metadata: run_metadata: 4 rows where experiment.library_layout = "SINGLE", technology = "10x" and tissue_curation

4 rows where experiment.library_layout = "SINGLE", technology = "10x" and tissue_curation_coarse = "Digestive 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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
9166	9166	ERR2788341	ERX2797590	ERS2709706	ERP110806	PRJEB28589	Single cell transcriptional analysis reveals ILC like cells in zebrafish	E-MTAB-7159	Transcriptome Analysis	Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 09 11	Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's …	5149STDY7292228	SAMEA4890710	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 16T17:03:30Z\|ENA LAST UPDATE:2018 09 11T09:38:07Z\|External Id:SAMEA4890710\|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 16T17:03:30Z\|INSDC last update:2018 09 11T09:38:07Z\|INSDC status:public\|Submitter Id:E MTAB 7159:5149STDY7292228\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP\|individual:pool 4\|organism part:intestine\|phenotype:lck positive\|sample name:E MTAB 7159:5149STDY7292228\|scientific name:Danio rerio\|sex:2 female 1 male\|strain:AB	Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish	E MTAB 7159:5149STDY7292228 p	5149STDY7292228 p	Single cell transcriptional analysis reveals ILC like cells in zebrafish	The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. B…	Experimental Factor: genotype:Tglck:EGFP\|Experimental Factor: infect:n1	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110806	Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16\|options: use QUAL	5149STDY7292228.bam 5149STDY7292228.bam.bai	bam bam	37970494940.0	387454030.0	E MTAB 7159:5149STDY7292228	0:98	A:11476520187;C:7571635167;G:8189594199;T:10701044279;N:31701108	98	11476520187	7571635167	8189594199	10701044279	31701108	ERX2797590	ERS2709706	ERA1594569	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	1	0.87568	0.2122	0.82582	0.5259	98	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2018-09-11	Adult	Adult	Gut	Digestive System
9167	9167	ERR2788340	ERX2797589	ERS2709705	ERP110806	PRJEB28589	Single cell transcriptional analysis reveals ILC like cells in zebrafish	E-MTAB-7159	Transcriptome Analysis	Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 09 11	Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's …	5149STDY7274848	SAMEA4890709	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 16T17:03:30Z\|ENA LAST UPDATE:2018 09 11T09:38:07Z\|External Id:SAMEA4890709\|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 16T17:03:30Z\|INSDC last update:2018 09 11T09:38:07Z\|INSDC status:public\|Submitter Id:E MTAB 7159:5149STDY7274848\|age:4\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 homozygous knockout\|individual:pool 3\|organism part:intestine\|phenotype:lck positive\|sample name:E MTAB 7159:5149STDY7274848\|scientific name:Danio rerio\|sex:female\|strain:AB	Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish	E MTAB 7159:5149STDY7274848 p	5149STDY7274848 p	Single cell transcriptional analysis reveals ILC like cells in zebrafish	The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. B…	Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout\|Experimental Factor: infect:Vibrio Anguillarum	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110806	Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16\|options: use QUAL	5149STDY7274848.bam 5149STDY7274848.bam.bai	bam bam	34517322840.0	352217580.0	E MTAB 7159:5149STDY7274848	0:98	A:10635243399;C:6658515314;G:7525079510;T:9695995344;N:2489273	98	10635243399	6658515314	7525079510	9695995344	2489273	ERX2797589	ERS2709705	ERA1594569	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	1	0.86206	0.18065	0.83514	0.53609	98	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2018-09-11	Adult	Adult	Gut	Digestive System
9168	9168	ERR2788339	ERX2797588	ERS2709704	ERP110806	PRJEB28589	Single cell transcriptional analysis reveals ILC like cells in zebrafish	E-MTAB-7159	Transcriptome Analysis	Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 09 11	Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's …	5149STDY7274847	SAMEA4890708	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 16T17:03:30Z\|ENA LAST UPDATE:2018 09 11T09:38:07Z\|External Id:SAMEA4890708\|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 16T17:03:30Z\|INSDC last update:2018 09 11T09:38:07Z\|INSDC status:public\|Submitter Id:E MTAB 7159:5149STDY7274847\|age:4\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 homozygous knockout\|individual:pool 2\|organism part:intestine\|phenotype:lck positive\|sample name:E MTAB 7159:5149STDY7274847\|scientific name:Danio rerio\|sex:female\|strain:AB	Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish	E MTAB 7159:5149STDY7274847 p	5149STDY7274847 p	Single cell transcriptional analysis reveals ILC like cells in zebrafish	The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. B…	Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout\|Experimental Factor: infect:Anisakis simplex	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110806	Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16\|options: use QUAL	5149STDY7274847.bam 5149STDY7274847.bam.bai	bam bam	34467649678.0	351710711.0	E MTAB 7159:5149STDY7274847	0:98	A:10609988948;C:6722093635;G:7464497879;T:9667814950;N:3254266	98	10609988948	6722093635	7464497879	9667814950	3254266	ERX2797588	ERS2709704	ERA1594569	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	1	0.88751	0.21835	0.83771	0.53927	98	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2018-09-11	Adult	Adult	Gut	Digestive System
9169	9169	ERR2788338	ERX2797587	ERS2709703	ERP110806	PRJEB28589	Single cell transcriptional analysis reveals ILC like cells in zebrafish	E-MTAB-7159	Transcriptome Analysis	Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 09 11	Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's …	5149STDY7274846	SAMEA4890707	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 16T17:03:30Z\|ENA LAST UPDATE:2018 09 11T09:38:07Z\|External Id:SAMEA4890707\|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 16T17:03:30Z\|INSDC last update:2018 09 11T09:38:07Z\|INSDC status:public\|Submitter Id:E MTAB 7159:5149STDY7274846\|age:4\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 homozygous knockout\|individual:pool 1\|organism part:intestine\|phenotype:lck positive\|sample name:E MTAB 7159:5149STDY7274846\|scientific name:Danio rerio\|sex:female\|strain:AB	Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish	E MTAB 7159:5149STDY7274846 p	5149STDY7274846 p	Single cell transcriptional analysis reveals ILC like cells in zebrafish	The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. B…	Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout\|Experimental Factor: infect:n1	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110806	Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16\|options: use QUAL	5149STDY7274846.bam 5149STDY7274846.bam.bai	bam bam	35052538472.0	357678964.0	E MTAB 7159:5149STDY7274846	0:98	A:10698116265;C:6858102477;G:7626019661;T:9866905792;N:3394277	98	10698116265	6858102477	7626019661	9866905792	3394277	ERX2797587	ERS2709703	ERA1594569	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	1	0.88916	0.21537	0.83802	0.5336	98	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2018-09-11	Adult	Adult	Gut	Digestive 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");;