-system
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
2411	2411	ERR1125022	ERX1204221	ERS959232	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 C12	SAMEA3652083	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:25:18Z\|External Id:SAMEA3652083\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:25:18Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 C12\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:1548.0\|experiment:Original\|fsc:37017.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 C12\|scientific name:Danio rerio\|ssc:144.0\|well:C12	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 C12	HIGH 2 C12	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 1548.0:egfp fluorescence\|Experimental Factor: 37017.0:fsc\|Experimental Factor: 144.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_C12_1.fq.gz HIGH_2_C12_2.fq.gz	fastq fastq	748434250.0	2993737.0	E MTAB 3947:HIGH 2 C12	0:125 1:125	A:212500284;C:167516552;G:156580935;T:211748631;N:87848	125	125	212500284	167516552	156580935	211748631	87848	ERX1204221	ERS959232	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.71827	0.59991	0.40986	0.33948	0.95434	0.95868	0.55538	0.55577	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2412	2412	ERR1125021	ERX1204220	ERS959231	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 C11	SAMEA3652082	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:25:18Z\|External Id:SAMEA3652082\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:25:18Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 C11\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:923.0\|experiment:Original\|fsc:25404.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 C11\|scientific name:Danio rerio\|ssc:99.0\|well:C11	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 C11	HIGH 2 C11	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 923.0:egfp fluorescence\|Experimental Factor: 25404.0:fsc\|Experimental Factor: 99.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_C11_1.fq.gz HIGH_2_C11_2.fq.gz	fastq fastq	602712500.0	2410850.0	E MTAB 3947:HIGH 2 C11	0:125 1:125	A:171304232;C:137143717;G:126295749;T:167898745;N:70057	125	125	171304232	137143717	126295749	167898745	70057	ERX1204220	ERS959231	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.71708	0.60506	0.37132	0.31027	0.95891	0.96284	0.46614	0.57196	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2413	2413	ERR1125020	ERX1204219	ERS959230	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 C10	SAMEA3652081	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:25:18Z\|External Id:SAMEA3652081\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:25:18Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 C10\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:448.0\|experiment:Original\|fsc:18198.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 C10\|scientific name:Danio rerio\|ssc:71.0\|well:C10	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 C10	HIGH 2 C10	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 448.0:egfp fluorescence\|Experimental Factor: 18198.0:fsc\|Experimental Factor: 71.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_C10_1.fq.gz HIGH_2_C10_2.fq.gz	fastq fastq	858632750.0	3434531.0	E MTAB 3947:HIGH 2 C10	0:125 1:125	A:236198102;C:199474873;G:186059198;T:236799346;N:101231	125	125	236198102	199474873	186059198	236799346	101231	ERX1204219	ERS959230	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.84557	0.72598	0.22661	0.19085	0.93596	0.93809	0.54847	0.54263	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2414	2414	ERR1125019	ERX1204218	ERS959229	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 C1	SAMEA3652080	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:24:42Z\|External Id:SAMEA3652080\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:24:42Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 C1\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:1645.0\|experiment:Original\|fsc:30620.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 C1\|scientific name:Danio rerio\|ssc:181.0\|well:C1	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 C1	HIGH 2 C1	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 1645.0:egfp fluorescence\|Experimental Factor: 30620.0:fsc\|Experimental Factor: 181.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_C1_1.fq.gz HIGH_2_C1_2.fq.gz	fastq fastq	677411000.0	2709644.0	E MTAB 3947:HIGH 2 C1	0:125 1:125	A:190739727;C:153866338;G:142400197;T:190324923;N:79815	125	125	190739727	153866338	142400197	190324923	79815	ERX1204218	ERS959229	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.73701	0.61953	0.3984	0.3309	0.95177	0.95487	0.52653	0.50846	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2415	2415	ERR1125018	ERX1204217	ERS959228	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 B9	SAMEA3652079	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:25:16Z\|External Id:SAMEA3652079\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:25:16Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 B9\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:2075.0\|experiment:Original\|fsc:29774.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 B9\|scientific name:Danio rerio\|ssc:75.0\|well:B9	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 B9	HIGH 2 B9	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 2075.0:egfp fluorescence\|Experimental Factor: 29774.0:fsc\|Experimental Factor: 75.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_B9_1.fq.gz HIGH_2_B9_2.fq.gz	fastq fastq	133472500.0	533890.0	E MTAB 3947:HIGH 2 B9	0:125 1:125	A:37586264;C:30785763;G:27455939;T:37628078;N:16456	125	125	37586264	30785763	27455939	37628078	16456	ERX1204217	ERS959228	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.68814	0.57566	0.40017	0.33032	0.95329	0.9559	0.56663	0.569	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2416	2416	ERR1125017	ERX1204216	ERS959227	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 B8	SAMEA3652078	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:26:23Z\|External Id:SAMEA3652078\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:26:23Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 B8\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:1169.0\|experiment:Original\|fsc:22602.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 B8\|scientific name:Danio rerio\|ssc:90.0\|well:B8	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 B8	HIGH 2 B8	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 1169.0:egfp fluorescence\|Experimental Factor: 22602.0:fsc\|Experimental Factor: 90.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_B8_1.fq.gz HIGH_2_B8_2.fq.gz	fastq fastq	746457500.0	2985830.0	E MTAB 3947:HIGH 2 B8	0:125 1:125	A:205351546;C:175332828;G:162976941;T:202706544;N:89641	125	125	205351546	175332828	162976941	202706544	89641	ERX1204216	ERS959227	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.70597	0.58768	0.41042	0.33777	0.95134	0.95631	0.52988	0.54797	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2417	2417	ERR1125016	ERX1204215	ERS959226	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 B7	SAMEA3652077	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:24:42Z\|External Id:SAMEA3652077\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:24:42Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 B7\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:913.0\|experiment:Original\|fsc:41241.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 B7\|scientific name:Danio rerio\|ssc:55.0\|well:B7	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 B7	HIGH 2 B7	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 913.0:egfp fluorescence\|Experimental Factor: 41241.0:fsc\|Experimental Factor: 55.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_B7_1.fq.gz HIGH_2_B7_2.fq.gz	fastq fastq	688559000.0	2754236.0	E MTAB 3947:HIGH 2 B7	0:125 1:125	A:189350327;C:162852633;G:144622699;T:191649792;N:83549	125	125	189350327	162852633	144622699	191649792	83549	ERX1204215	ERS959226	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.75396	0.63965	0.26609	0.22087	0.94339	0.94667	0.57972	0.48587	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2418	2418	ERR1125015	ERX1204214	ERS959225	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 B6	SAMEA3652076	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:25:16Z\|External Id:SAMEA3652076\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:25:16Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 B6\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:1206.0\|experiment:Original\|fsc:15919.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 B6\|scientific name:Danio rerio\|ssc:152.0\|well:B6	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 B6	HIGH 2 B6	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 1206.0:egfp fluorescence\|Experimental Factor: 15919.0:fsc\|Experimental Factor: 152.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_B6_1.fq.gz HIGH_2_B6_2.fq.gz	fastq fastq	567376250.0	2269505.0	E MTAB 3947:HIGH 2 B6	0:125 1:125	A:161665583;C:126592766;G:115829607;T:163219915;N:68379	125	125	161665583	126592766	115829607	163219915	68379	ERX1204214	ERS959225	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.53901	0.44383	0.33165	0.26966	0.94878	0.95422	0.56193	0.5569	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2419	2419	ERR1125014	ERX1204213	ERS959224	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 B5	SAMEA3652075	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:26:23Z\|External Id:SAMEA3652075\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:26:23Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 B5\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:940.0\|experiment:Original\|fsc:29177.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 B5\|scientific name:Danio rerio\|ssc:176.0\|well:B5	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 B5	HIGH 2 B5	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 940.0:egfp fluorescence\|Experimental Factor: 29177.0:fsc\|Experimental Factor: 176.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_B5_1.fq.gz HIGH_2_B5_2.fq.gz	fastq fastq	597814000.0	2391256.0	E MTAB 3947:HIGH 2 B5	0:125 1:125	A:166324027;C:138643893;G:124996333;T:167776897;N:72850	125	125	166324027	138643893	124996333	167776897	72850	ERX1204213	ERS959224	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.70584	0.5871	0.43466	0.35728	0.95396	0.95791	0.52584	0.53163	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2420	2420	ERR1125013	ERX1204212	ERS959223	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 B4	SAMEA3652074	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:26:23Z\|External Id:SAMEA3652074\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:26:23Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 B4\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:1665.0\|experiment:Original\|fsc:29051.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 B4\|scientific name:Danio rerio\|ssc:98.0\|well:B4	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 B4	HIGH 2 B4	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 1665.0:egfp fluorescence\|Experimental Factor: 29051.0:fsc\|Experimental Factor: 98.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_B4_1.fq.gz HIGH_2_B4_2.fq.gz	fastq fastq	492056000.0	1968224.0	E MTAB 3947:HIGH 2 B4	0:125 1:125	A:136121951;C:115110359;G:103436733;T:137328520;N:58437	125	125	136121951	115110359	103436733	137328520	58437	ERX1204212	ERS959223	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.70874	0.59035	0.40819	0.33557	0.9515	0.95582	0.52997	0.5225	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2421	2421	ERR1125012	ERX1204211	ERS959222	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 B3	SAMEA3652073	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:24:38Z\|External Id:SAMEA3652073\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:24:38Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 B3\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:810.0\|experiment:Original\|fsc:33036.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 B3\|scientific name:Danio rerio\|ssc:124.0\|well:B3	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 B3	HIGH 2 B3	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 810.0:egfp fluorescence\|Experimental Factor: 33036.0:fsc\|Experimental Factor: 124.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_B3_1.fq.gz HIGH_2_B3_2.fq.gz	fastq fastq	702391750.0	2809567.0	E MTAB 3947:HIGH 2 B3	0:125 1:125	A:199736058;C:159583440;G:146984666;T:196005402;N:82184	125	125	199736058	159583440	146984666	196005402	82184	ERX1204211	ERS959222	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.74355	0.6283	0.38429	0.32192	0.9587	0.96132	0.57614	0.57726	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2422	2422	ERR1125011	ERX1204210	ERS959221	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 B2	SAMEA3652072	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:26:23Z\|External Id:SAMEA3652072\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:26:23Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 B2\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:1020.0\|experiment:Original\|fsc:28657.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 B2\|scientific name:Danio rerio\|ssc:103.0\|well:B2	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 B2	HIGH 2 B2	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 1020.0:egfp fluorescence\|Experimental Factor: 28657.0:fsc\|Experimental Factor: 103.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_B2_1.fq.gz HIGH_2_B2_2.fq.gz	fastq fastq	497307750.0	1989231.0	E MTAB 3947:HIGH 2 B2	0:125 1:125	A:143025030;C:111720974;G:99552715;T:142948908;N:60123	125	125	143025030	111720974	99552715	142948908	60123	ERX1204210	ERS959221	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.69598	0.57901	0.41271	0.33912	0.9554	0.95921	0.57302	0.5561	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2423	2423	ERR1125010	ERX1204209	ERS959220	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 B12	SAMEA3652071	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:25:16Z\|External Id:SAMEA3652071\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:25:16Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 B12\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:845.0\|experiment:Original\|fsc:28871.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 B12\|scientific name:Danio rerio\|ssc:85.0\|well:B12	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 B12	HIGH 2 B12	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 845.0:egfp fluorescence\|Experimental Factor: 28871.0:fsc\|Experimental Factor: 85.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_B12_1.fq.gz HIGH_2_B12_2.fq.gz	fastq fastq	724324500.0	2897298.0	E MTAB 3947:HIGH 2 B12	0:125 1:125	A:206976059;C:161393744;G:150157708;T:205709843;N:87146	125	125	206976059	161393744	150157708	205709843	87146	ERX1204209	ERS959220	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.70374	0.5852	0.4239	0.34937	0.9554	0.95946	0.5618	0.55814	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2424	2424	ERR1125009	ERX1204208	ERS959219	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 B11	SAMEA3652070	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:24:38Z\|External Id:SAMEA3652070\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:24:38Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 B11\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:2080.0\|experiment:Original\|fsc:30888.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 B11\|scientific name:Danio rerio\|ssc:121.0\|well:B11	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 B11	HIGH 2 B11	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 2080.0:egfp fluorescence\|Experimental Factor: 30888.0:fsc\|Experimental Factor: 121.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_B11_1.fq.gz HIGH_2_B11_2.fq.gz	fastq fastq	686882000.0	2747528.0	E MTAB 3947:HIGH 2 B11	0:125 1:125	A:193878282;C:158790264;G:145680246;T:188450276;N:82932	125	125	193878282	158790264	145680246	188450276	82932	ERX1204208	ERS959219	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.73609	0.62279	0.39912	0.33433	0.95937	0.9623	0.53785	0.50022	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2425	2425	ERR1125008	ERX1204207	ERS959218	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 B10	SAMEA3652069	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:26:23Z\|External Id:SAMEA3652069\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:26:23Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 B10\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:1943.0\|experiment:Original\|fsc:20791.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 B10\|scientific name:Danio rerio\|ssc:177.0\|well:B10	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 B10	HIGH 2 B10	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 1943.0:egfp fluorescence\|Experimental Factor: 20791.0:fsc\|Experimental Factor: 177.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_B10_1.fq.gz HIGH_2_B10_2.fq.gz	fastq fastq	619664500.0	2478658.0	E MTAB 3947:HIGH 2 B10	0:125 1:125	A:171491122;C:143787528;G:132588275;T:171725121;N:72454	125	125	171491122	143787528	132588275	171725121	72454	ERX1204207	ERS959218	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.72673	0.61127	0.44346	0.37072	0.96004	0.96408	0.47438	0.51929	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2426	2426	ERR1125007	ERX1204206	ERS959217	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 B1	SAMEA3652068	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:26:23Z\|External Id:SAMEA3652068\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:26:23Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 B1\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:683.0\|experiment:Original\|fsc:37507.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 B1\|scientific name:Danio rerio\|ssc:81.0\|well:B1	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 B1	HIGH 2 B1	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 683.0:egfp fluorescence\|Experimental Factor: 37507.0:fsc\|Experimental Factor: 81.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_B1_1.fq.gz HIGH_2_B1_2.fq.gz	fastq fastq	598727250.0	2394909.0	E MTAB 3947:HIGH 2 B1	0:125 1:125	A:168763713;C:136230060;G:126047079;T:167614630;N:71768	125	125	168763713	136230060	126047079	167614630	71768	ERX1204206	ERS959217	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.75198	0.63571	0.35872	0.29818	0.95753	0.96023	0.51035	0.51105	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2427	2427	ERR1125006	ERX1204205	ERS959216	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 A9	SAMEA3652067	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:25:16Z\|External Id:SAMEA3652067\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:25:16Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 A9\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:1062.0\|experiment:Original\|fsc:20462.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 A9\|scientific name:Danio rerio\|ssc:112.0\|well:A9	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 A9	HIGH 2 A9	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 1062.0:egfp fluorescence\|Experimental Factor: 20462.0:fsc\|Experimental Factor: 112.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_A9_1.fq.gz HIGH_2_A9_2.fq.gz	fastq fastq	235150500.0	940602.0	E MTAB 3947:HIGH 2 A9	0:125 1:125	A:64709727;C:55290040;G:48683567;T:66439385;N:27781	125	125	64709727	55290040	48683567	66439385	27781	ERX1204205	ERS959216	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.71466	0.60195	0.36862	0.30781	0.95846	0.96221	0.52784	0.52989	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2428	2428	ERR1125005	ERX1204204	ERS959215	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 A8	SAMEA3652066	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:24:38Z\|External Id:SAMEA3652066\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:24:38Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 A8\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:1816.0\|experiment:Original\|fsc:23959.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 A8\|scientific name:Danio rerio\|ssc:131.0\|well:A8	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 A8	HIGH 2 A8	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 1816.0:egfp fluorescence\|Experimental Factor: 23959.0:fsc\|Experimental Factor: 131.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_A8_1.fq.gz HIGH_2_A8_2.fq.gz	fastq fastq	411990250.0	1647961.0	E MTAB 3947:HIGH 2 A8	0:125 1:125	A:115633720;C:95512217;G:84820282;T:115976883;N:47148	125	125	115633720	95512217	84820282	115976883	47148	ERX1204204	ERS959215	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.62078	0.51083	0.38526	0.3145	0.95572	0.96128	0.58604	0.59225	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2429	2429	ERR1125004	ERX1204203	ERS959214	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 A7	SAMEA3652065	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:26:23Z\|External Id:SAMEA3652065\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:26:23Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 A7\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:415.0\|experiment:Original\|fsc:33487.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 A7\|scientific name:Danio rerio\|ssc:74.0\|well:A7	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 A7	HIGH 2 A7	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 415.0:egfp fluorescence\|Experimental Factor: 33487.0:fsc\|Experimental Factor: 74.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_A7_1.fq.gz HIGH_2_A7_2.fq.gz	fastq fastq	391732000.0	1566928.0	E MTAB 3947:HIGH 2 A7	0:125 1:125	A:109169573;C:91581017;G:78073153;T:112865475;N:42782	125	125	109169573	91581017	78073153	112865475	42782	ERX1204203	ERS959214	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.71097	0.60098	0.27937	0.23216	0.94763	0.95124	0.54099	0.54521	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2430	2430	ERR1125003	ERX1204202	ERS959213	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 A6	SAMEA3652064	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:24:38Z\|External Id:SAMEA3652064\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:24:38Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 A6\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:2724.0\|experiment:Original\|fsc:11087.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 A6\|scientific name:Danio rerio\|ssc:138.0\|well:A6	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 A6	HIGH 2 A6	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 2724.0:egfp fluorescence\|Experimental Factor: 11087.0:fsc\|Experimental Factor: 138.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_A6_1.fq.gz HIGH_2_A6_2.fq.gz	fastq fastq	469393250.0	1877573.0	E MTAB 3947:HIGH 2 A6	0:125 1:125	A:131867414;C:107036944;G:94545740;T:135887751;N:55401	125	125	131867414	107036944	94545740	135887751	55401	ERX1204202	ERS959213	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.64527	0.52872	0.44989	0.36587	0.94909	0.95493	0.50356	0.52818	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2431	2431	ERR1125002	ERX1204201	ERS959212	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 A5	SAMEA3652063	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:24:38Z\|External Id:SAMEA3652063\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:24:38Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 A5\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:1338.0\|experiment:Original\|fsc:27554.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 A5\|scientific name:Danio rerio\|ssc:106.0\|well:A5	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 A5	HIGH 2 A5	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 1338.0:egfp fluorescence\|Experimental Factor: 27554.0:fsc\|Experimental Factor: 106.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_A5_1.fq.gz HIGH_2_A5_2.fq.gz	fastq fastq	358499750.0	1433999.0	E MTAB 3947:HIGH 2 A5	0:125 1:125	A:99967262;C:83245116;G:72063378;T:103182965;N:41029	125	125	99967262	83245116	72063378	103182965	41029	ERX1204201	ERS959212	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.68434	0.5683	0.36795	0.30069	0.95041	0.95592	0.54282	0.53689	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2432	2432	ERR1125001	ERX1204200	ERS959211	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 A4	SAMEA3652062	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:26:18Z\|External Id:SAMEA3652062\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:26:18Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 A4\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:1030.0\|experiment:Original\|fsc:28335.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 A4\|scientific name:Danio rerio\|ssc:78.0\|well:A4	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 A4	HIGH 2 A4	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 1030.0:egfp fluorescence\|Experimental Factor: 28335.0:fsc\|Experimental Factor: 78.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_A4_1.fq.gz HIGH_2_A4_2.fq.gz	fastq fastq	409690000.0	1638760.0	E MTAB 3947:HIGH 2 A4	0:125 1:125	A:113400195;C:95200471;G:83889014;T:117157086;N:43234	125	125	113400195	95200471	83889014	117157086	43234	ERX1204200	ERS959211	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.7238	0.61361	0.32938	0.27581	0.95457	0.95785	0.5107	0.52897	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2433	2433	ERR1125000	ERX1204199	ERS959210	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 A3	SAMEA3652061	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:25:16Z\|External Id:SAMEA3652061\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:25:16Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 A3\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:1719.0\|experiment:Original\|fsc:27281.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 A3\|scientific name:Danio rerio\|ssc:133.0\|well:A3	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 A3	HIGH 2 A3	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 1719.0:egfp fluorescence\|Experimental Factor: 27281.0:fsc\|Experimental Factor: 133.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_A3_1.fq.gz HIGH_2_A3_2.fq.gz	fastq fastq	491303500.0	1965214.0	E MTAB 3947:HIGH 2 A3	0:125 1:125	A:140223481;C:111407934;G:98985396;T:140631370;N:55319	125	125	140223481	111407934	98985396	140631370	55319	ERX1204199	ERS959210	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.69552	0.57579	0.4253	0.34973	0.95361	0.95824	0.59743	0.60657	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2434	2434	ERR1124999	ERX1204198	ERS959209	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 A2	SAMEA3652060	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:26:18Z\|External Id:SAMEA3652060\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:26:18Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 A2\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:1181.0\|experiment:Original\|fsc:31794.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 A2\|scientific name:Danio rerio\|ssc:170.0\|well:A2	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 A2	HIGH 2 A2	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 1181.0:egfp fluorescence\|Experimental Factor: 31794.0:fsc\|Experimental Factor: 170.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_A2_1.fq.gz HIGH_2_A2_2.fq.gz	fastq fastq	691993250.0	2767973.0	E MTAB 3947:HIGH 2 A2	0:125 1:125	A:194386250;C:158850498;G:140892698;T:197783348;N:80456	125	125	194386250	158850498	140892698	197783348	80456	ERX1204198	ERS959209	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.76026	0.64643	0.30724	0.25626	0.9599	0.9629	0.67287	0.66786	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2435	2435	ERR1124998	ERX1204197	ERS959208	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 A12	SAMEA3652059	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:24:38Z\|External Id:SAMEA3652059\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:24:38Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 A12\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:803.0\|experiment:Original\|fsc:31770.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 A12\|scientific name:Danio rerio\|ssc:88.0\|well:A12	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 A12	HIGH 2 A12	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 803.0:egfp fluorescence\|Experimental Factor: 31770.0:fsc\|Experimental Factor: 88.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_A12_1.fq.gz HIGH_2_A12_2.fq.gz	fastq fastq	255037750.0	1020151.0	E MTAB 3947:HIGH 2 A12	0:125 1:125	A:74627903;C:55765462;G:49131966;T:75484997;N:27422	125	125	74627903	55765462	49131966	75484997	27422	ERX1204197	ERS959208	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.63571	0.54379	0.23048	0.20073	0.97934	0.97991	0.55209	0.55372	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2436	2436	ERR1124997	ERX1204196	ERS959207	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 A11	SAMEA3652058	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:24:38Z\|External Id:SAMEA3652058\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:24:38Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 A11\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:881.0\|experiment:Original\|fsc:30036.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 A11\|scientific name:Danio rerio\|ssc:81.0\|well:A11	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 A11	HIGH 2 A11	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 881.0:egfp fluorescence\|Experimental Factor: 30036.0:fsc\|Experimental Factor: 81.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_A11_1.fq.gz HIGH_2_A11_2.fq.gz	fastq fastq	695946750.0	2783787.0	E MTAB 3947:HIGH 2 A11	0:125 1:125	A:195562723;C:160296142;G:144532913;T:195475645;N:79327	125	125	195562723	160296142	144532913	195475645	79327	ERX1204196	ERS959207	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.75254	0.63608	0.35139	0.29487	0.95566	0.95883	0.57191	0.57231	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2437	2437	ERR1124996	ERX1204195	ERS959206	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 A10	SAMEA3652057	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:26:18Z\|External Id:SAMEA3652057\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:26:18Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 A10\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:1164.0\|experiment:Original\|fsc:22577.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 A10\|scientific name:Danio rerio\|ssc:93.0\|well:A10	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 A10	HIGH 2 A10	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 1164.0:egfp fluorescence\|Experimental Factor: 22577.0:fsc\|Experimental Factor: 93.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_A10_1.fq.gz HIGH_2_A10_2.fq.gz	fastq fastq	363569000.0	1454276.0	E MTAB 3947:HIGH 2 A10	0:125 1:125	A:101980108;C:83267465;G:73917235;T:104360917;N:43275	125	125	101980108	83267465	73917235	104360917	43275	ERX1204195	ERS959206	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.68052	0.56825	0.39196	0.32456	0.95383	0.95787	0.48891	0.518	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United Kingdom	2016-01-08	Undetermined	Undetermined	Multi-tissue	Multi-system
2438	2438	ERR1124995	ERX1204194	ERS959205	ERP013160	PRJEB11748	Analysis of single CD41 cell transcriptomes from Zebrafish	E-MTAB-3947	Transcriptome Analysis	Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.	ArrayExpress:E MTAB 3947	Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	HIGH 2 A1	SAMEA3652056	EMBL-EBI	ENA FIRST PUBLIC:2016 01 08T17:01:53Z\|ENA LAST UPDATE:2018 03 09T09:25:16Z\|External Id:SAMEA3652056\|INSDC center name:EMBL EBI\|INSDC first public:2016 01 08T17:01:53Z\|INSDC last update:2018 03 09T09:25:16Z\|INSDC status:public\|Submitter Id:E MTAB 3947:HIGH 2 A1\|broker name:ArrayExpress\|cells:1.0\|common name:zebrafish\|condition:EGFP high\|egfp fluorescence:1033.0\|experiment:Original\|fsc:10616.0\|location:Kidney\|plate:HIGH 2\|sample name:E MTAB 3947:HIGH 2 A1\|scientific name:Danio rerio\|ssc:26.0\|well:A1	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	E MTAB 3947:HIGH 2 A1	HIGH 2 A1	Analysis of single CD41 cell transcriptomes from Zebrafish	A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture.	Experimental Factor: Kidney:location\|Experimental Factor: EGFP high:condition\|Experimental Factor: 1033.0:egfp fluorescence\|Experimental Factor: 10616.0:fsc\|Experimental Factor: 26.0:ssc	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP013160	Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish	ENA FIRST PUBLIC:2016 01 08\|ENA LAST UPDATE:2018 11 16	HIGH_2_A1_1.fq.gz HIGH_2_A1_2.fq.gz	fastq fastq	246022000.0	984088.0	E MTAB 3947:HIGH 2 A1	0:125 1:125	A:70752554;C:55977404;G:48181259;T:71082134;N:28649	125	125	70752554	55977404	48181259	71082134	28649	ERX1204194	ERS959205	ERA533479	EMBL-EBI\|European Nucleotide Archive	EMBL-EBI\|European Nucleotide Archive	2	0.4781	0.4168	0.31626	0.28114	0.99312	0.99399	0.5701	0.57228	125	125	B	B	biological fallback assumption	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");;