metadata: run_metadata: 1,099 rows where experiment.library_selection = "Oligo-dT", experiment.library_strategy = "RNA-Seq" and tissue_curation

1,099 rows where experiment.library_selection = "Oligo-dT", 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
8110	8110	ERR2724023	ERX2737792	ERS2635243	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney F1	SAMEA4815345	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815345\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney F1\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney F1\|scientific name:Danio rerio\|sex:female\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney F1 p	Rag1 kidney F1 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney F1	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i716_i520.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i716_i520.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	37287900.0	124293.0	E MTAB 7117:SLX 12114.i716 i520.HKKG2BBXX.s 1.r	0:150 1:150	A:9752914;C:9040023;G:8665437;T:9829107;N:419	150	150	9752914	9040023	8665437	9829107	419	ERX2737792	ERS2635243	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.84559	0.84961	0.25366	0.2614	0.87371	0.88172	0.59878	0.59883	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8111	8111	ERR2724022	ERX2737791	ERS2635242	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney E1	SAMEA4815344	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815344\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney E1\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney E1\|scientific name:Danio rerio\|sex:female\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney E1 p	Rag1 kidney E1 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney E1	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i716_i518.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i716_i518.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	11274000.0	37580.0	E MTAB 7117:SLX 12114.i716 i518.HKKG2BBXX.s 1.r	0:150 1:150	A:2926114;C:2747598;G:2634051;T:2966113;N:124	150	150	2926114	2747598	2634051	2966113	124	ERX2737791	ERS2635242	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.8296	0.8425	0.26896	0.27904	0.92364	0.93077	0.6102	0.61311	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8112	8112	ERR2724021	ERX2737790	ERS2635241	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney D1	SAMEA4815343	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815343\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney D1\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney D1\|scientific name:Danio rerio\|sex:female\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney D1 p	Rag1 kidney D1 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney D1	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i716_i517.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i716_i517.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	12474900.0	41583.0	E MTAB 7117:SLX 12114.i716 i517.HKKG2BBXX.s 1.r	0:150 1:150	A:3257834;C:3043701;G:2896026;T:3277216;N:123	150	150	3257834	3043701	2896026	3277216	123	ERX2737790	ERS2635241	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.83651	0.85178	0.24924	0.26112	0.90914	0.91942	0.55363	0.56789	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8113	8113	ERR2724020	ERX2737789	ERS2635240	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 gut F1	SAMEA4815342	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815342\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 gut F1\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:gut\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 gut F1\|scientific name:Danio rerio\|sex:female\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 gut F1 p	Rag1 gut F1 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:gut\|Experimental Factor: single cell identifier:Rag1 gut F1	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i701_i508.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i701_i508.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	12988500.0	43295.0	E MTAB 7117:SLX 12114.i701 i508.HKKG2BBXX.s 1.r	0:150 1:150	A:3461959;C:3059299;G:2933330;T:3533768;N:144	150	150	3461959	3059299	2933330	3533768	144	ERX2737789	ERS2635240	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.85611	0.86366	0.20961	0.21567	0.90782	0.91557	0.60043	0.54265	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8114	8114	ERR2724019	ERX2737788	ERS2635239	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 gut E1	SAMEA4815341	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815341\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 gut E1\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:gut\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 gut E1\|scientific name:Danio rerio\|sex:female\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 gut E1 p	Rag1 gut E1 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:gut\|Experimental Factor: single cell identifier:Rag1 gut E1	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i701_i507.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i701_i507.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	16703700.0	55679.0	E MTAB 7117:SLX 12114.i701 i507.HKKG2BBXX.s 1.r	0:150 1:150	A:4474340;C:3934992;G:3734743;T:4559406;N:219	150	150	4474340	3934992	3734743	4559406	219	ERX2737788	ERS2635239	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.86009	0.86698	0.21869	0.21703	0.9009	0.90863	0.61396	0.62254	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8115	8115	ERR2724018	ERX2737787	ERS2635238	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 gut D1	SAMEA4815340	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815340\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 gut D1\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:gut\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 gut D1\|scientific name:Danio rerio\|sex:female\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 gut D1 p	Rag1 gut D1 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:gut\|Experimental Factor: single cell identifier:Rag1 gut D1	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i701_i506.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i701_i506.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	20109900.0	67033.0	E MTAB 7117:SLX 12114.i701 i506.HKKG2BBXX.s 1.r	0:150 1:150	A:5462955;C:4667929;G:4478326;T:5500442;N:248	150	150	5462955	4667929	4478326	5500442	248	ERX2737787	ERS2635238	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.87317	0.88395	0.22588	0.22941	0.88836	0.89635	0.59254	0.59398	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8116	8116	ERR2724017	ERX2737786	ERS2635237	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	mhc2dab kidney pl2 G2	SAMEA4815339	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815339\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:mhc2dab kidney pl2 G2\|age:10\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tgmhc2dab:GFP cd45:dsRed\|individual:3\|organism part:kidney\|phenotype:GFP and dsRed positive cell\|sample name:E MTAB 7117:mhc2dab kidney pl2 G2\|scientific name:Danio rerio\|sex:female\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:mhc2dab kidney pl2 G2 p	mhc2dab kidney pl2 G2 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgmhc2dab:GFP cd45:dsRed\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:mhc2dab kidney pl2 G2	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i702_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i702_i521.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	165358800.0	551196.0	E MTAB 7117:SLX 12114.i702 i521.HKKG2BBXX.s 1.r	0:150 1:150	A:42147164;C:40764409;G:38853267;T:43591839;N:2121	150	150	42147164	40764409	38853267	43591839	2121	ERX2737786	ERS2635237	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.51525	0.50872	0.27056	0.26811	0.98817	0.98863	0.57694	0.57913	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8117	8117	ERR2724016	ERX2737785	ERS2635236	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	mhc2dab kidney pl2 G1	SAMEA4815338	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815338\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:mhc2dab kidney pl2 G1\|age:10\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tgmhc2dab:GFP cd45:dsRed\|individual:3\|organism part:kidney\|phenotype:GFP and dsRed positive cell\|sample name:E MTAB 7117:mhc2dab kidney pl2 G1\|scientific name:Danio rerio\|sex:female\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:mhc2dab kidney pl2 G1 p	mhc2dab kidney pl2 G1 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgmhc2dab:GFP cd45:dsRed\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:mhc2dab kidney pl2 G1	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i701_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i701_i521.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	148696500.0	495655.0	E MTAB 7117:SLX 12114.i701 i521.HKKG2BBXX.s 1.r	0:150 1:150	A:37512136;C:36958044;G:35224815;T:38999534;N:1971	150	150	37512136	36958044	35224815	38999534	1971	ERX2737785	ERS2635236	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.43607	0.42817	0.31231	0.30716	0.98837	0.98926	0.63049	0.62338	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8118	8118	ERR2724015	ERX2737784	ERS2635235	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	mhc2dab kidney pl2 E2	SAMEA4815337	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815337\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:mhc2dab kidney pl2 E2\|age:10\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tgmhc2dab:GFP cd45:dsRed\|individual:3\|organism part:kidney\|phenotype:GFP and dsRed positive cell\|sample name:E MTAB 7117:mhc2dab kidney pl2 E2\|scientific name:Danio rerio\|sex:female\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:mhc2dab kidney pl2 E2 p	mhc2dab kidney pl2 E2 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgmhc2dab:GFP cd45:dsRed\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:mhc2dab kidney pl2 E2	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i702_i518.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i702_i518.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	187041000.0	623470.0	E MTAB 7117:SLX 12114.i702 i518.HKKG2BBXX.s 1.r	0:150 1:150	A:49389638;C:44123341;G:42141034;T:51384635;N:2352	150	150	49389638	44123341	42141034	51384635	2352	ERX2737784	ERS2635235	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.64392	0.64634	0.3608	0.36339	0.98859	0.989	0.5416	0.54533	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8119	8119	ERR2724014	ERX2737783	ERS2635234	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	mhc2dab kidney pl1 H10	SAMEA4815336	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815336\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:mhc2dab kidney pl1 H10\|age:10\|broker name:ArrayExpress\|cell type:blood cell\|cluster:2\|common name:zebrafish\|developmental stage:adult\|genotype:Tgmhc2dab:GFP cd45:dsRed\|individual:3\|organism part:kidney\|phenotype:dsRed positive cell\|sample name:E MTAB 7117:mhc2dab kidney pl1 H10\|scientific name:Danio rerio\|sex:female\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:mhc2dab kidney pl1 H10 p	mhc2dab kidney pl1 H10 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgmhc2dab:GFP cd45:dsRed\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:mhc2dab kidney pl1 H10	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i727_i511.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i727_i511.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	220240200.0	734134.0	E MTAB 7117:SLX 12114.i727 i511.HKKG2BBXX.s 1.r	0:150 1:150	A:54938529;C:55870591;G:53804950;T:55623473;N:2657	150	150	54938529	55870591	53804950	55623473	2657	ERX2737783	ERS2635234	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.65146	0.63182	0.21753	0.21931	0.97555	0.97676	0.64203	0.61402	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8120	8120	ERR2724013	ERX2737782	ERS2635233	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	mhc2dab kidney pl1 F9	SAMEA4815335	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815335\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:mhc2dab kidney pl1 F9\|age:10\|broker name:ArrayExpress\|cell type:blood cell\|cluster:2\|common name:zebrafish\|developmental stage:adult\|genotype:Tgmhc2dab:GFP cd45:dsRed\|individual:3\|organism part:kidney\|phenotype:dsRed positive cell\|sample name:E MTAB 7117:mhc2dab kidney pl1 F9\|scientific name:Danio rerio\|sex:female\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:mhc2dab kidney pl1 F9 p	mhc2dab kidney pl1 F9 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgmhc2dab:GFP cd45:dsRed\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:mhc2dab kidney pl1 F9	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i726_i508.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i726_i508.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	177822900.0	592743.0	E MTAB 7117:SLX 12114.i726 i508.HKKG2BBXX.s 1.r	0:150 1:150	A:45477562;C:43694070;G:42010119;T:46638998;N:2151	150	150	45477562	43694070	42010119	46638998	2151	ERX2737782	ERS2635233	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.61993	0.60069	0.1457	0.14507	0.96039	0.96157	0.58852	0.59377	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8121	8121	ERR2724012	ERX2737781	ERS2635232	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	mhc2dab kidney pl1 E8	SAMEA4815334	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815334\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:mhc2dab kidney pl1 E8\|age:10\|broker name:ArrayExpress\|cell type:blood cell\|cluster:2\|common name:zebrafish\|developmental stage:adult\|genotype:Tgmhc2dab:GFP cd45:dsRed\|individual:3\|organism part:kidney\|phenotype:dsRed positive cell\|sample name:E MTAB 7117:mhc2dab kidney pl1 E8\|scientific name:Danio rerio\|sex:female\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:mhc2dab kidney pl1 E8 p	mhc2dab kidney pl1 E8 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgmhc2dab:GFP cd45:dsRed\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:mhc2dab kidney pl1 E8	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i724_i507.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i724_i507.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	53810700.0	179369.0	E MTAB 7117:SLX 12114.i724 i507.HKKG2BBXX.s 1.r	0:150 1:150	A:13871534;C:13212554;G:12616252;T:14109780;N:580	150	150	13871534	13212554	12616252	14109780	580	ERX2737781	ERS2635232	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.89611	0.90099	0.08881	0.0909	0.90262	0.90611	0.52812	0.52726	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8122	8122	ERR2724011	ERX2737780	ERS2635231	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	CD4 thymus H1	SAMEA4815333	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815333\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:CD4 thymus H1\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tgcd4 1:mCherry\|individual:2\|organism part:thymus\|phenotype:mCherry positive cell\|sample name:E MTAB 7117:CD4 thymus H1\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:CD4 thymus H1 p	CD4 thymus H1 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgcd4 1:mCherry\|Experimental Factor: organism part:thymus\|Experimental Factor: single cell identifier:CD4 thymus H1	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12119.i716_i511.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i716_i511.HKCTNBBXX.s_1.r_2.fq.gz	fastq fastq	65942400.0	219808.0	E MTAB 7117:SLX 12119.i716 i511.HKCTNBBXX.s 1.r	0:150 1:150	A:15633170;C:17548955;G:17103880;T:15654910;N:1485	150	150	15633170	17548955	17103880	15654910	1485	ERX2737780	ERS2635231	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.30317	0.2954	0.19698	0.19711	0.98599	0.98808	0.58605	0.57143	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8123	8123	ERR2724010	ERX2737779	ERS2635230	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	CD4 thymus G5	SAMEA4815332	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815332\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:CD4 thymus G5\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tgcd4 1:mCherry\|individual:2\|organism part:thymus\|phenotype:mCherry positive cell\|sample name:E MTAB 7117:CD4 thymus G5\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:CD4 thymus G5 p	CD4 thymus G5 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgcd4 1:mCherry\|Experimental Factor: organism part:thymus\|Experimental Factor: single cell identifier:CD4 thymus G5	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12119.i721_i510.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i721_i510.HKCTNBBXX.s_1.r_2.fq.gz	fastq fastq	346846800.0	1156156.0	E MTAB 7117:SLX 12119.i721 i510.HKCTNBBXX.s 1.r	0:150 1:150	A:95363866;C:78024771;G:75165091;T:98285320;N:7752	150	150	95363866	78024771	75165091	98285320	7752	ERX2737779	ERS2635230	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.93335	0.93318	0.60406	0.61164	0.99001	0.99078	0.49673	0.49258	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8124	8124	ERR2724009	ERX2737778	ERS2635229	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	CD4 thymus G4	SAMEA4815331	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815331\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:CD4 thymus G4\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tgcd4 1:mCherry\|individual:2\|organism part:thymus\|phenotype:mCherry positive cell\|sample name:E MTAB 7117:CD4 thymus G4\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:CD4 thymus G4 p	CD4 thymus G4 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgcd4 1:mCherry\|Experimental Factor: organism part:thymus\|Experimental Factor: single cell identifier:CD4 thymus G4	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12119.i720_i510.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i720_i510.HKCTNBBXX.s_1.r_2.fq.gz	fastq fastq	461552100.0	1538507.0	E MTAB 7117:SLX 12119.i720 i510.HKCTNBBXX.s 1.r	0:150 1:150	A:126164428;C:105641045;G:101502649;T:128233257;N:10721	150	150	126164428	105641045	101502649	128233257	10721	ERX2737778	ERS2635229	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.93958	0.93555	0.41416	0.42894	0.99194	0.99247	0.51712	0.52812	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8125	8125	ERR2724008	ERX2737777	ERS2635228	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	CD4 kidney D3	SAMEA4815330	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815330\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:CD4 kidney D3\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tgcd4 1:mCherry\|individual:2\|organism part:kidney\|phenotype:mCherry positive cell\|sample name:E MTAB 7117:CD4 kidney D3\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:CD4 kidney D3 p	CD4 kidney D3 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgcd4 1:mCherry\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:CD4 kidney D3	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-10874.N703_S506.C9FTNANXX.s_4.r_1.fq.gz SLX-10874.N703_S506.C9FTNANXX.s_4.r_2.fq.gz	fastq fastq	566790750.0	2267163.0	E MTAB 7117:SLX 10874.N703 S506.C9FTNANXX.s 4.r	0:125 1:125	A:171738679;C:113474320;G:105652185;T:175917546;N:8020	125	125	171738679	113474320	105652185	175917546	8020	ERX2737777	ERS2635228	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.90273	0.90184	0.55846	0.5605	0.99904	0.9991	0.99722	0.82975	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8126	8126	ERR2724007	ERX2737776	ERS2635227	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	CD4 kidney D2	SAMEA4815329	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815329\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:CD4 kidney D2\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tgcd4 1:mCherry\|individual:2\|organism part:kidney\|phenotype:mCherry positive cell\|sample name:E MTAB 7117:CD4 kidney D2\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:CD4 kidney D2 p	CD4 kidney D2 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgcd4 1:mCherry\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:CD4 kidney D2	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-10874.N702_S506.C9FTNANXX.s_4.r_1.fq.gz SLX-10874.N702_S506.C9FTNANXX.s_4.r_2.fq.gz	fastq fastq	277111250.0	1108445.0	E MTAB 7117:SLX 10874.N702 S506.C9FTNANXX.s 4.r	0:125 1:125	A:82435920;C:57203613;G:52019151;T:85448114;N:4452	125	125	82435920	57203613	52019151	85448114	4452	ERX2737776	ERS2635227	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.82299	0.82476	0.57143	0.57476	0.98415	0.98449	0.58875	0.58969	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8127	8127	ERR2724006	ERX2737775	ERS2635226	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	CD4 kidney D12	SAMEA4815328	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815328\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:CD4 kidney D12\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tgcd4 1:mCherry\|individual:2\|organism part:kidney\|phenotype:mCherry positive cell\|sample name:E MTAB 7117:CD4 kidney D12\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:CD4 kidney D12 p	CD4 kidney D12 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgcd4 1:mCherry\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:CD4 kidney D12	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-10874.N715_S506.C9FTNANXX.s_4.r_1.fq.gz SLX-10874.N715_S506.C9FTNANXX.s_4.r_2.fq.gz	fastq fastq	120347500.0	481390.0	E MTAB 7117:SLX 10874.N715 S506.C9FTNANXX.s 4.r	0:125 1:125	A:34833149;C:25858968;G:23765495;T:35888156;N:1732	125	125	34833149	25858968	23765495	35888156	1732	ERX2737775	ERS2635226	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.74258	0.74099	0.4164	0.42068	0.99086	0.99109	0.69164	0.68237	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8128	8128	ERR2724005	ERX2737774	ERS2635225	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	CD4 gill C11	SAMEA4815327	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815327\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:CD4 gill C11\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tgcd4 1:mCherry\|individual:2\|organism part:gill\|phenotype:mCherry positive cell\|sample name:E MTAB 7117:CD4 gill C11\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:CD4 gill C11 p	CD4 gill C11 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgcd4 1:mCherry\|Experimental Factor: organism part:gill\|Experimental Factor: single cell identifier:CD4 gill C11	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-10875.N714_S516.C9FTNANXX.s_5.r_1.fq.gz SLX-10875.N714_S516.C9FTNANXX.s_5.r_2.fq.gz	fastq fastq	165997000.0	663988.0	E MTAB 7117:SLX 10875.N714 S516.C9FTNANXX.s 5.r	0:125 1:125	A:49371380;C:34732413;G:31052964;T:50839053;N:1190	125	125	49371380	34732413	31052964	50839053	1190	ERX2737774	ERS2635225	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.82287	0.82566	0.53775	0.54259	0.98798	0.9881	0.63953	0.62734	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8129	8129	ERR2724004	ERX2737773	ERS2635224	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	CD4 gill B10	SAMEA4815326	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815326\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:CD4 gill B10\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tgcd4 1:mCherry\|individual:2\|organism part:gill\|phenotype:mCherry positive cell\|sample name:E MTAB 7117:CD4 gill B10\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:CD4 gill B10 p	CD4 gill B10 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgcd4 1:mCherry\|Experimental Factor: organism part:gill\|Experimental Factor: single cell identifier:CD4 gill B10	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-10875.N712_S515.C9FTNANXX.s_5.r_1.fq.gz SLX-10875.N712_S515.C9FTNANXX.s_5.r_2.fq.gz	fastq fastq	383976500.0	1535906.0	E MTAB 7117:SLX 10875.N712 S515.C9FTNANXX.s 5.r	0:125 1:125	A:118831629;C:76296476;G:69785982;T:119059622;N:2791	125	125	118831629	76296476	69785982	119059622	2791	ERX2737773	ERS2635224	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.85658	0.85722	0.65298	0.65529	0.98973	0.98995	0.57674	0.54701	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8130	8130	ERR2724003	ERX2737772	ERS2635223	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	CD4 spleen G7	SAMEA4815325	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815325\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:CD4 spleen G7\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|cluster:3\|common name:zebrafish\|developmental stage:adult\|genotype:Tgcd4 1:mCherry\|individual:2\|organism part:spleen\|phenotype:mCherry positive cell\|sample name:E MTAB 7117:CD4 spleen G7\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:CD4 spleen G7 p	CD4 spleen G7 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgcd4 1:mCherry\|Experimental Factor: organism part:spleen\|Experimental Factor: single cell identifier:CD4 spleen G7	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-10875.N723_S510.C9FTNANXX.s_5.r_1.fq.gz SLX-10875.N723_S510.C9FTNANXX.s_5.r_2.fq.gz	fastq fastq	177573500.0	710294.0	E MTAB 7117:SLX 10875.N723 S510.C9FTNANXX.s 5.r	0:125 1:125	A:48445252;C:41183835;G:38570754;T:49372448;N:1211	125	125	48445252	41183835	38570754	49372448	1211	ERX2737772	ERS2635223	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.76107	0.76087	0.2578	0.2632	0.96331	0.96404	0.59545	0.60013	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8131	8131	ERR2724002	ERX2737771	ERS2635222	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	CD4 spleen E8	SAMEA4815324	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815324\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:CD4 spleen E8\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|cluster:3\|common name:zebrafish\|developmental stage:adult\|genotype:Tgcd4 1:mCherry\|individual:2\|organism part:spleen\|phenotype:mCherry positive cell\|sample name:E MTAB 7117:CD4 spleen E8\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:CD4 spleen E8 p	CD4 spleen E8 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgcd4 1:mCherry\|Experimental Factor: organism part:spleen\|Experimental Factor: single cell identifier:CD4 spleen E8	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-10875.N724_S507.C9FTNANXX.s_5.r_1.fq.gz SLX-10875.N724_S507.C9FTNANXX.s_5.r_2.fq.gz	fastq fastq	257265750.0	1029063.0	E MTAB 7117:SLX 10875.N724 S507.C9FTNANXX.s 5.r	0:125 1:125	A:72268420;C:57460553;G:53691082;T:73843922;N:1773	125	125	72268420	57460553	53691082	73843922	1773	ERX2737771	ERS2635222	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.78515	0.78466	0.29915	0.30955	0.97047	0.97112	0.53525	0.53581	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8132	8132	ERR2724001	ERX2737770	ERS2635221	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	CD4 gill A11	SAMEA4815323	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815323\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:CD4 gill A11\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|cluster:3\|common name:zebrafish\|developmental stage:adult\|genotype:Tgcd4 1:mCherry\|individual:2\|organism part:gill\|phenotype:mCherry positive cell\|sample name:E MTAB 7117:CD4 gill A11\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:CD4 gill A11 p	CD4 gill A11 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgcd4 1:mCherry\|Experimental Factor: organism part:gill\|Experimental Factor: single cell identifier:CD4 gill A11	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-10875.N714_S513.C9FTNANXX.s_5.r_1.fq.gz SLX-10875.N714_S513.C9FTNANXX.s_5.r_2.fq.gz	fastq fastq	124536000.0	498144.0	E MTAB 7117:SLX 10875.N714 S513.C9FTNANXX.s 5.r	0:125 1:125	A:33962304;C:28877389;G:27029516;T:34665844;N:947	125	125	33962304	28877389	27029516	34665844	947	ERX2737770	ERS2635221	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.78979	0.79005	0.2588	0.26313	0.97981	0.98044	0.57157	0.56676	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8133	8133	ERR2724000	ERX2737769	ERS2635220	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	CD4 kidney F7	SAMEA4815322	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815322\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:CD4 kidney F7\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|cluster:2\|common name:zebrafish\|developmental stage:adult\|genotype:Tgcd4 1:mCherry\|individual:2\|organism part:kidney\|phenotype:mCherry positive cell\|sample name:E MTAB 7117:CD4 kidney F7\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:CD4 kidney F7 p	CD4 kidney F7 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgcd4 1:mCherry\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:CD4 kidney F7	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-10874.N707_S508.C9FTNANXX.s_4.r_1.fq.gz SLX-10874.N707_S508.C9FTNANXX.s_4.r_2.fq.gz	fastq fastq	113655500.0	454622.0	E MTAB 7117:SLX 10874.N707 S508.C9FTNANXX.s 4.r	0:125 1:125	A:33870000;C:23611974;G:21194053;T:34977343;N:2130	125	125	33870000	23611974	21194053	34977343	2130	ERX2737769	ERS2635220	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.85267	0.85506	0.25904	0.26014	0.943	0.94383	0.59233	0.60505	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8134	8134	ERR2723999	ERX2737768	ERS2635219	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	CD4 kidney B12	SAMEA4815321	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815321\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:CD4 kidney B12\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|cluster:2\|common name:zebrafish\|developmental stage:adult\|genotype:Tgcd4 1:mCherry\|individual:2\|organism part:kidney\|phenotype:mCherry positive cell\|sample name:E MTAB 7117:CD4 kidney B12\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:CD4 kidney B12 p	CD4 kidney B12 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgcd4 1:mCherry\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:CD4 kidney B12	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-10874.N715_S503.C9FTNANXX.s_4.r_1.fq.gz SLX-10874.N715_S503.C9FTNANXX.s_4.r_2.fq.gz	fastq fastq	41609000.0	166436.0	E MTAB 7117:SLX 10874.N715 S503.C9FTNANXX.s 4.r	0:125 1:125	A:11753969;C:9216161;G:8702127;T:11935923;N:820	125	125	11753969	9216161	8702127	11935923	820	ERX2737768	ERS2635219	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.82459	0.82764	0.17061	0.17378	0.93854	0.93878	0.54477	0.55123	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8135	8135	ERR2723998	ERX2737767	ERS2635218	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	CD4 spleen A12	SAMEA4815320	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815320\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:CD4 spleen A12\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|cluster:1\|common name:zebrafish\|developmental stage:adult\|genotype:Tgcd4 1:mCherry\|individual:2\|organism part:spleen\|phenotype:mCherry positive cell\|sample name:E MTAB 7117:CD4 spleen A12\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:CD4 spleen A12 p	CD4 spleen A12 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgcd4 1:mCherry\|Experimental Factor: organism part:spleen\|Experimental Factor: single cell identifier:CD4 spleen A12	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-10875.N729_S502.C9FTNANXX.s_5.r_1.fq.gz SLX-10875.N729_S502.C9FTNANXX.s_5.r_2.fq.gz	fastq fastq	236353500.0	945414.0	E MTAB 7117:SLX 10875.N729 S502.C9FTNANXX.s 5.r	0:125 1:125	A:64839700;C:54488967;G:51265476;T:65757276;N:2081	125	125	64839700	54488967	51265476	65757276	2081	ERX2737767	ERS2635218	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.69382	0.69224	0.33275	0.33643	0.9833	0.98346	0.54137	0.53281	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8136	8136	ERR2723997	ERX2737766	ERS2635217	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	CD4 spleen A11	SAMEA4815319	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815319\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:CD4 spleen A11\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|cluster:1\|common name:zebrafish\|developmental stage:adult\|genotype:Tgcd4 1:mCherry\|individual:2\|organism part:spleen\|phenotype:mCherry positive cell\|sample name:E MTAB 7117:CD4 spleen A11\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:CD4 spleen A11 p	CD4 spleen A11 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgcd4 1:mCherry\|Experimental Factor: organism part:spleen\|Experimental Factor: single cell identifier:CD4 spleen A11	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-10875.N728_S502.C9FTNANXX.s_5.r_1.fq.gz SLX-10875.N728_S502.C9FTNANXX.s_5.r_2.fq.gz	fastq fastq	308428500.0	1233714.0	E MTAB 7117:SLX 10875.N728 S502.C9FTNANXX.s 5.r	0:125 1:125	A:83665727;C:71720130;G:68234442;T:84805861;N:2340	125	125	83665727	71720130	68234442	84805861	2340	ERX2737766	ERS2635217	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.70583	0.70452	0.29793	0.30065	0.97885	0.97906	0.62417	0.61241	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8137	8137	ERR2723996	ERX2737765	ERS2635216	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	CD4 spleen A10	SAMEA4815318	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815318\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:CD4 spleen A10\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|cluster:1\|common name:zebrafish\|developmental stage:adult\|genotype:Tgcd4 1:mCherry\|individual:2\|organism part:spleen\|phenotype:mCherry positive cell\|sample name:E MTAB 7117:CD4 spleen A10\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:CD4 spleen A10 p	CD4 spleen A10 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgcd4 1:mCherry\|Experimental Factor: organism part:spleen\|Experimental Factor: single cell identifier:CD4 spleen A10	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-10875.N727_S502.C9FTNANXX.s_5.r_1.fq.gz SLX-10875.N727_S502.C9FTNANXX.s_5.r_2.fq.gz	fastq fastq	328761500.0	1315046.0	E MTAB 7117:SLX 10875.N727 S502.C9FTNANXX.s 5.r	0:125 1:125	A:89742953;C:76043831;G:72070914;T:90901345;N:2457	125	125	89742953	76043831	72070914	90901345	2457	ERX2737765	ERS2635216	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.7281	0.72679	0.30613	0.30863	0.98137	0.98184	0.61337	0.61341	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8138	8138	ERR2723995	ERX2737764	ERS2635215	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	CD4 kidney H11	SAMEA4815317	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815317\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:CD4 kidney H11\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|cluster:1\|common name:zebrafish\|developmental stage:adult\|genotype:Tgcd4 1:mCherry\|individual:2\|organism part:kidney\|phenotype:mCherry positive cell\|sample name:E MTAB 7117:CD4 kidney H11\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:CD4 kidney H11 p	CD4 kidney H11 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgcd4 1:mCherry\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:CD4 kidney H11	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-10874.N714_S511.C9FTNANXX.s_4.r_1.fq.gz SLX-10874.N714_S511.C9FTNANXX.s_4.r_2.fq.gz	fastq fastq	38522250.0	154089.0	E MTAB 7117:SLX 10874.N714 S511.C9FTNANXX.s 4.r	0:125 1:125	A:10506506;C:8914382;G:8393250;T:10707317;N:795	125	125	10506506	8914382	8393250	10707317	795	ERX2737764	ERS2635215	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.67795	0.67789	0.33735	0.34027	0.98478	0.98512	0.5973	0.58484	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8139	8139	ERR2723994	ERX2737763	ERS2635214	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	CD4 kidney G9	SAMEA4815316	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815316\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:CD4 kidney G9\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|cluster:1\|common name:zebrafish\|developmental stage:adult\|genotype:Tgcd4 1:mCherry\|individual:2\|organism part:kidney\|phenotype:mCherry positive cell\|sample name:E MTAB 7117:CD4 kidney G9\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:CD4 kidney G9 p	CD4 kidney G9 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tgcd4 1:mCherry\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:CD4 kidney G9	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-10874.N711_S510.C9FTNANXX.s_4.r_1.fq.gz SLX-10874.N711_S510.C9FTNANXX.s_4.r_2.fq.gz	fastq fastq	221927750.0	887711.0	E MTAB 7117:SLX 10874.N711 S510.C9FTNANXX.s 4.r	0:125 1:125	A:67713095;C:44853314;G:41236151;T:68121004;N:4186	125	125	67713095	44853314	41236151	68121004	4186	ERX2737763	ERS2635214	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.86217	0.86277	0.36625	0.36915	0.97137	0.97155	0.61749	0.61418	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8140	8140	ERR2723993	ERX2737762	ERS2635213	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	LCK thymus C1	SAMEA4815315	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815315\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:LCK thymus C1\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP\|individual:1\|organism part:thymus\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:LCK thymus C1\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:LCK thymus C1 p	LCK thymus C1 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP\|Experimental Factor: organism part:thymus\|Experimental Factor: single cell identifier:LCK thymus C1	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12119.i701_i505.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i701_i505.HKCTNBBXX.s_1.r_2.fq.gz	fastq fastq	214753500.0	715845.0	E MTAB 7117:SLX 12119.i701 i505.HKCTNBBXX.s 1.r	0:150 1:150	A:58043697;C:49133850;G:47539293;T:60032128;N:4532	150	150	58043697	49133850	47539293	60032128	4532	ERX2737762	ERS2635213	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.90796	0.9075	0.47549	0.49027	0.98733	0.98784	0.44635	0.44113	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8141	8141	ERR2723992	ERX2737761	ERS2635212	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	LCK thymus B8	SAMEA4815314	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815314\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:LCK thymus B8\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP\|individual:1\|organism part:thymus\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:LCK thymus B8\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:LCK thymus B8 p	LCK thymus B8 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP\|Experimental Factor: organism part:thymus\|Experimental Factor: single cell identifier:LCK thymus B8	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12119.i710_i503.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i710_i503.HKCTNBBXX.s_1.r_2.fq.gz	fastq fastq	301541400.0	1005138.0	E MTAB 7117:SLX 12119.i710 i503.HKCTNBBXX.s 1.r	0:150 1:150	A:80889588;C:70114577;G:68676561;T:81854043;N:6631	150	150	80889588	70114577	68676561	81854043	6631	ERX2737761	ERS2635212	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.90679	0.90475	0.5614	0.56522	0.99291	0.99302	0.45816	0.45886	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8142	8142	ERR2723991	ERX2737760	ERS2635211	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	LCK thymus B6	SAMEA4815313	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815313\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:LCK thymus B6\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP\|individual:1\|organism part:thymus\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:LCK thymus B6\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:LCK thymus B6 p	LCK thymus B6 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP\|Experimental Factor: organism part:thymus\|Experimental Factor: single cell identifier:LCK thymus B6	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12119.i706_i503.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i706_i503.HKCTNBBXX.s_1.r_2.fq.gz	fastq fastq	184856100.0	616187.0	E MTAB 7117:SLX 12119.i706 i503.HKCTNBBXX.s 1.r	0:150 1:150	A:49138791;C:43366279;G:42353773;T:49993540;N:3717	150	150	49138791	43366279	42353773	49993540	3717	ERX2737760	ERS2635211	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.88928	0.88981	0.53378	0.54911	0.98802	0.98912	0.53874	0.51283	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8143	8143	ERR2723990	ERX2737759	ERS2635210	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	LCK thymus B2	SAMEA4815312	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815312\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:LCK thymus B2\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP\|individual:1\|organism part:thymus\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:LCK thymus B2\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:LCK thymus B2 p	LCK thymus B2 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP\|Experimental Factor: organism part:thymus\|Experimental Factor: single cell identifier:LCK thymus B2	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12119.i702_i503.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i702_i503.HKCTNBBXX.s_1.r_2.fq.gz	fastq fastq	505800.0	1686.0	E MTAB 7117:SLX 12119.i702 i503.HKCTNBBXX.s 1.r	0:150 1:150	A:130422;C:126765;G:117769;T:130837;N:7	150	150	130422	126765	117769	130837	7	ERX2737759	ERS2635210	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.59969	0.58629	0.2609	0.2583	0.99354	0.99527	0.53571	0.55405	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8144	8144	ERR2723989	ERX2737758	ERS2635209	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	LCK thymus B10	SAMEA4815311	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815311\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:LCK thymus B10\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP\|individual:1\|organism part:thymus\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:LCK thymus B10\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:LCK thymus B10 p	LCK thymus B10 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP\|Experimental Factor: organism part:thymus\|Experimental Factor: single cell identifier:LCK thymus B10	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12119.i712_i503.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i712_i503.HKCTNBBXX.s_1.r_2.fq.gz	fastq fastq	247476300.0	824921.0	E MTAB 7117:SLX 12119.i712 i503.HKCTNBBXX.s 1.r	0:150 1:150	A:68013465;C:55551292;G:54322136;T:69583621;N:5786	150	150	68013465	55551292	54322136	69583621	5786	ERX2737758	ERS2635209	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.9046	0.90455	0.49135	0.50578	0.98677	0.98739	0.4365	0.39972	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8145	8145	ERR2723988	ERX2737757	ERS2635208	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	LCK kidney E7	SAMEA4815310	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815310\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:LCK kidney E7\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|cluster:1\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP\|individual:1\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:LCK kidney E7\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:LCK kidney E7 p	LCK kidney E7 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:LCK kidney E7	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12119.i723_i518.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i723_i518.HKCTNBBXX.s_1.r_2.fq.gz	fastq fastq	232390500.0	774635.0	E MTAB 7117:SLX 12119.i723 i518.HKCTNBBXX.s 1.r	0:150 1:150	A:61370741;C:54657214;G:52783802;T:63573865;N:4878	150	150	61370741	54657214	52783802	63573865	4878	ERX2737757	ERS2635208	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.88735	0.89152	0.31373	0.32461	0.97319	0.97465	0.52638	0.53463	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8146	8146	ERR2723987	ERX2737756	ERS2635207	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	LCK kidney E10	SAMEA4815309	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815309\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:LCK kidney E10\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|cluster:1\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP\|individual:1\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:LCK kidney E10\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:LCK kidney E10 p	LCK kidney E10 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:LCK kidney E10	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12119.i727_i518.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i727_i518.HKCTNBBXX.s_1.r_2.fq.gz	fastq fastq	364697700.0	1215659.0	E MTAB 7117:SLX 12119.i727 i518.HKCTNBBXX.s 1.r	0:150 1:150	A:95675868;C:86934996;G:84117263;T:97961987;N:7586	150	150	95675868	86934996	84117263	97961987	7586	ERX2737756	ERS2635207	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.88034	0.88626	0.39506	0.4105	0.98443	0.98516	0.52064	0.52752	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8147	8147	ERR2723986	ERX2737755	ERS2635206	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	LCK kidney D3	SAMEA4815308	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815308\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:LCK kidney D3\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|cluster:1\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP\|individual:1\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:LCK kidney D3\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:LCK kidney D3 p	LCK kidney D3 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:LCK kidney D3	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12119.i719_i517.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i719_i517.HKCTNBBXX.s_1.r_2.fq.gz	fastq fastq	189068100.0	630227.0	E MTAB 7117:SLX 12119.i719 i517.HKCTNBBXX.s 1.r	0:150 1:150	A:49359046;C:45298627;G:43481326;T:50925211;N:3890	150	150	49359046	45298627	43481326	50925211	3890	ERX2737755	ERS2635206	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.90143	0.89821	0.27981	0.29122	0.97741	0.97847	0.52388	0.52707	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8148	8148	ERR2723985	ERX2737754	ERS2635205	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	LCK kidney A9	SAMEA4815307	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815307\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:LCK kidney A9\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|cluster:1\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP\|individual:1\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:LCK kidney A9\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:LCK kidney A9 p	LCK kidney A9 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:LCK kidney A9	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12119.i726_i513.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i726_i513.HKCTNBBXX.s_1.r_2.fq.gz	fastq fastq	337984500.0	1126615.0	E MTAB 7117:SLX 12119.i726 i513.HKCTNBBXX.s 1.r	0:150 1:150	A:92362762;C:76764558;G:73890731;T:94958687;N:7762	150	150	92362762	76764558	73890731	94958687	7762	ERX2737754	ERS2635205	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.92075	0.9174	0.36307	0.37491	0.98301	0.98348	0.50947	0.52782	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8149	8149	ERR2723984	ERX2737753	ERS2635204	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	LCK kidney A8	SAMEA4815306	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815306\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:LCK kidney A8\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|cluster:1\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP\|individual:1\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:LCK kidney A8\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:LCK kidney A8 p	LCK kidney A8 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:LCK kidney A8	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12119.i724_i513.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i724_i513.HKCTNBBXX.s_1.r_2.fq.gz	fastq fastq	256610100.0	855367.0	E MTAB 7117:SLX 12119.i724 i513.HKCTNBBXX.s 1.r	0:150 1:150	A:68825150;C:59610677;G:57682582;T:70486458;N:5233	150	150	68825150	59610677	57682582	70486458	5233	ERX2737753	ERS2635204	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.90086	0.89794	0.35242	0.36169	0.98088	0.98147	0.48826	0.50311	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8150	8150	ERR2723983	ERX2737752	ERS2635203	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	LCK kidney A7	SAMEA4815305	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:27Z\|External Id:SAMEA4815305\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:27Z\|INSDC status:public\|Submitter Id:E MTAB 7117:LCK kidney A7\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|cluster:1\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP\|individual:1\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:LCK kidney A7\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:LCK kidney A7 p	LCK kidney A7 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:LCK kidney A7	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12119.i723_i513.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i723_i513.HKCTNBBXX.s_1.r_2.fq.gz	fastq fastq	277473600.0	924912.0	E MTAB 7117:SLX 12119.i723 i513.HKCTNBBXX.s 1.r	0:150 1:150	A:74081873;C:64503157;G:62299967;T:76582517;N:6086	150	150	74081873	64503157	62299967	76582517	6086	ERX2737752	ERS2635203	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.90225	0.90246	0.35509	0.36408	0.98027	0.98098	0.54551	0.53005	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8151	8151	ERR2723982	ERX2737751	ERS2635202	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	LCK kidney A6	SAMEA4815304	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815304\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:LCK kidney A6\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|cluster:1\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP\|individual:1\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:LCK kidney A6\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:LCK kidney A6 p	LCK kidney A6 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:LCK kidney A6	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12119.i722_i513.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i722_i513.HKCTNBBXX.s_1.r_2.fq.gz	fastq fastq	199380300.0	664601.0	E MTAB 7117:SLX 12119.i722 i513.HKCTNBBXX.s 1.r	0:150 1:150	A:53339247;C:46384000;G:44842527;T:54810170;N:4356	150	150	53339247	46384000	44842527	54810170	4356	ERX2737751	ERS2635202	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.90656	0.90507	0.28527	0.29363	0.9727	0.97384	0.50665	0.52084	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8152	8152	ERR2723981	ERX2737750	ERS2635201	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	LCK kidney A5	SAMEA4815303	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815303\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:LCK kidney A5\|age:6\|broker name:ArrayExpress\|cell type:blood cell\|cluster:1\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP\|individual:1\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:LCK kidney A5\|scientific name:Danio rerio\|sex:male\|single cell well quality:not OK\|strain:AB\|well information:50 cells	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:LCK kidney A5 p	LCK kidney A5 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP\|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:LCK kidney A5	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12119.i721_i513.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i721_i513.HKCTNBBXX.s_1.r_2.fq.gz	fastq fastq	228681900.0	762273.0	E MTAB 7117:SLX 12119.i721 i513.HKCTNBBXX.s 1.r	0:150 1:150	A:62064639;C:52192654;G:50570771;T:63849396;N:4440	150	150	62064639	52192654	50570771	63849396	4440	ERX2737750	ERS2635201	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.91143	0.9113	0.38029	0.38612	0.97812	0.97938	0.5556	0.55549	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8153	8153	ERR2723980	ERX2737749	ERS2635200	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney H9	SAMEA4815302	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815302\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney H9\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney H9\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney H9 p	Rag1 kidney H9 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney H9	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i726_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i726_i522.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	266967000.0	889890.0	E MTAB 7117:SLX 12114.i726 i522.HKKG2BBXX.s 1.r	0:150 1:150	A:72936497;C:61564543;G:58506328;T:73956365;N:3267	150	150	72936497	61564543	58506328	73956365	3267	ERX2737749	ERS2635200	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.89229	0.89466	0.28452	0.29065	0.98593	0.98618	0.49404	0.48931	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8154	8154	ERR2723979	ERX2737748	ERS2635199	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney H8	SAMEA4815301	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815301\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney H8\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney H8\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney H8 p	Rag1 kidney H8 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney H8	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i724_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i724_i522.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	142694100.0	475647.0	E MTAB 7117:SLX 12114.i724 i522.HKKG2BBXX.s 1.r	0:150 1:150	A:38465370;C:33223562;G:32019646;T:38983841;N:1681	150	150	38465370	33223562	32019646	38983841	1681	ERX2737748	ERS2635199	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.88313	0.88606	0.24707	0.25454	0.97153	0.9726	0.49136	0.50097	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8155	8155	ERR2723978	ERX2737747	ERS2635198	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney H7	SAMEA4815300	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815300\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney H7\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney H7\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney H7 p	Rag1 kidney H7 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney H7	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i723_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i723_i522.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	74628600.0	248762.0	E MTAB 7117:SLX 12114.i723 i522.HKKG2BBXX.s 1.r	0:150 1:150	A:16733962;C:20859916;G:20170167;T:16863672;N:883	150	150	16733962	20859916	20170167	16863672	883	ERX2737747	ERS2635198	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.5047	0.52498	0.16597	0.17713	0.9726	0.97352	0.60194	0.62146	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8156	8156	ERR2723977	ERX2737746	ERS2635197	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney H6	SAMEA4815299	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815299\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney H6\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney H6\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney H6 p	Rag1 kidney H6 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney H6	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i722_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i722_i522.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	122152500.0	407175.0	E MTAB 7117:SLX 12114.i722 i522.HKKG2BBXX.s 1.r	0:150 1:150	A:32764089;C:28490846;G:27469008;T:33427148;N:1409	150	150	32764089	28490846	27469008	33427148	1409	ERX2737746	ERS2635197	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.79287	0.80107	0.30929	0.32026	0.97206	0.97313	0.55781	0.55838	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8157	8157	ERR2723976	ERX2737745	ERS2635196	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney H5	SAMEA4815298	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815298\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney H5\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney H5\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney H5 p	Rag1 kidney H5 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney H5	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i721_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i721_i522.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	129788100.0	432627.0	E MTAB 7117:SLX 12114.i721 i522.HKKG2BBXX.s 1.r	0:150 1:150	A:35236161;C:30081249;G:29009363;T:35459913;N:1414	150	150	35236161	30081249	29009363	35459913	1414	ERX2737745	ERS2635196	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.89451	0.89576	0.19999	0.20491	0.96625	0.96743	0.50804	0.49439	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8158	8158	ERR2723975	ERX2737744	ERS2635195	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney H4	SAMEA4815297	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815297\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney H4\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney H4\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney H4 p	Rag1 kidney H4 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney H4	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i720_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i720_i522.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	119907300.0	399691.0	E MTAB 7117:SLX 12114.i720 i522.HKKG2BBXX.s 1.r	0:150 1:150	A:32516536;C:27737809;G:26669245;T:32982313;N:1397	150	150	32516536	27737809	26669245	32982313	1397	ERX2737744	ERS2635195	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.85448	0.85693	0.28483	0.29668	0.96861	0.9699	0.51867	0.51004	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8159	8159	ERR2723974	ERX2737743	ERS2635194	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney H3	SAMEA4815296	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815296\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney H3\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney H3\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney H3 p	Rag1 kidney H3 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney H3	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i719_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i719_i522.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	717900.0	2393.0	E MTAB 7117:SLX 12114.i719 i522.HKKG2BBXX.s 1.r	0:150 1:150	A:184605;C:180972;G:168309;T:184011;N:3	150	150	184605	180972	168309	184011	3	ERX2737743	ERS2635194	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.5248	0.47818	0.18826	0.19849	0.99151	0.99411	0.60743	0.56575	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8160	8160	ERR2723973	ERX2737742	ERS2635193	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney H2	SAMEA4815295	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815295\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney H2\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney H2\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney H2 p	Rag1 kidney H2 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney H2	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i718_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i718_i522.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	251043900.0	836813.0	E MTAB 7117:SLX 12114.i718 i522.HKKG2BBXX.s 1.r	0:150 1:150	A:68320114;C:58141192;G:55866806;T:68712922;N:2866	150	150	68320114	58141192	55866806	68712922	2866	ERX2737742	ERS2635193	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.85705	0.86239	0.26656	0.27442	0.97273	0.97354	0.54258	0.53766	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8161	8161	ERR2723972	ERX2737741	ERS2635192	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney H12	SAMEA4815294	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815294\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney H12\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney H12\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney H12 p	Rag1 kidney H12 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney H12	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i729_i522.HKKG2BBXX.s_1.r_2.fq.gz SLX-12114.i729_i522.HKKG2BBXX.s_1.r_1.fq.gz	fastq fastq	205536300.0	685121.0	E MTAB 7117:SLX 12114.i729 i522.HKKG2BBXX.s 1.r	0:150 1:150	A:54575803;C:48923788;G:46554826;T:55479471;N:2412	150	150	54575803	48923788	46554826	55479471	2412	ERX2737741	ERS2635192	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.88176	0.88607	0.44943	0.45367	0.98346	0.98332	0.59478	0.58035	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8162	8162	ERR2723971	ERX2737740	ERS2635191	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney H11	SAMEA4815293	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815293\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney H11\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney H11\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney H11 p	Rag1 kidney H11 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney H11	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i728_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i728_i522.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	218551200.0	728504.0	E MTAB 7117:SLX 12114.i728 i522.HKKG2BBXX.s 1.r	0:150 1:150	A:59914721;C:49712610;G:47874165;T:61047094;N:2610	150	150	59914721	49712610	47874165	61047094	2610	ERX2737740	ERS2635191	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.89681	0.89967	0.31764	0.32917	0.97924	0.97973	0.51522	0.51708	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8163	8163	ERR2723970	ERX2737739	ERS2635190	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney H10	SAMEA4815292	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815292\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney H10\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney H10\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney H10 p	Rag1 kidney H10 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney H10	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i727_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i727_i522.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	148134600.0	493782.0	E MTAB 7117:SLX 12114.i727 i522.HKKG2BBXX.s 1.r	0:150 1:150	A:40215105;C:34309220;G:32968610;T:40639940;N:1725	150	150	40215105	34309220	32968610	40639940	1725	ERX2737739	ERS2635190	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.85472	0.86027	0.3246	0.33485	0.9735	0.97494	0.53066	0.50715	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8164	8164	ERR2723969	ERX2737738	ERS2635189	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney H1	SAMEA4815291	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815291\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney H1\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney H1\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney H1 p	Rag1 kidney H1 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney H1	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i716_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i716_i522.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	210196800.0	700656.0	E MTAB 7117:SLX 12114.i716 i522.HKKG2BBXX.s 1.r	0:150 1:150	A:52816299;C:53122529;G:51064568;T:53191053;N:2351	150	150	52816299	53122529	51064568	53191053	2351	ERX2737738	ERS2635189	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.82744	0.84153	0.16889	0.17748	0.9542	0.95493	0.55348	0.55212	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8165	8165	ERR2723968	ERX2737737	ERS2635188	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney G9	SAMEA4815290	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815290\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney G9\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney G9\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney G9 p	Rag1 kidney G9 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney G9	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i726_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i726_i521.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	205987500.0	686625.0	E MTAB 7117:SLX 12114.i726 i521.HKKG2BBXX.s 1.r	0:150 1:150	A:57262398;C:46388763;G:43950404;T:58383283;N:2652	150	150	57262398	46388763	43950404	58383283	2652	ERX2737737	ERS2635188	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.8772	0.87939	0.37456	0.37809	0.97871	0.97934	0.56985	0.58161	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8166	8166	ERR2723967	ERX2737736	ERS2635187	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney G8	SAMEA4815289	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815289\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney G8\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney G8\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney G8 p	Rag1 kidney G8 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney G8	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i724_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i724_i521.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	138236700.0	460789.0	E MTAB 7117:SLX 12114.i724 i521.HKKG2BBXX.s 1.r	0:150 1:150	A:38231050;C:31102804;G:30059891;T:38841286;N:1669	150	150	38231050	31102804	30059891	38841286	1669	ERX2737736	ERS2635187	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.89024	0.8918	0.32094	0.32933	0.97437	0.97536	0.51993	0.52818	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8167	8167	ERR2723966	ERX2737735	ERS2635186	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney G7	SAMEA4815288	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815288\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney G7\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney G7\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney G7 p	Rag1 kidney G7 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney G7	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i723_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i723_i521.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	77073300.0	256911.0	E MTAB 7117:SLX 12114.i723 i521.HKKG2BBXX.s 1.r	0:150 1:150	A:18220192;C:20562829;G:19856183;T:18433242;N:854	150	150	18220192	20562829	19856183	18433242	854	ERX2737735	ERS2635186	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.48981	0.57084	0.17877	0.21647	0.9684	0.96852	0.63691	0.64125	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8168	8168	ERR2723965	ERX2737734	ERS2635185	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney G6	SAMEA4815287	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815287\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney G6\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney G6\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney G6 p	Rag1 kidney G6 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney G6	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i722_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i722_i521.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	66912000.0	223040.0	E MTAB 7117:SLX 12114.i722 i521.HKKG2BBXX.s 1.r	0:150 1:150	A:16469009;C:17213266;G:16620613;T:16608292;N:820	150	150	16469009	17213266	16620613	16608292	820	ERX2737734	ERS2635185	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.54771	0.63559	0.19195	0.23078	0.96534	0.96512	0.57228	0.5806	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8169	8169	ERR2723964	ERX2737733	ERS2635184	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney G5	SAMEA4815286	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815286\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney G5\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney G5\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney G5 p	Rag1 kidney G5 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney G5	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i721_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i721_i521.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	127597200.0	425324.0	E MTAB 7117:SLX 12114.i721 i521.HKKG2BBXX.s 1.r	0:150 1:150	A:34778626;C:29213451;G:28164730;T:35438856;N:1537	150	150	34778626	29213451	28164730	35438856	1537	ERX2737733	ERS2635184	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.86881	0.87329	0.35885	0.36707	0.96962	0.97183	0.50972	0.50832	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8170	8170	ERR2723963	ERX2737732	ERS2635183	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney G4	SAMEA4815285	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815285\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney G4\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney G4\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney G4 p	Rag1 kidney G4 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney G4	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i720_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i720_i521.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	208706100.0	695687.0	E MTAB 7117:SLX 12114.i720 i521.HKKG2BBXX.s 1.r	0:150 1:150	A:49506811;C:55639927;G:53649832;T:49906916;N:2614	150	150	49506811	55639927	53649832	49906916	2614	ERX2737732	ERS2635183	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.59828	0.62274	0.23345	0.24511	0.98837	0.9891	0.52332	0.54143	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8171	8171	ERR2723962	ERX2737731	ERS2635182	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney G3	SAMEA4815284	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815284\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney G3\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney G3\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney G3 p	Rag1 kidney G3 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney G3	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i719_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i719_i521.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	78470100.0	261567.0	E MTAB 7117:SLX 12114.i719 i521.HKKG2BBXX.s 1.r	0:150 1:150	A:20861944;C:18531657;G:17910833;T:21164717;N:949	150	150	20861944	18531657	17910833	21164717	949	ERX2737731	ERS2635182	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.84211	0.84705	0.21181	0.21987	0.96197	0.9639	0.52563	0.53396	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8172	8172	ERR2723961	ERX2737730	ERS2635181	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney G2	SAMEA4815283	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815283\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney G2\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney G2\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney G2 p	Rag1 kidney G2 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney G2	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i718_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i718_i521.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	170317500.0	567725.0	E MTAB 7117:SLX 12114.i718 i521.HKKG2BBXX.s 1.r	0:150 1:150	A:46279278;C:39388939;G:38119248;T:46528005;N:2030	150	150	46279278	39388939	38119248	46528005	2030	ERX2737730	ERS2635181	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.86893	0.87291	0.26507	0.27212	0.97007	0.97163	0.53986	0.51551	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8173	8173	ERR2723960	ERX2737729	ERS2635180	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney G12	SAMEA4815282	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815282\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney G12\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney G12\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney G12 p	Rag1 kidney G12 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney G12	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i729_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i729_i521.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	184555800.0	615186.0	E MTAB 7117:SLX 12114.i729 i521.HKKG2BBXX.s 1.r	0:150 1:150	A:49685531;C:42960556;G:41166991;T:50740527;N:2195	150	150	49685531	42960556	41166991	50740527	2195	ERX2737729	ERS2635180	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.87399	0.878	0.32312	0.33071	0.97423	0.97433	0.47728	0.47512	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8174	8174	ERR2723959	ERX2737728	ERS2635179	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney G11	SAMEA4815281	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815281\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney G11\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney G11\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney G11 p	Rag1 kidney G11 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney G11	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i728_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i728_i521.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	174227700.0	580759.0	E MTAB 7117:SLX 12114.i728 i521.HKKG2BBXX.s 1.r	0:150 1:150	A:47124445;C:40338390;G:38827876;T:47934892;N:2097	150	150	47124445	40338390	38827876	47934892	2097	ERX2737728	ERS2635179	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.87068	0.87397	0.32244	0.33114	0.97924	0.98037	0.5677	0.58727	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8175	8175	ERR2723958	ERX2737727	ERS2635178	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney G10	SAMEA4815280	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815280\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney G10\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney G10\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney G10 p	Rag1 kidney G10 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney G10	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i727_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i727_i521.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	119128800.0	397096.0	E MTAB 7117:SLX 12114.i727 i521.HKKG2BBXX.s 1.r	0:150 1:150	A:32538117;C:27143637;G:26209284;T:33236228;N:1534	150	150	32538117	27143637	26209284	33236228	1534	ERX2737727	ERS2635178	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.88413	0.88973	0.34973	0.35892	0.97321	0.97415	0.53322	0.55266	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8176	8176	ERR2723957	ERX2737726	ERS2635177	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney G1	SAMEA4815279	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815279\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney G1\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney G1\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney G1 p	Rag1 kidney G1 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney G1	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i716_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i716_i521.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	192269700.0	640899.0	E MTAB 7117:SLX 12114.i716 i521.HKKG2BBXX.s 1.r	0:150 1:150	A:52209157;C:44619638;G:42999231;T:52439338;N:2336	150	150	52209157	44619638	42999231	52439338	2336	ERX2737726	ERS2635177	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.903	0.90329	0.2165	0.22388	0.96956	0.97055	0.51313	0.49792	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8177	8177	ERR2723956	ERX2737725	ERS2635176	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney F9	SAMEA4815278	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815278\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney F9\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney F9\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney F9 p	Rag1 kidney F9 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney F9	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i726_i520.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i726_i520.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	156714600.0	522382.0	E MTAB 7117:SLX 12114.i726 i520.HKKG2BBXX.s 1.r	0:150 1:150	A:43302587;C:35378974;G:33959883;T:44071238;N:1918	150	150	43302587	35378974	33959883	44071238	1918	ERX2737725	ERS2635176	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.88305	0.88608	0.27135	0.28056	0.96895	0.96997	0.5322	0.54601	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8178	8178	ERR2723955	ERX2737724	ERS2635175	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney F8	SAMEA4815277	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815277\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney F8\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney F8\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney F8 p	Rag1 kidney F8 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney F8	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i724_i520.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i724_i520.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	113784000.0	379280.0	E MTAB 7117:SLX 12114.i724 i520.HKKG2BBXX.s 1.r	0:150 1:150	A:31395414;C:25669850;G:24673269;T:32043993;N:1474	150	150	31395414	25669850	24673269	32043993	1474	ERX2737724	ERS2635175	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.91199	0.91535	0.25974	0.26473	0.97017	0.97163	0.51679	0.49978	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8179	8179	ERR2723954	ERX2737723	ERS2635174	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney F7	SAMEA4815276	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815276\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney F7\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney F7\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney F7 p	Rag1 kidney F7 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney F7	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i723_i520.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i723_i520.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	103296000.0	344320.0	E MTAB 7117:SLX 12114.i723 i520.HKKG2BBXX.s 1.r	0:150 1:150	A:28453461;C:23160364;G:22306024;T:29374931;N:1220	150	150	28453461	23160364	22306024	29374931	1220	ERX2737723	ERS2635174	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.7944	0.8019	0.42293	0.43282	0.97467	0.97544	0.59231	0.56276	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8180	8180	ERR2723953	ERX2737722	ERS2635173	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney F6	SAMEA4815275	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815275\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney F6\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney F6\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney F6 p	Rag1 kidney F6 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney F6	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i722_i520.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i722_i520.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	122835300.0	409451.0	E MTAB 7117:SLX 12114.i722 i520.HKKG2BBXX.s 1.r	0:150 1:150	A:33228500;C:28399606;G:27461890;T:33743848;N:1456	150	150	33228500	28399606	27461890	33743848	1456	ERX2737722	ERS2635173	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.88054	0.88159	0.3098	0.3173	0.96666	0.96767	0.48577	0.4915	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8181	8181	ERR2723952	ERX2737721	ERS2635172	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney F5	SAMEA4815274	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815274\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney F5\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney F5\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney F5 p	Rag1 kidney F5 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney F5	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i721_i520.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i721_i520.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	81664200.0	272214.0	E MTAB 7117:SLX 12114.i721 i520.HKKG2BBXX.s 1.r	0:150 1:150	A:20085749;C:20965813;G:20180320;T:20431294;N:1024	150	150	20085749	20965813	20180320	20431294	1024	ERX2737721	ERS2635172	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.52933	0.5184	0.16984	0.16981	0.96682	0.9684	0.5888	0.60509	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8182	8182	ERR2723951	ERX2737720	ERS2635171	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney F4	SAMEA4815273	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815273\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney F4\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney F4\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney F4 p	Rag1 kidney F4 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney F4	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i720_i520.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i720_i520.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	103027500.0	343425.0	E MTAB 7117:SLX 12114.i720 i520.HKKG2BBXX.s 1.r	0:150 1:150	A:28021710;C:23710651;G:22850056;T:28443901;N:1182	150	150	28021710	23710651	22850056	28443901	1182	ERX2737720	ERS2635171	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.85183	0.85762	0.31545	0.32595	0.96228	0.96414	0.53403	0.55566	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8183	8183	ERR2723950	ERX2737719	ERS2635170	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney F3	SAMEA4815272	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815272\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney F3\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney F3\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney F3 p	Rag1 kidney F3 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney F3	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i719_i520.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i719_i520.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	83391900.0	277973.0	E MTAB 7117:SLX 12114.i719 i520.HKKG2BBXX.s 1.r	0:150 1:150	A:20159748;C:21755945;G:21010139;T:20464992;N:1076	150	150	20159748	21755945	21010139	20464992	1076	ERX2737719	ERS2635170	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.65217	0.6639	0.2232	0.23162	0.96258	0.96364	0.55651	0.61674	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8184	8184	ERR2723949	ERX2737718	ERS2635169	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney F2	SAMEA4815271	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815271\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney F2\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney F2\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney F2 p	Rag1 kidney F2 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney F2	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i718_i520.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i718_i520.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	125776800.0	419256.0	E MTAB 7117:SLX 12114.i718 i520.HKKG2BBXX.s 1.r	0:150 1:150	A:33333183;C:29722378;G:28767637;T:33952164;N:1438	150	150	33333183	29722378	28767637	33952164	1438	ERX2737718	ERS2635169	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.84847	0.85771	0.31507	0.32474	0.96165	0.96278	0.56034	0.56274	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8185	8185	ERR2723948	ERX2737717	ERS2635168	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney F12	SAMEA4815270	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815270\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney F12\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney F12\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney F12 p	Rag1 kidney F12 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney F12	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i729_i520.HKKG2BBXX.s_1.r_2.fq.gz SLX-12114.i729_i520.HKKG2BBXX.s_1.r_1.fq.gz	fastq fastq	184441200.0	614804.0	E MTAB 7117:SLX 12114.i729 i520.HKKG2BBXX.s 1.r	0:150 1:150	A:50457939;C:42068226;G:40383683;T:51529167;N:2185	150	150	50457939	42068226	40383683	51529167	2185	ERX2737717	ERS2635168	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.88501	0.88842	0.32277	0.33018	0.9808	0.98133	0.52482	0.53634	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8186	8186	ERR2723947	ERX2737716	ERS2635167	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney F11	SAMEA4815269	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815269\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney F11\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney F11\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney F11 p	Rag1 kidney F11 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney F11	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i728_i520.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i728_i520.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	116534400.0	388448.0	E MTAB 7117:SLX 12114.i728 i520.HKKG2BBXX.s 1.r	0:150 1:150	A:31755909;C:26396912;G:25437290;T:32942906;N:1383	150	150	31755909	26396912	25437290	32942906	1383	ERX2737716	ERS2635167	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.87538	0.88378	0.36008	0.36315	0.97784	0.97885	0.54811	0.55909	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8187	8187	ERR2723946	ERX2737715	ERS2635166	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney F10	SAMEA4815268	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815268\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney F10\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney F10\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney F10 p	Rag1 kidney F10 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney F10	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i727_i520.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i727_i520.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	169185300.0	563951.0	E MTAB 7117:SLX 12114.i727 i520.HKKG2BBXX.s 1.r	0:150 1:150	A:46115868;C:38693685;G:37272079;T:47101595;N:2073	150	150	46115868	38693685	37272079	47101595	2073	ERX2737715	ERS2635166	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.87454	0.87979	0.35463	0.36602	0.97897	0.97968	0.58126	0.58044	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8188	8188	ERR2723945	ERX2737714	ERS2635165	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney E9	SAMEA4815267	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815267\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney E9\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney E9\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney E9 p	Rag1 kidney E9 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney E9	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i726_i518.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i726_i518.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	194760000.0	649200.0	E MTAB 7117:SLX 12114.i726 i518.HKKG2BBXX.s 1.r	0:150 1:150	A:54695945;C:43179429;G:41190553;T:55691695;N:2378	150	150	54695945	43179429	41190553	55691695	2378	ERX2737714	ERS2635165	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.90048	0.90334	0.34514	0.35585	0.97522	0.97569	0.55438	0.55166	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8189	8189	ERR2723944	ERX2737713	ERS2635164	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney E8	SAMEA4815266	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815266\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney E8\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney E8\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney E8 p	Rag1 kidney E8 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney E8	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i724_i518.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i724_i518.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	55993200.0	186644.0	E MTAB 7117:SLX 12114.i724 i518.HKKG2BBXX.s 1.r	0:150 1:150	A:15045698;C:12998692;G:12576252;T:15371942;N:616	150	150	15045698	12998692	12576252	15371942	616	ERX2737713	ERS2635164	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.53124	0.53074	0.18925	0.19187	0.9695	0.97098	0.50782	0.51777	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8190	8190	ERR2723943	ERX2737712	ERS2635163	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney E7	SAMEA4815265	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:28Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815265\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:28Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney E7\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney E7\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney E7 p	Rag1 kidney E7 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney E7	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i723_i518.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i723_i518.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	130283700.0	434279.0	E MTAB 7117:SLX 12114.i723 i518.HKKG2BBXX.s 1.r	0:150 1:150	A:33706324;C:31755963;G:30723170;T:34096785;N:1458	150	150	33706324	31755963	30723170	34096785	1458	ERX2737712	ERS2635163	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.79753	0.80724	0.20933	0.21563	0.9738	0.97473	0.45384	0.45402	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8191	8191	ERR2723942	ERX2737711	ERS2635162	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney E6	SAMEA4815264	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815264\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney E6\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney E6\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney E6 p	Rag1 kidney E6 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney E6	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i722_i518.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i722_i518.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	169597800.0	565326.0	E MTAB 7117:SLX 12114.i722 i518.HKKG2BBXX.s 1.r	0:150 1:150	A:45279108;C:39866861;G:38708534;T:45741284;N:2013	150	150	45279108	39866861	38708534	45741284	2013	ERX2737711	ERS2635162	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.86363	0.86925	0.30665	0.3137	0.97634	0.97727	0.52425	0.51674	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8192	8192	ERR2723941	ERX2737710	ERS2635161	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney E5	SAMEA4815263	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815263\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney E5\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney E5\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney E5 p	Rag1 kidney E5 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney E5	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i721_i518.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i721_i518.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	41675400.0	138918.0	E MTAB 7117:SLX 12114.i721 i518.HKKG2BBXX.s 1.r	0:150 1:150	A:11489479;C:9368580;G:9029224;T:11787598;N:519	150	150	11489479	9368580	9029224	11787598	519	ERX2737710	ERS2635161	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.86382	0.86857	0.28096	0.28577	0.95905	0.96114	0.5458	0.53792	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8193	8193	ERR2723940	ERX2737709	ERS2635160	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney E4	SAMEA4815262	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815262\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney E4\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney E4\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney E4 p	Rag1 kidney E4 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney E4	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i720_i518.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i720_i518.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	50454600.0	168182.0	E MTAB 7117:SLX 12114.i720 i518.HKKG2BBXX.s 1.r	0:150 1:150	A:13676299;C:11695130;G:11262069;T:13820515;N:587	150	150	13676299	11695130	11262069	13820515	587	ERX2737709	ERS2635160	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.85769	0.86535	0.31263	0.32013	0.96538	0.96761	0.52994	0.51906	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8194	8194	ERR2723939	ERX2737708	ERS2635159	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney E3	SAMEA4815261	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815261\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney E3\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney E3\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney E3 p	Rag1 kidney E3 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney E3	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i719_i518.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i719_i518.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	81588600.0	271962.0	E MTAB 7117:SLX 12114.i719 i518.HKKG2BBXX.s 1.r	0:150 1:150	A:22263230;C:18690875;G:18137519;T:22496029;N:947	150	150	22263230	18690875	18137519	22496029	947	ERX2737708	ERS2635159	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.87083	0.87096	0.23436	0.23975	0.96262	0.96414	0.52272	0.51165	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8195	8195	ERR2723938	ERX2737707	ERS2635158	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney E2	SAMEA4815260	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815260\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney E2\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney E2\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney E2 p	Rag1 kidney E2 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney E2	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i718_i518.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i718_i518.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	154968900.0	516563.0	E MTAB 7117:SLX 12114.i718 i518.HKKG2BBXX.s 1.r	0:150 1:150	A:42197529;C:35965196;G:33880773;T:42923589;N:1813	150	150	42197529	35965196	33880773	42923589	1813	ERX2737707	ERS2635158	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.76822	0.77389	0.34825	0.35066	0.9755	0.97666	0.46424	0.48646	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8196	8196	ERR2723937	ERX2737706	ERS2635157	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney E12	SAMEA4815259	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815259\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney E12\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney E12\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney E12 p	Rag1 kidney E12 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney E12	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i729_i518.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i729_i518.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	196124700.0	653749.0	E MTAB 7117:SLX 12114.i729 i518.HKKG2BBXX.s 1.r	0:150 1:150	A:53232683;C:45163301;G:43381738;T:54344782;N:2196	150	150	53232683	45163301	43381738	54344782	2196	ERX2737706	ERS2635157	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.89768	0.90227	0.3133	0.32098	0.98019	0.98046	0.59472	0.59049	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8197	8197	ERR2723936	ERX2737705	ERS2635156	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney E11	SAMEA4815258	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815258\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney E11\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney E11\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney E11 p	Rag1 kidney E11 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney E11	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i728_i518.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i728_i518.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	147688500.0	492295.0	E MTAB 7117:SLX 12114.i728 i518.HKKG2BBXX.s 1.r	0:150 1:150	A:40797287;C:33172041;G:32032241;T:41685284;N:1647	150	150	40797287	33172041	32032241	41685284	1647	ERX2737705	ERS2635156	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.88943	0.89218	0.3012	0.30985	0.9727	0.97376	0.54793	0.5563	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8198	8198	ERR2723935	ERX2737704	ERS2635155	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney E10	SAMEA4815257	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815257\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney E10\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney E10\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney E10 p	Rag1 kidney E10 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney E10	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i727_i518.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i727_i518.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	130359000.0	434530.0	E MTAB 7117:SLX 12114.i727 i518.HKKG2BBXX.s 1.r	0:150 1:150	A:36557639;C:28803227;G:27730637;T:37265981;N:1516	150	150	36557639	28803227	27730637	37265981	1516	ERX2737704	ERS2635155	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.87745	0.88245	0.36937	0.37885	0.97256	0.9737	0.55336	0.52059	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8199	8199	ERR2723934	ERX2737703	ERS2635154	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney D9	SAMEA4815256	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815256\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney D9\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney D9\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney D9 p	Rag1 kidney D9 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney D9	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i726_i517.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i726_i517.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	202864500.0	676215.0	E MTAB 7117:SLX 12114.i726 i517.HKKG2BBXX.s 1.r	0:150 1:150	A:56251653;C:45769354;G:43567505;T:57273526;N:2462	150	150	56251653	45769354	43567505	57273526	2462	ERX2737703	ERS2635154	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.92303	0.92592	0.3075	0.31718	0.97737	0.97798	0.55614	0.55921	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8200	8200	ERR2723933	ERX2737702	ERS2635153	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney D8	SAMEA4815255	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815255\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney D8\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney D8\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney D8 p	Rag1 kidney D8 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney D8	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i724_i517.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i724_i517.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	107951100.0	359837.0	E MTAB 7117:SLX 12114.i724 i517.HKKG2BBXX.s 1.r	0:150 1:150	A:29376362;C:24872489;G:23918337;T:29782678;N:1234	150	150	29376362	24872489	23918337	29782678	1234	ERX2737702	ERS2635153	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.91313	0.91381	0.24962	0.25673	0.96345	0.96528	0.55883	0.57172	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8201	8201	ERR2723932	ERX2737701	ERS2635152	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney D7	SAMEA4815254	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815254\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney D7\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney D7\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney D7 p	Rag1 kidney D7 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney D7	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i723_i517.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i723_i517.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	152595300.0	508651.0	E MTAB 7117:SLX 12114.i723 i517.HKKG2BBXX.s 1.r	0:150 1:150	A:41386474;C:35268410;G:33772870;T:42165658;N:1888	150	150	41386474	35268410	33772870	42165658	1888	ERX2737701	ERS2635152	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.80459	0.81182	0.32	0.32902	0.97658	0.97788	0.52169	0.50052	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8202	8202	ERR2723931	ERX2737700	ERS2635151	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney D6	SAMEA4815253	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815253\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney D6\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney D6\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney D6 p	Rag1 kidney D6 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney D6	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i722_i517.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i722_i517.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	99709200.0	332364.0	E MTAB 7117:SLX 12114.i722 i517.HKKG2BBXX.s 1.r	0:150 1:150	A:25903226;C:24192029;G:23231351;T:26381477;N:1117	150	150	25903226	24192029	23231351	26381477	1117	ERX2737700	ERS2635151	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.75741	0.7638	0.27723	0.28857	0.9699	0.97094	0.55045	0.55739	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8203	8203	ERR2723930	ERX2737699	ERS2635150	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney D5	SAMEA4815252	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815252\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney D5\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney D5\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney D5 p	Rag1 kidney D5 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney D5	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i721_i517.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i721_i517.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	88570800.0	295236.0	E MTAB 7117:SLX 12114.i721 i517.HKKG2BBXX.s 1.r	0:150 1:150	A:24035629;C:20411313;G:19531313;T:24591503;N:1042	150	150	24035629	20411313	19531313	24591503	1042	ERX2737699	ERS2635150	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.83087	0.83151	0.28673	0.2973	0.96646	0.96857	0.53652	0.54093	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8204	8204	ERR2723929	ERX2737698	ERS2635149	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney D4	SAMEA4815251	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:26Z\|External Id:SAMEA4815251\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:26Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney D4\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney D4\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney D4 p	Rag1 kidney D4 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney D4	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i720_i517.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i720_i517.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	107283300.0	357611.0	E MTAB 7117:SLX 12114.i720 i517.HKKG2BBXX.s 1.r	0:150 1:150	A:24611082;C:29520367;G:28334156;T:24816370;N:1325	150	150	24611082	29520367	28334156	24816370	1325	ERX2737698	ERS2635149	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.57757	0.60767	0.21159	0.22836	0.97861	0.97968	0.57609	0.58855	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8205	8205	ERR2723928	ERX2737697	ERS2635148	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney D3	SAMEA4815250	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:25Z\|External Id:SAMEA4815250\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:25Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney D3\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney D3\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney D3 p	Rag1 kidney D3 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney D3	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i719_i517.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i719_i517.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	162542400.0	541808.0	E MTAB 7117:SLX 12114.i719 i517.HKKG2BBXX.s 1.r	0:150 1:150	A:36856751;C:45103637;G:43309991;T:37270171;N:1850	150	150	36856751	45103637	43309991	37270171	1850	ERX2737697	ERS2635148	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.56716	0.59718	0.18919	0.20585	0.97262	0.97366	0.63174	0.6191	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8206	8206	ERR2723927	ERX2737696	ERS2635147	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney D2	SAMEA4815249	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:25Z\|External Id:SAMEA4815249\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:25Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney D2\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney D2\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney D2 p	Rag1 kidney D2 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney D2	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i718_i517.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i718_i517.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	68668800.0	228896.0	E MTAB 7117:SLX 12114.i718 i517.HKKG2BBXX.s 1.r	0:150 1:150	A:15319834;C:19355376;G:18575674;T:15417130;N:786	150	150	15319834	19355376	18575674	15417130	786	ERX2737696	ERS2635147	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.55143	0.57804	0.17519	0.19189	0.97066	0.97301	0.63691	0.52056	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8207	8207	ERR2723926	ERX2737695	ERS2635146	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney D12	SAMEA4815248	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:25Z\|External Id:SAMEA4815248\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:25Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney D12\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney D12\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney D12 p	Rag1 kidney D12 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney D12	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i729_i517.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i729_i517.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	179389800.0	597966.0	E MTAB 7117:SLX 12114.i729 i517.HKKG2BBXX.s 1.r	0:150 1:150	A:49243999;C:40790057;G:39166348;T:50187175;N:2221	150	150	49243999	40790057	39166348	50187175	2221	ERX2737695	ERS2635146	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.91776	0.9195	0.28736	0.29412	0.97987	0.98003	0.5404	0.52479	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8208	8208	ERR2723925	ERX2737694	ERS2635145	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney D11	SAMEA4815247	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:25Z\|External Id:SAMEA4815247\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:25Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney D11\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney D11\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney D11 p	Rag1 kidney D11 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney D11	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i728_i517.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i728_i517.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	163471500.0	544905.0	E MTAB 7117:SLX 12114.i728 i517.HKKG2BBXX.s 1.r	0:150 1:150	A:44482061;C:37481802;G:36018593;T:45487118;N:1926	150	150	44482061	37481802	36018593	45487118	1926	ERX2737694	ERS2635145	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.86747	0.87395	0.27918	0.29087	0.97384	0.97437	0.54118	0.54401	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	Multi-tissue	Multi-system
8209	8209	ERR2723924	ERX2737693	ERS2635144	ERP110227	PRJEB28062	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E-MTAB-7117	Transcriptome Analysis	Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry Tglck:EGFP Tgmhc2dab:GFP cd45:dsRed AB.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 08 03	Protocols: Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Rag1 kidney D10	SAMEA4815246	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:29Z\|ENA LAST UPDATE:2018 08 03T10:54:25Z\|External Id:SAMEA4815246\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:29Z\|INSDC last update:2018 08 03T10:54:25Z\|INSDC status:public\|Submitter Id:E MTAB 7117:Rag1 kidney D10\|age:4\|broker name:ArrayExpress\|cell type:blood cell\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 / \|individual:4\|organism part:kidney\|phenotype:EGFP positive cell\|sample name:E MTAB 7117:Rag1 kidney D10\|scientific name:Danio rerio\|sex:female\|single cell well quality:OK\|strain:AB\|well information:single cell	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	E MTAB 7117:Rag1 kidney D10 p	Rag1 kidney D10 p	Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys guts spleens gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney gut gills spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation we used the Illumina Nextera XT DNA kit incubating the mixture for 5 min at 55 °C. post stripping the transposase enzyme adaptor ligation was carried out using the Nextera PCR master mix and index primers cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check the libraries were pooled and diluted to the concentration required for sequencing.	Experimental Factor: genotype:Tglck:EGFP; Rag1 / \|Experimental Factor: organism part:kidney\|Experimental Factor: single cell identifier:Rag1 kidney D10	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110227	Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16	SLX-12114.i727_i517.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i727_i517.HKKG2BBXX.s_1.r_2.fq.gz	fastq fastq	195072000.0	650240.0	E MTAB 7117:SLX 12114.i727 i517.HKKG2BBXX.s 1.r	0:150 1:150	A:53399879;C:44543683;G:42733426;T:54392686;N:2326	150	150	53399879	44543683	42733426	54392686	2326	ERX2737693	ERS2635144	ERA1555808	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	2	0.87836	0.88503	0.333	0.34239	0.97833	0.97893	0.5307	0.52597	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2018-08-03	Adult	Adult	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");;