metadata: run_metadata: 50 rows where experiment.library_strategy = "AMPLICON", experiment.platform = "ILLUMINA" and tissue

50 rows where experiment.library_strategy = "AMPLICON", experiment.platform = "ILLUMINA" and tissue_curation = "Whole Organism"

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
11130	11130	ERR9979395	ERX9520370	ERS12499848	ERP139765	PRJEB54901	Single cell RNA sequencing of germ free zebrafish embryos	E-MTAB-11984	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish. Here we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22	Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Sample 2 WT GO+BA	SAMEA110401656	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22\|External Id:SAMEA110401656\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 22T16:26:50Z\|INSDC last update:2022 07 22T16:26:50Z\|INSDC status:public\|Submitter Id:E MTAB 11984:Sample 2 WT GO+BA\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|genotype:wild type genotype\|individual:pool of 80 individuals\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11984:Sample 2 WT GO+BA\|sex:not available\|stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos	E MTAB 11984:Sample 2 WT GO+BA p	Sample 2 WT GO+BA p	Single cell RNA sequencing of germ free zebrafish embryos	The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM with 10% FBS…	Experimental Factor: stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP139765	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22	P22202_7002_S2_L002_R1_001.fastq.gz P22202_7002_S2_L002_R2_001.fastq.gz	fastq fastq	18144406998.0	153766161.0	E MTAB 11984:P22202 7002 S2 L002	0:28 1:90	A:5277424121;C:3880928155;G:4118706097;T:4866649878;N:698747	28	90	5277424121	3880928155	4118706097	4866649878	698747	ERX9520370	ERS12499848	ERA16483151	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.0109	0.90145	0.0053	0.21373	0.98746	0.79423	0.41198	0.54447	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-22	Multi-stage	Embryo	Whole Organism	All anatomical structures
11131	11131	ERR9979394	ERX9520370	ERS12499848	ERP139765	PRJEB54901	Single cell RNA sequencing of germ free zebrafish embryos	E-MTAB-11984	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish. Here we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22	Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Sample 2 WT GO+BA	SAMEA110401656	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22\|External Id:SAMEA110401656\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 22T16:26:50Z\|INSDC last update:2022 07 22T16:26:50Z\|INSDC status:public\|Submitter Id:E MTAB 11984:Sample 2 WT GO+BA\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|genotype:wild type genotype\|individual:pool of 80 individuals\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11984:Sample 2 WT GO+BA\|sex:not available\|stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos	E MTAB 11984:Sample 2 WT GO+BA p	Sample 2 WT GO+BA p	Single cell RNA sequencing of germ free zebrafish embryos	The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM with 10% FBS…	Experimental Factor: stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP139765	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22	P22202_7002_S2_L001_R1_001.fastq.gz P22202_7002_S2_L001_R2_001.fastq.gz	fastq fastq	18458951574.0	156431793.0	E MTAB 11984:P22202 7002 S2 L001	0:28 1:90	A:5372920926;C:3946687814;G:4185647697;T:4953205454;N:489683	28	90	5372920926	3946687814	4185647697	4953205454	489683	ERX9520370	ERS12499848	ERA16483151	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.01037	0.90168	0.0048	0.21246	0.98752	0.79297	0.42601	0.54996	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-22	Multi-stage	Embryo	Whole Organism	All anatomical structures
11132	11132	ERR9979392	ERX9520369	ERS12499847	ERP139765	PRJEB54901	Single cell RNA sequencing of germ free zebrafish embryos	E-MTAB-11984	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish. Here we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22	Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Sample 1 WT control	SAMEA110401655	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22\|External Id:SAMEA110401655\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 22T16:26:50Z\|INSDC last update:2022 07 22T16:26:50Z\|INSDC status:public\|Submitter Id:E MTAB 11984:Sample 1 WT control\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|genotype:wild type genotype\|individual:pool of 80 individuals\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11984:Sample 1 WT control\|sex:not available\|stimulus:n1\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos	E MTAB 11984:Sample 1 WT control p	Sample 1 WT control p	Single cell RNA sequencing of germ free zebrafish embryos	The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM with 10% FBS…	Experimental Factor: stimulus:n1	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP139765	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22	P22202_7001_S1_L001_R1_001.fastq.gz P22202_7001_S1_L001_R2_001.fastq.gz	fastq fastq	19396994226.0	164381307.0	E MTAB 11984:P22202 7001 S1 L001	0:28 1:90	A:5665199484;C:4091196594;G:4415211076;T:5224866754;N:520318	28	90	5665199484	4091196594	4415211076	5224866754	520318	ERX9520369	ERS12499847	ERA16483151	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.01093	0.89238	0.00557	0.232	0.98764	0.79444	0.40806	0.54781	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-22	Multi-stage	Embryo	Whole Organism	All anatomical structures
11133	11133	ERR9979393	ERX9520369	ERS12499847	ERP139765	PRJEB54901	Single cell RNA sequencing of germ free zebrafish embryos	E-MTAB-11984	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish. Here we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22	Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Sample 1 WT control	SAMEA110401655	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22\|External Id:SAMEA110401655\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 22T16:26:50Z\|INSDC last update:2022 07 22T16:26:50Z\|INSDC status:public\|Submitter Id:E MTAB 11984:Sample 1 WT control\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|genotype:wild type genotype\|individual:pool of 80 individuals\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11984:Sample 1 WT control\|sex:not available\|stimulus:n1\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos	E MTAB 11984:Sample 1 WT control p	Sample 1 WT control p	Single cell RNA sequencing of germ free zebrafish embryos	The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM with 10% FBS…	Experimental Factor: stimulus:n1	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP139765	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22	P22202_7001_S1_L002_R1_001.fastq.gz P22202_7001_S1_L002_R2_001.fastq.gz	fastq fastq	19063958224.0	161558968.0	E MTAB 11984:P22202 7001 S1 L002	0:28 1:90	A:5563588848;C:4022930643;G:4344549562;T:5132136743;N:752428	28	90	5563588848	4022930643	4344549562	5132136743	752428	ERX9520369	ERS12499847	ERA16483151	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.01118	0.89308	0.00573	0.23128	0.98737	0.79354	0.39264	0.54552	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-22	Multi-stage	Embryo	Whole Organism	All anatomical structures
11134	11134	ERR9981089	ERX9522049	ERS12503451	ERP139797	PRJEB54930	Single cell RNA sequencing of lck GFP transgenic zebrafish	E-MTAB-11991	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing u…	Sample 1 lck control	SAMEA110406305	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23\|External Id:SAMEA110406305\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 23T04:33:35Z\|INSDC last update:2022 07 23T04:33:35Z\|INSDC status:public\|Submitter Id:E MTAB 11991:Sample 1 lck control\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larva\|disease:normal\|genotype:wild type genotype\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11991:Sample 1 lck control\|strain:Tglck:GFP	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	E MTAB 11991:Sample 1 lck control p	Sample 1 lck control p	Single cell RNA sequencing of lck GFP transgenic zebrafish	The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Experimental Factor: stimulus:n1	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP139797	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	P25452_2002_S2_L001_R1_001.fastq.gz P25452_2002_S2_L001_R2_001.fastq.gz	fastq fastq	60177283876.0	509976982.0	E MTAB 11991:P25452 2002 S2 L001	0:28 1:90	A:17254566438;C:13547211711;G:14188233429;T:15185192817;N:2079481	28	90	17254566438	13547211711	14188233429	15185192817	2079481	ERX9522049	ERS12503451	ERA16488297	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.00671	0.93031	0.00231	0.11028	0.9932	0.82227	0.30887	0.58272	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-23	Larval	Larval	Whole Organism	All anatomical structures
11135	11135	ERR9981090	ERX9522049	ERS12503451	ERP139797	PRJEB54930	Single cell RNA sequencing of lck GFP transgenic zebrafish	E-MTAB-11991	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing u…	Sample 1 lck control	SAMEA110406305	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23\|External Id:SAMEA110406305\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 23T04:33:35Z\|INSDC last update:2022 07 23T04:33:35Z\|INSDC status:public\|Submitter Id:E MTAB 11991:Sample 1 lck control\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larva\|disease:normal\|genotype:wild type genotype\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11991:Sample 1 lck control\|strain:Tglck:GFP	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	E MTAB 11991:Sample 1 lck control p	Sample 1 lck control p	Single cell RNA sequencing of lck GFP transgenic zebrafish	The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Experimental Factor: stimulus:n1	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP139797	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	P25452_2002_S2_L002_R1_001.fastq.gz P25452_2002_S2_L002_R2_001.fastq.gz	fastq fastq	60597886144.0	513541408.0	E MTAB 11991:P25452 2002 S2 L002	0:28 1:90	A:17368154358;C:13649089056;G:14296037620;T:15282869484;N:1735626	28	90	17368154358	13649089056	14296037620	15282869484	1735626	ERX9522049	ERS12503451	ERA16488297	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.00656	0.92899	0.00211	0.11059	0.99334	0.82335	0.32311	0.57644	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-23	Larval	Larval	Whole Organism	All anatomical structures
11136	11136	ERR9981087	ERX9522048	ERS12503450	ERP139797	PRJEB54930	Single cell RNA sequencing of lck GFP transgenic zebrafish	E-MTAB-11991	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing u…	Sample 2 lck GO+BA	SAMEA110406304	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23\|External Id:SAMEA110406304\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 23T04:33:35Z\|INSDC last update:2022 07 23T04:33:35Z\|INSDC status:public\|Submitter Id:E MTAB 11991:Sample 2 lck GO+BA\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larva\|disease:normal\|genotype:wild type genotype\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11991:Sample 2 lck GO+BA\|strain:Tglck:GFP	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	E MTAB 11991:Sample 2 lck GO+BA p	Sample 2 lck GO+BA p	Single cell RNA sequencing of lck GFP transgenic zebrafish	The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Experimental Factor: stimulus:graphene oxide 30 microgram per milliliter\|Experimental Factor: compound:butyrate\|Experimental Factor: dose:2.5	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP139797	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	P25452_2001_S1_L001_R1_001.fastq.gz P25452_2001_S1_L001_R2_001.fastq.gz	fastq fastq	20866120186.0	176831527.0	E MTAB 11991:P25452 2001 S1 L001	0:28 1:90	A:5933525376;C:4737179804;G:5025711080;T:5168983880;N:720046	28	90	5933525376	4737179804	5025711080	5168983880	720046	ERX9522048	ERS12503450	ERA16488297	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.00805	0.92622	0.00259	0.11842	0.99302	0.83027	0.2729	0.57699	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-23	Larval	Larval	Whole Organism	All anatomical structures
11137	11137	ERR9981088	ERX9522048	ERS12503450	ERP139797	PRJEB54930	Single cell RNA sequencing of lck GFP transgenic zebrafish	E-MTAB-11991	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing u…	Sample 2 lck GO+BA	SAMEA110406304	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23\|External Id:SAMEA110406304\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 23T04:33:35Z\|INSDC last update:2022 07 23T04:33:35Z\|INSDC status:public\|Submitter Id:E MTAB 11991:Sample 2 lck GO+BA\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larva\|disease:normal\|genotype:wild type genotype\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11991:Sample 2 lck GO+BA\|strain:Tglck:GFP	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	E MTAB 11991:Sample 2 lck GO+BA p	Sample 2 lck GO+BA p	Single cell RNA sequencing of lck GFP transgenic zebrafish	The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Experimental Factor: stimulus:graphene oxide 30 microgram per milliliter\|Experimental Factor: compound:butyrate\|Experimental Factor: dose:2.5	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP139797	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	P25452_2001_S1_L002_R1_001.fastq.gz P25452_2001_S1_L002_R2_001.fastq.gz	fastq fastq	21068682172.0	178548154.0	E MTAB 11991:P25452 2001 S1 L002	0:28 1:90	A:5987758267;C:4786100132;G:5078292970;T:5215926275;N:604528	28	90	5987758267	4786100132	5078292970	5215926275	604528	ERX9522048	ERS12503450	ERA16488297	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.00813	0.92702	0.00264	0.11874	0.99283	0.82737	0.30228	0.56929	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-23	Larval	Larval	Whole Organism	All anatomical structures
40376	40376	SRR3166964	SRX1583817	SRS1295580	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRA library 28d Calm4		breed:AB\|chain:alpha\|index:26\|sex:male\|time point:28d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRa sequencing of zebrafish: whole zebrafish: Sample TCRA library 28d Calm4	116 28d Calm4 alpha	116 28d Calm4 alpha	five prime RACE amplification of TCRa transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_116_28d_Calm4_alpha.fq.gz read2_116_28d_Calm4_alpha.fq.gz	fastq fastq	12052440600.0	40174802.0	116 28d Calm4 alpha files	0:150 1:150	A:3274476247;C:2324807837;G:3578878507;T:2848354560;N:25923449	150	150	3274476247	2324807837	3578878507	2848354560	25923449	SRX1583817	SRS1295580	SRA353254	SRA	Bar-Ilan University	2	0.00096	0.22917	0.00017	0.19822	0.99906	0.99762	0.35172	0.6189	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40377	40377	SRR3166963	SRX1583816	SRS1295581	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRA library 28d Calm2		breed:AB\|chain:alpha\|index:25\|sex:male\|time point:28d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRa sequencing of zebrafish: whole zebrafish: Sample TCRA library 28d Calm2	114 28d Calm2 alpha	114 28d Calm2 alpha	five prime RACE amplification of TCRa transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_114_28d_Calm2_alpha.fq.gz read2_114_28d_Calm2_alpha.fq.gz	fastq fastq	4957122900.0	16523743.0	114 28d Calm2 alpha files	0:150 1:150	A:1398510544;C:988027281;G:1244120221;T:1316350204;N:10114650	150	150	1398510544	988027281	1244120221	1316350204	10114650	SRX1583816	SRS1295581	SRA353254	SRA	Bar-Ilan University	2	0.00167	0.03332	0.00146	0.028	0.99967	0.99896	0.15789	0.60731	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40378	40378	SRR3166962	SRX1583815	SRS1295582	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRA library 28d KLH6		breed:AB\|chain:alpha\|index:21\|sex:male\|time point:28d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRa sequencing of zebrafish: whole zebrafish: Sample TCRA library 28d KLH6	110 28d KLH6 alpha	110 28d KLH6 alpha	five prime RACE amplification of TCRa transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_110_28d_KLH6_alpha.fq.gz read2_110_28d_KLH6_alpha.fq.gz	fastq fastq	6270530700.0	20901769.0	110 28d KLH6 alpha files	0:150 1:150	A:1802311183;C:1236560108;G:1561615962;T:1659163742;N:10879705	150	150	1802311183	1236560108	1561615962	1659163742	10879705	SRX1583815	SRS1295582	SRA353254	SRA	Bar-Ilan University	2	0.00179	0.13512	0.00073	0.11592	0.99967	0.99855	0.21568	0.87835	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40379	40379	SRR3166961	SRX1583814	SRS1295583	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRA library 28d PHA6		breed:AB\|chain:alpha\|index:32\|sex:male\|time point:28d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRa sequencing of zebrafish: whole zebrafish: Sample TCRA library 28d PHA6	102 28d PHA6 alpha	102 28d PHA6 alpha	five prime RACE amplification of TCRa transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_102_28d_PHA6_alpha.fq.gz read2_102_28d_PHA6_alpha.fq.gz	fastq fastq	10067723700.0	33559079.0	102 28d PHA6 alpha files	0:150 1:150	A:2803515995;C:2027880463;G:2649055724;T:2566963260;N:20308258	150	150	2803515995	2027880463	2649055724	2566963260	20308258	SRX1583814	SRS1295583	SRA353254	SRA	Bar-Ilan University	2	0.00158	0.04576	0.00056	0.03839	0.99922	0.99831	0.3246	0.40078	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2016-02-14	Undetermined	Undetermined	Whole Organism	All anatomical structures
40380	40380	SRR3166960	SRX1583813	SRS1295584	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRA library 7d KLH2		breed:AB\|chain:alpha\|index:34\|sex:male\|time point:7d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRa sequencing of zebrafish: whole zebrafish: Sample TCRA library 7d KLH2	16 7d KLH2 alpha	16 7d KLH2 alpha	five prime RACE amplification of TCRa transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_16_7d_KLH2_alpha.fq.gz read2_16_7d_KLH2_alpha.fq.gz	fastq fastq	2783317500.0	9277725.0	16 7d KLH2 alpha files	0:150 1:150	A:761370556;C:556705024;G:719835894;T:727504605;N:17901421	150	150	761370556	556705024	719835894	727504605	17901421	SRX1583813	SRS1295584	SRA353254	SRA	Bar-Ilan University	2	0.00143	0.13658	0.0008	0.11879	0.99935	0.99876	0.25409	0.87567	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2016-02-14	Undetermined	Undetermined	Whole Organism	All anatomical structures
40381	40381	SRR3166959	SRX1583812	SRS1295585	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRA library 21d KLH6		breed:AB\|chain:alpha\|index:24\|sex:male\|time point:21d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRa sequencing of zebrafish: whole zebrafish: Sample TCRA library 21d KLH6	78 21d KLH6 alpha	78 21d KLH6 alpha	five prime RACE amplification of TCRa transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_78_21d_KLH6_alpha.fq.gz read2_78_21d_KLH6_alpha.fq.gz	fastq fastq	7720614900.0	25735383.0	78 21d KLH6 alpha files	0:150 1:150	A:2163229607;C:1591913203;G:1963558161;T:1998596363;N:3317566	150	150	2163229607	1591913203	1963558161	1998596363	3317566	SRX1583812	SRS1295585	SRA353254	SRA	Bar-Ilan University	2	0.00105	0.04913	0.00036	0.04186	0.99937	0.99835	0.14393	0.4819	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40382	40382	SRR3166958	SRX1583811	SRS1295586	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRA library 7d Calm6		breed:AB\|chain:alpha\|index:33\|sex:male\|time point:7d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRa sequencing of zebrafish: whole zebrafish: Sample TCRA library 7d Calm6	27 7d Calm6 alpha	27 7d Calm6 alpha	five prime RACE amplification of TCRa transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_27_7d_Calm6_alpha.fq.gz read2_27_7d_Calm6_alpha.fq.gz	fastq fastq	4337226600.0	14457422.0	27 7d Calm6 alpha files	0:150 1:150	A:1174401516;C:871068073;G:1145864920;T:1118174763;N:27717328	150	150	1174401516	871068073	1145864920	1118174763	27717328	SRX1583811	SRS1295586	SRA353254	SRA	Bar-Ilan University	2	0.002	0.032	0.0007	0.02494	0.99924	0.99912	0.38	0.38606	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2016-02-14	Undetermined	Undetermined	Whole Organism	All anatomical structures
40383	40383	SRR3166957	SRX1583810	SRS1295587	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRA library 7d PHA7		breed:AB\|chain:alpha\|index:36\|sex:male\|time point:7d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRa sequencing of zebrafish: whole zebrafish: Sample TCRA library 7d PHA7	14 7d PHA7 alpha	14 7d PHA7 alpha	five prime RACE amplification of TCRa transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_14_7d_PHA7_alpha.fq.gz read2_14_7d_PHA7_alpha.fq.gz	fastq fastq	3401366100.0	11337887.0	14 7d PHA7 alpha files										SRX1583810	SRS1295587	SRA353254	SRA	Bar-Ilan University	2	0.00357	0.02242	0.00202	0.01952	0.99902	0.99811	0.35016	0.5424	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40384	40384	SRR3166956	SRX1583809	SRS1295588	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRA library 7d PHA3		breed:AB\|chain:alpha\|index:35\|sex:male\|time point:7d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRa sequencing of zebrafish: whole zebrafish: Sample TCRA library 7d PHA3	10 7d PHA3 alpha	10 7d PHA3 alpha	five prime RACE amplification of TCRa transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read2_10_7d_PHA3_alpha.fq.gz read1_10_7d_PHA3_alpha.fq.gz	fastq fastq	4293459300.0	14311531.0	10 7d PHA3 alpha files	0:150 1:150	A:1208054755;C:855800391;G:1072212534;T:1129932131;N:27459489	150	150	1208054755	855800391	1072212534	1129932131	27459489	SRX1583809	SRS1295588	SRA353254	SRA	Bar-Ilan University	2	0.00174	0.05155	0.0009	0.0472	0.99937	0.9989	0.2256	0.60714	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40385	40385	SRR3166955	SRX1583808	SRS1295589	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 28d Calm7		breed:AB\|chain:beta\|index:56\|sex:male\|time point:28d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d Calm7	119 28d Calm7 beta	119 28d Calm7 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_119_28d_Calm7_beta.fq.gz read2_119_28d_Calm7_beta.fq.gz	fastq fastq	3494941800.0	11649806.0	119 28d Calm7 beta files	0:150 1:150	A:1262121526;C:602497563;G:790544892;T:738346792;N:101431027	150	150	1262121526	602497563	790544892	738346792	101431027	SRX1583808	SRS1295589	SRA353254	SRA	Bar-Ilan University	2	3e-05	0.00179	0.0	7e-05	0.99997	0.99831	0.0	0.42009	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40386	40386	SRR3166954	SRX1583807	SRS1295590	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 28d Calm5		breed:AB\|chain:beta\|index:55\|sex:male\|time point:28d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d Calm5	117 28d Calm5 beta	117 28d Calm5 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read2_117_28d_Calm5_beta.fq.gz read1_117_28d_Calm5_beta.fq.gz	fastq fastq	2950876200.0	9836254.0	117 28d Calm5 beta files	0:150 1:150	A:1025845698;C:505599350;G:688977765;T:634738210;N:95715177	150	150	1025845698	505599350	688977765	634738210	95715177	SRX1583807	SRS1295590	SRA353254	SRA	Bar-Ilan University	2	0.0	0.00023	0.0	0.0	1.0	0.99987		0.07692	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2016-03-02	Undetermined	Undetermined	Whole Organism	All anatomical structures
40387	40387	SRR3166953	SRX1583806	SRS1295591	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 28d Calm3		breed:AB\|chain:beta\|index:54\|sex:male\|time point:28d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d Calm3	115 28d Calm3 beta	115 28d Calm3 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_115_28d_Calm3_beta.fq.gz read2_115_28d_Calm3_beta.fq.gz	fastq fastq	1913218200.0	6377394.0	115 28d Calm3 beta files	0:150 1:150	A:637646003;C:349779874;G:435732113;T:430619528;N:59440682	150	150	637646003	349779874	435732113	430619528	59440682	SRX1583806	SRS1295591	SRA353254	SRA	Bar-Ilan University	2	0.0	0.02438	0.0	0.00184	1.0	0.99908		0.01511	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40388	40388	SRR3166952	SRX1583805	SRS1295592	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 28d KLH6		breed:AB\|chain:beta\|index:27\|sex:male\|time point:28d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d KLH6	110 28d KLH6 beta	110 28d KLH6 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_110_28d_KLH6_beta.fq.gz read2_110_28d_KLH6_beta.fq.gz	fastq fastq	2689206600.0	8964022.0	110 28d KLH6 beta files	0:150 1:150	A:807762783;C:503825062;G:585283183;T:703818890;N:88516682	150	150	807762783	503825062	585283183	703818890	88516682	SRX1583805	SRS1295592	SRA353254	SRA	Bar-Ilan University	2	0.00014	0.3078	0.0	0.02202	0.99975	0.99095	0.38888	0.10297	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40389	40389	SRR3166951	SRX1583804	SRS1295593	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 28d KLH2		breed:AB\|chain:beta\|index:23\|sex:male\|time point:28d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d KLH2	106 28d KLH2 beta	106 28d KLH2 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read2_106_28d_KLH2_beta.fq.gz read1_106_28d_KLH2_beta.fq.gz	fastq fastq	2795086200.0	9316954.0	106 28d KLH2 beta files	0:150 1:150	A:897420089;C:470460508;G:621809014;T:712999451;N:92397138	150	150	897420089	470460508	621809014	712999451	92397138	SRX1583804	SRS1295593	SRA353254	SRA	Bar-Ilan University	2	0.0	0.05106	0.0	0.00859	1.0	0.99943		0.01388	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2016-03-02	Undetermined	Undetermined	Whole Organism	All anatomical structures
40390	40390	SRR3166950	SRX1583803	SRS1295594	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 28d KLH1		breed:AB\|chain:beta\|index:22\|sex:male\|time point:28d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d KLH1	105 28d KLH1 beta	105 28d KLH1 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_105_28d_KLH1_beta.fq.gz read2_105_28d_KLH1_beta.fq.gz	fastq fastq	1768628700.0	5895429.0	105 28d KLH1 beta files	0:150 1:150	A:486366963;C:366398128;G:389871583;T:478235213;N:47756813	150	150	486366963	366398128	389871583	478235213	47756813	SRX1583803	SRS1295594	SRA353254	SRA	Bar-Ilan University	2	4e-05	0.09054	3e-05	0.01597	1.0	0.99931		0.00767	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40391	40391	SRR3166949	SRX1583802	SRS1295595	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 28d PHA7		breed:AB\|chain:beta\|index:30\|sex:male\|time point:28d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d PHA7	103 28d PHA7 beta	103 28d PHA7 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_103_28d_PHA7_beta.fq.gz read2_103_28d_PHA7_beta.fq.gz	fastq fastq	2234344500.0	7447815.0	103 28d PHA7 beta files	0:150 1:150	A:628358242;C:462371909;G:526170885;T:548473987;N:68969477	150	150	628358242	462371909	526170885	548473987	68969477	SRX1583802	SRS1295595	SRA353254	SRA	Bar-Ilan University	2	0.00104	0.68691	5e-05	0.01999	0.99894	0.97281	0.23076	0.44172	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2016-03-02	Undetermined	Undetermined	Whole Organism	All anatomical structures
40392	40392	SRR3166948	SRX1583801	SRS1295596	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 28d PHA5		breed:AB\|chain:beta\|index:29\|sex:male\|time point:28d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d PHA5	101 28d PHA5 beta	101 28d PHA5 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_101_28d_PHA5_beta.fq.gz read2_101_28d_PHA5_beta.fq.gz	fastq fastq	1356278400.0	4520928.0	101 28d PHA5 beta files	0:150 1:150	A:372190640;C:278464953;G:294268430;T:378226253;N:33128124	150	150	372190640	278464953	294268430	378226253	33128124	SRX1583801	SRS1295596	SRA353254	SRA	Bar-Ilan University	2	0.00254	0.10913	0.0001	0.01715	0.99995	0.99904	0.01106	0.01084	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40393	40393	SRR3166947	SRX1583800	SRS1295597	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 28d PHA2		breed:AB\|chain:beta\|index:28\|sex:male\|time point:28d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d PHA2	98 28d PHA2 beta	98 28d PHA2 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read2_98_28d_PHA2_beta.fq.gz read1_98_28d_PHA2_beta.fq.gz	fastq fastq	4533755400.0	15112518.0	98 28d PHA2 beta files	0:150 1:150	A:1508096116;C:749853448;G:1051562277;T:1142392486;N:81851073	150	150	1508096116	749853448	1051562277	1142392486	81851073	SRX1583800	SRS1295597	SRA353254	SRA	Bar-Ilan University	2	0.0	0.33493	0.0	0.02388	1.0	0.99758		0.15819	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40394	40394	SRR3166946	SRX1583799	SRS1295598	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 28d IFA 5		breed:AB\|chain:beta\|index:11\|sex:male\|time point:28d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d IFA 5	93 28d IFA 5 beta	93 28d IFA 5 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_93_28d_IFA_5_beta.fq.gz read2_93_28d_IFA_5_beta.fq.gz	fastq fastq	1526394600.0	5087982.0	93 28d IFA 5 beta files	0:150 1:150	A:431910708;C:323148774;G:334806769;T:417586287;N:18942062	150	150	431910708	323148774	334806769	417586287	18942062	SRX1583799	SRS1295598	SRA353254	SRA	Bar-Ilan University	2	0.00039	0.31457	0.00015	0.00771	0.99963	0.98468	0.28947	0.16209	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40395	40395	SRR3166945	SRX1583798	SRS1295599	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 28d IFA 2		breed:AB\|chain:beta\|index:10\|sex:male\|time point:28d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d IFA 2	90 28d IFA 2 beta	90 28d IFA 2 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_90_28d_IFA_2_beta.fq.gz read2_90_28d_IFA_2_beta.fq.gz	fastq fastq	2345298300.0	7817661.0	90 28d IFA 2 beta files	0:150 1:150	A:753823005;C:419081900;G:516233583;T:613533931;N:42625881	150	150	753823005	419081900	516233583	613533931	42625881	SRX1583798	SRS1295599	SRA353254	SRA	Bar-Ilan University	2	0.00015	0.38592	3e-05	0.00508	0.99985	0.99385	0.33333	0.06202	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40396	40396	SRR3166944	SRX1583797	SRS1295600	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 28d IFA 1		breed:AB\|chain:beta\|index:28\|sex:male\|time point:28d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d IFA 1	89 28d IFA 1 beta	89 28d IFA 1 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_89_28d_IFA_1_beta.fq.gz read2_89_28d_IFA_1_beta.fq.gz	fastq fastq	2029349400.0	6764498.0	89 28d IFA 1 beta files	0:150 1:150	A:714287901;C:360307311;G:472841677;T:446872160;N:35040351	150	150	714287901	360307311	472841677	446872160	35040351	SRX1583797	SRS1295600	SRA353254	SRA	Bar-Ilan University	2	0.0	0.06313	0.0	0.01031	1.0	0.99703		0.15591	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40397	40397	SRR3166943	SRX1583796	SRS1295601	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 21d Calm6		breed:AB\|chain:beta\|index:44\|sex:male\|time point:21d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d Calm6	86 21d Calm6 beta	86 21d Calm6 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read2_86_21d_Calm6_beta.fq.gz read1_86_21d_Calm6_beta.fq.gz	fastq fastq	2610499200.0	8701664.0	86 21d Calm6 beta files	0:150 1:150	A:764524163;C:544491001;G:601533912;T:654396223;N:45553901	150	150	764524163	544491001	601533912	654396223	45553901	SRX1583796	SRS1295601	SRA353254	SRA	Bar-Ilan University	2	0.00108	0.63356	0.00012	0.12284	0.99837	0.96193	0.21768	0.38237	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2016-03-02	Undetermined	Undetermined	Whole Organism	All anatomical structures
40398	40398	SRR3166942	SRX1583795	SRS1295602	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 21d Calm5		breed:AB\|chain:beta\|index:43\|sex:male\|time point:21d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d Calm5	85 21d Calm5 beta	85 21d Calm5 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_85_21d_Calm5_beta.fq.gz read2_85_21d_Calm5_beta.fq.gz	fastq fastq	2700056100.0	9000187.0	85 21d Calm5 beta files	0:150 1:150	A:755011216;C:593419169;G:623123170;T:688658373;N:39844172	150	150	755011216	593419169	623123170	688658373	39844172	SRX1583795	SRS1295602	SRA353254	SRA	Bar-Ilan University	2	0.00244	0.68155	0.00026	0.01492	0.99766	0.96597	0.24863	0.31823	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40399	40399	SRR3166941	SRX1583794	SRS1295603	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 21d Calm1		breed:AB\|chain:beta\|index:42\|sex:male\|time point:21d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d Calm1	81 21d Calm1 beta	81 21d Calm1 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_81_21d_Calm1_beta.fq.gz read2_81_21d_Calm1_beta.fq.gz	fastq fastq	2296683900.0	7655613.0	81 21d Calm1 beta files	0:150 1:150	A:776751441;C:430253074;G:528909259;T:525320137;N:35449989	150	150	776751441	430253074	528909259	525320137	35449989	SRX1583794	SRS1295603	SRA353254	SRA	Bar-Ilan University	2	2e-05	0.0464	0.0	0.00091	0.99997	0.99882	0.0	0.0134	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2016-03-02	Undetermined	Undetermined	Whole Organism	All anatomical structures
40400	40400	SRR3166940	SRX1583793	SRS1295604	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 21d KLH6		breed:AB\|chain:beta\|index:50\|sex:male\|time point:21d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d KLH6	78 21d KLH6 beta	78 21d KLH6 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_78_21d_KLH6_beta.fq.gz read2_78_21d_KLH6_beta.fq.gz	fastq fastq	1500221100.0	5000737.0	78 21d KLH6 beta files	0:150 1:150	A:435807096;C:294707078;G:337922064;T:361615328;N:70169534	150	150	435807096	294707078	337922064	361615328	70169534	SRX1583793	SRS1295604	SRA353254	SRA	Bar-Ilan University	2	5e-05	0.37212	3e-05	0.03128	0.99997	0.99358	0.0	0.11962	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40401	40401	SRR3166939	SRX1583792	SRS1295605	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 21d KLH5		breed:AB\|chain:beta\|index:49\|sex:male\|time point:21d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d KLH5	77 21d KLH5 beta	77 21d KLH5 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_77_21d_KLH5_beta.fq.gz read2_77_21d_KLH5_beta.fq.gz	fastq fastq	2106732600.0	7022442.0	77 21d KLH5 beta files	0:150 1:150	A:696373936;C:376059887;G:465978414;T:465485185;N:102835178	150	150	696373936	376059887	465978414	465485185	102835178	SRX1583792	SRS1295605	SRA353254	SRA	Bar-Ilan University	2	0.0	0.04625	0.0	0.00381	1.0	0.99979		0.00123	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40402	40402	SRR3166938	SRX1583791	SRS1295606	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 21d KLH1		breed:AB\|chain:beta\|index:48\|sex:male\|time point:21d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d KLH1	73 21d KLH1 beta	73 21d KLH1 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read2_73_21d_KLH1_beta.fq.gz read1_73_21d_KLH1_beta.fq.gz	fastq fastq	3554391900.0	11847973.0	73 21d KLH1 beta files	0:150 1:150	A:1312477977;C:598886813;G:787337227;T:686894043;N:168795840	150	150	1312477977	598886813	787337227	686894043	168795840	SRX1583791	SRS1295606	SRA353254	SRA	Bar-Ilan University	2	6e-05	0.00136	5e-05	0.00019	1.0	0.99983		0.0303	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40403	40403	SRR3166937	SRX1583790	SRS1295607	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 21d PHA6		breed:AB\|chain:beta\|index:53\|sex:male\|time point:21d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d PHA6	70 21d PHA6 beta	70 21d PHA6 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read2_70_21d_PHA6_beta.fq.gz read1_70_21d_PHA6_beta.fq.gz	fastq fastq	4238076900.0	14126923.0	70 21d PHA6 beta files	0:150 1:150	A:1519543327;C:710498920;G:932091678;T:844220454;N:231722521	150	150	1519543327	710498920	932091678	844220454	231722521	SRX1583790	SRS1295607	SRA353254	SRA	Bar-Ilan University	2	0.00023	0.00772	7e-05	0.00068	0.99991	0.99851	0.25	0.08615	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40404	40404	SRR3166936	SRX1583789	SRS1295608	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 21d PHA4		breed:AB\|chain:beta\|index:52\|sex:male\|time point:21d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d PHA4	68 21d PHA4 beta	68 21d PHA4 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_68_21d_PHA4_beta.fq.gz read2_68_21d_PHA4_beta.fq.gz	fastq fastq	2030511600.0	6768372.0	68 21d PHA4 beta files	0:150 1:150	A:659873688;C:307551211;G:388669539;T:566328083;N:108089079	150	150	659873688	307551211	388669539	566328083	108089079	SRX1583789	SRS1295608	SRA353254	SRA	Bar-Ilan University	2	0.00029	0.24246	3e-05	0.05929	0.99971	0.99214	0.4	0.16492	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40405	40405	SRR3166935	SRX1583788	SRS1295609	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 21d PHA1		breed:AB\|chain:beta\|index:51\|sex:male\|time point:21d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d PHA1	65 21d PHA1 beta	65 21d PHA1 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_65_21d_PHA1_beta.fq.gz read2_65_21d_PHA1_beta.fq.gz	fastq fastq	930240600.0	3100802.0	65 21d PHA1 beta files	0:150 1:150	A:259486434;C:184043790;G:197463162;T:250422190;N:38825024	150	150	259486434	184043790	197463162	250422190	38825024	SRX1583788	SRS1295609	SRA353254	SRA	Bar-Ilan University	2	0.00012	0.14868	0.0	0.02051	0.99963	0.99111	0.36842	0.258	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40406	40406	SRR3166934	SRX1583787	SRS1295610	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 21d IFA 8		breed:AB\|chain:beta\|index:47\|sex:male\|time point:21d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d IFA 8	64 21d IFA 8 beta	64 21d IFA 8 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_64_21d_IFA_8_beta.fq.gz read2_64_21d_IFA_8_beta.fq.gz	fastq fastq	1461868800.0	4872896.0	64 21d IFA 8 beta files	0:150 1:150	A:462418747;C:247121586;G:284662907;T:394116911;N:73548649	150	150	462418747	247121586	284662907	394116911	73548649	SRX1583787	SRS1295610	SRA353254	SRA	Bar-Ilan University	2	0.0001	0.17532	0.0	0.04988	0.99983	0.99843	0.25	0.01908	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40407	40407	SRR3166933	SRX1583786	SRS1295611	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 21d IFA 4		breed:AB\|chain:beta\|index:46\|sex:male\|time point:21d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d IFA 4	60 21d IFA 4 beta	60 21d IFA 4 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read2_60_21d_IFA_4_beta.fq.gz read1_60_21d_IFA_4_beta.fq.gz	fastq fastq	4128399900.0	13761333.0	60 21d IFA 4 beta files	0:150 1:150	A:1332478795;C:800389451;G:937176538;T:950735272;N:107619844	150	150	1332478795	800389451	937176538	950735272	107619844	SRX1583786	SRS1295611	SRA353254	SRA	Bar-Ilan University	2	0.00043	0.19668	5e-05	0.00597	0.99953	0.9782	0.2647	0.35656	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40408	40408	SRR3166932	SRX1583785	SRS1295612	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 21d IFA 2		breed:AB\|chain:beta\|index:45\|sex:male\|time point:21d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d IFA 2	58 21d IFA 2 beta	58 21d IFA 2 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read2_58_21d_IFA_2_beta.fq.gz read1_58_21d_IFA_2_beta.fq.gz	fastq fastq	5035078800.0	16783596.0	58 21d IFA 2 beta files	0:150 1:150	A:1714919930;C:839542402;G:1121993893;T:1220614755;N:138007820	150	150	1714919930	839542402	1121993893	1220614755	138007820	SRX1583785	SRS1295612	SRA353254	SRA	Bar-Ilan University	2	0.0	0.17551	0.0	0.00318	1.0	0.99833		0.10802	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2016-03-02	Undetermined	Undetermined	Whole Organism	All anatomical structures
40409	40409	SRR3166931	SRX1583784	SRS1295613	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 14d Calm6		breed:AB\|chain:beta\|index:37\|sex:male\|time point:14d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 14d Calm6	55 14d Calm6 beta	55 14d Calm6 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_55_14d_Calm6_beta.fq.gz read2_55_14d_Calm6_beta.fq.gz	fastq fastq	1028012700.0	3426709.0	55 14d Calm6 beta files	0:150 1:150	A:295958360;C:207583542;G:216651025;T:284035600;N:23784173	150	150	295958360	207583542	216651025	284035600	23784173	SRX1583784	SRS1295613	SRA353254	SRA	Bar-Ilan University	2	5e-05	0.16498	0.0	0.01748	0.99989	0.99253	0.33333	0.12385	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2016-03-02	Undetermined	Undetermined	Whole Organism	All anatomical structures
40410	40410	SRR3166930	SRX1583783	SRS1295614	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library Naive6		breed:AB\|chain:beta\|index:31\|sex:male\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library Naive6	126 Naive6 beta	126 Naive6 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read2_126_Naive6_beta.fq.gz read1_126_Naive6_beta.fq.gz	fastq fastq	1984909800.0	6616366.0	126 Naive6 beta files	0:150 1:150	A:574002364;C:411972224;G:452963561;T:493883048;N:52088603	150	150	574002364	411972224	452963561	493883048	52088603	SRX1583783	SRS1295614	SRA353254	SRA	Bar-Ilan University	2	0.0007	0.73767	5e-05	0.01562	0.99928	0.9754	0.16	0.44061	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40411	40411	SRR3166929	SRX1583782	SRS1295615	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 14d IFA1		breed:AB\|chain:beta\|index:38\|sex:male\|time point:14d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 14d IFA1	36 14d IFA1 beta	36 14d IFA1 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read2_36_14d_IFA1_beta.fq.gz read1_36_14d_IFA1_beta.fq.gz	fastq fastq	2641709400.0	8805698.0	36 14d IFA1 beta files	0:150 1:150	A:828430279;C:516389015;G:603137557;T:652458512;N:41294037	150	150	828430279	516389015	603137557	652458512	41294037	SRX1583782	SRS1295615	SRA353254	SRA	Bar-Ilan University	2	6e-05	0.17777	1e-05	0.00441	0.99991	0.99243	0.5	0.07212	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40412	40412	SRR3166928	SRX1583781	SRS1295616	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 14d PHA7		breed:AB\|chain:beta\|index:41\|sex:male\|time point:14d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 14d PHA7	35 14d PHA7 beta	35 14d PHA7 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read2_35_14d_PHA7_beta.fq.gz read1_35_14d_PHA7_beta.fq.gz	fastq fastq	2481744900.0	8272483.0	35 14d PHA7 beta files	0:150 1:150	A:684148801;C:534638425;G:555073374;T:671216692;N:36667608	150	150	684148801	534638425	555073374	671216692	36667608	SRX1583781	SRS1295616	SRA353254	SRA	Bar-Ilan University	2	0.00054	0.3447	8e-05	0.03511	0.9991	0.97049	0.29411	0.37357	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2017-02-12	Undetermined	Undetermined	Whole Organism	All anatomical structures
40413	40413	SRR3166927	SRX1583780	SRS1295617	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 14d PHA6		breed:AB\|chain:beta\|index:40\|sex:male\|time point:14d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 14d PHA6	34 14d PHA6 beta	34 14d PHA6 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_34_14d_PHA6_beta.fq.gz read2_34_14d_PHA6_beta.fq.gz	fastq fastq	2149899000.0	7166330.0	34 14d PHA6 beta files	0:150 1:150	A:603640552;C:452244383;G:474826068;T:587177894;N:32010103	150	150	603640552	452244383	474826068	587177894	32010103	SRX1583780	SRS1295617	SRA353254	SRA	Bar-Ilan University	2	4e-05	0.16994	0.0	0.14727	0.99991	0.99342	0.0	0.31047	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2016-03-02	Undetermined	Undetermined	Whole Organism	All anatomical structures
40414	40414	SRR3166926	SRX1583779	SRS1295618	SRP070056	PRJNA309588	Analysis of the T cell response in Zebrafish	PRJNA309588	Other	Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.				TCRB library 14d PHA5		breed:AB\|chain:beta\|index:39\|sex:male\|time point:14d\|tissue:whole fish\|age:1y\|BioSampleModel:Model organism or animal	TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 14d PHA5	33 14d PHA5 beta	33 14d PHA5 beta	five prime RACE amplification of TCRb transcript			AMPLICON	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070056			read1_33_14d_PHA5_beta.fq.gz read2_33_14d_PHA5_beta.fq.gz	fastq fastq	4781329500.0	15937765.0	33 14d PHA5 beta files	0:150 1:150	A:1564269921;C:790001191;G:1015752339;T:1331170138;N:80135911	150	150	1564269921	790001191	1015752339	1331170138	80135911	SRX1583779	SRS1295618	SRA353254	SRA	Bar-Ilan University	2	0.00034	0.20127	0.00018	0.00887	0.99989	0.99567	0.05263	0.08667	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Israel	2016-03-02	Undetermined	Undetermined	Whole Organism	All anatomical structures
58873	58873	SRR11509894	SRX8082006	SRS6450124	SRP255712	PRJNA623798	Single cell lineage tracing on endogenous scarring sites scLOESS	PRJNA623798	Other	Lineage recording of zebrafish embryogenesis reveals early cell fate commitment		1g cDNA library fetch from 10x Genomics Chromium Single Cell 3 Library was amplified by extra 15 cycles. and then split into 90 equal aliquots to amplify each target by 25 cycles and purified amplicons were pooled into an equimolar mixture. 3 independent replicates in total.	Target specific Amplification of Single Cell cDNA Library	SCC		strain:AB line\|age:7dpf\|dev stage:larvae\|sex:not applicable\|tissue:Whole organism\|collection date:2018 07 26\|BioSampleModel:Model organism or animal	Single cell cDNA library Amplicon of zebrafish larva replicate 3	SCC replicate3	SCC replicate3	1g cDNA library fetch from 10x Genomics Chromium Single Cell 3 Library was amplified by extra 15 cycles. and then split into 90 equal aliquots to amplify each target by 25 cycles and purified amplicons were pooled into an equimolar mixture. PCR replicate 3.			AMPLICON	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	HiSeq X Ten		SRP255712			SCC-replicate3_R1.fq.gz SCC-replicate3_R2.fq.gz	fastq fastq	14811756300.0	49372521.0	SCC replicate3 R1.fq.gz	0:150 1:150	A:3255250699;C:3018244265;G:3088919277;T:5446140655;N:3201404	150	150	3255250699	3018244265	3088919277	5446140655	3201404	SRX8082006	SRS6450124	SRA1063780	Sun Yat- sen University\|Life Sicence School	Sun Yat- sen University	2	0.01015	0.97122	0.00049	0.00158	0.99841	0.97569	0.54867	0.48858	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	China	2020-04-10	Larval	Larval	Whole Organism	All anatomical structures
58874	58874	SRR11509895	SRX8082005	SRS6450124	SRP255712	PRJNA623798	Single cell lineage tracing on endogenous scarring sites scLOESS	PRJNA623798	Other	Lineage recording of zebrafish embryogenesis reveals early cell fate commitment		1g cDNA library fetch from 10x Genomics Chromium Single Cell 3 Library was amplified by extra 15 cycles. and then split into 90 equal aliquots to amplify each target by 25 cycles and purified amplicons were pooled into an equimolar mixture. 3 independent replicates in total.	Target specific Amplification of Single Cell cDNA Library	SCC		strain:AB line\|age:7dpf\|dev stage:larvae\|sex:not applicable\|tissue:Whole organism\|collection date:2018 07 26\|BioSampleModel:Model organism or animal	Single cell cDNA library Amplicon of zebrafish larva replicate 2	SCC replicate2	SCC replicate2	1g cDNA library fetch from 10x Genomics Chromium Single Cell 3 Library was amplified by extra 15 cycles. and then split into 90 equal aliquots to amplify each target by 25 cycles and purified amplicons were pooled into an equimolar mixture. PCR replicate 2.			AMPLICON	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	HiSeq X Ten		SRP255712			SCC-replicate2_R2.fq.gz SCC-replicate2_R1.fq.gz	fastq fastq	19858547700.0	66195159.0	SCC replicate2 R1.fq.gz	0:150 1:150	A:4363166112;C:4066433314;G:4155737160;T:7269480395;N:3730719	150	150	4363166112	4066433314	4155737160	7269480395	3730719	SRX8082005	SRS6450124	SRA1063780	Sun Yat- sen University\|Life Sicence School	Sun Yat- sen University	2	0.025	0.97152	0.00079	0.00143	0.99746	0.97668	0.74358	0.46727	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	China	2020-04-09	Larval	Larval	Whole Organism	All anatomical structures
58875	58875	SRR11509896	SRX8082004	SRS6450124	SRP255712	PRJNA623798	Single cell lineage tracing on endogenous scarring sites scLOESS	PRJNA623798	Other	Lineage recording of zebrafish embryogenesis reveals early cell fate commitment		1g cDNA library fetch from 10x Genomics Chromium Single Cell 3 Library was amplified by extra 15 cycles. and then split into 90 equal aliquots to amplify each target by 25 cycles and purified amplicons were pooled into an equimolar mixture. 3 independent replicates in total.	Target specific Amplification of Single Cell cDNA Library	SCC		strain:AB line\|age:7dpf\|dev stage:larvae\|sex:not applicable\|tissue:Whole organism\|collection date:2018 07 26\|BioSampleModel:Model organism or animal	Single cell cDNA library Amplicon of zebrafish larva replicate 1	SCC replicate1	SCC replicate1	1g cDNA library fetch from 10x Genomics Chromium Single Cell 3 Library was amplified by extra 15 cycles. and then split into 90 equal aliquots to amplify each target by 25 cycles and purified amplicons were pooled into an equimolar mixture. PCR replicate 1.			AMPLICON	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	HiSeq X Ten		SRP255712			SCC-replicate1_R1.fq.gz SCC-replicate1_R2.fq.gz	fastq fastq	18191440200.0	60638134.0	SCC replicate1 R1.fq.gz	0:150 1:150	A:3994446536;C:3726446852;G:3814798796;T:6652431833;N:3316183	150	150	3994446536	3726446852	3814798796	6652431833	3316183	SRX8082004	SRS6450124	SRA1063780	Sun Yat- sen University\|Life Sicence School	Sun Yat- sen University	2	0.03094	0.97334	0.00045	0.00127	0.99774	0.97824	0.80981	0.45378	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	China	2020-04-09	Larval	Larval	Whole Organism	All anatomical structures

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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");;