metadata: run_metadata: 28 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "size fractionation" and tissue_curation

28 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "size fractionation" and tissue_curation_coarse = "All anatomical structures"

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	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.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
28490	28490	SRR26319601	SRX22027740	SRS19100857	SRP465070	PRJNA1025141	Danio rerio Raw sequence reads	PRJNA1025141	Other	Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.		Treatment	CX3 for transcriptome 3	CX3		strain:AB\|cultivar:WT\|ecotype:China: Jiangsu\|age:7 dpf\|dev stage:Larvae\|collection date:2022 11\|geo loc name:China: Jiangsu suzhou\|sex:pooled male and female\|tissue:larvae\|lat lon:31.32 N 120.67 E\|treatment:Treatment Group\|BioSampleModel:Model organism or animal								ALST3 for transcriptome 3	CX3 for transcriptome 3	CX3 for transcriptome 3	CX3 for transcriptome 3			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Ten		SRP465070			Unknown_AY803-03T0006_good_1.fq.gz Unknown_AY803-03T0006_good_2.fq.gz	fastq fastq	6255596356.0	20929531.0	Unknown AY803 03T0006 good 1.fq.gz	0:149.44 1:149.44	A:1657365560;C:1463722268;G:1467057724;T:1667269298;N:181506	149	149	1657365560	1463722268	1467057724	1667269298	181506	SRX22027740	SRS19100857	SRA1727563	Soochow University\|School of biology & basic medical sciences	Soochow University	2	0.89228	0.91654	0.09286	0.09714	0.6588	0.65604	0.4631	0.45773	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-10-11	Larval	Larval	Whole Organism	All anatomical structures
28491	28491	SRR26319602	SRX22027739	SRS19100854	SRP465070	PRJNA1025141	Danio rerio Raw sequence reads	PRJNA1025141	Other	Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.		Treatment	CX2 for transcriptome 2	CX2		strain:AB\|cultivar:WT\|ecotype:China: Jiangsu\|age:7 dpf\|dev stage:Larvae\|collection date:2022 11\|geo loc name:China: Jiangsu suzhou\|sex:pooled male and female\|tissue:larvae\|lat lon:31.32 N 120.66 E\|treatment:Treatment Group\|BioSampleModel:Model organism or animal								ALST2 for transcriptome 2	CX2 for transcriptome 2	CX2 for transcriptome 2	CX2 for transcriptome 2			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Ten		SRP465070			Unknown_AY803-03T0005_good_1.fq.gz Unknown_AY803-03T0005_good_2.fq.gz	fastq fastq	6598066464.0	22061446.0	Unknown AY803 03T0005 good 1.fq.gz	0:149.54 1:149.54	A:1747291499;C:1543289262;G:1549193118;T:1758088368;N:204217	149	149	1747291499	1543289262	1549193118	1758088368	204217	SRX22027739	SRS19100854	SRA1727563	Soochow University\|School of biology & basic medical sciences	Soochow University	2	0.88949	0.92148	0.08893	0.0947	0.65596	0.65228	0.46045	0.47087	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-10-11	Larval	Larval	Whole Organism	All anatomical structures
28492	28492	SRR26319603	SRX22027738	SRS19100853	SRP465070	PRJNA1025141	Danio rerio Raw sequence reads	PRJNA1025141	Other	Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.		Treatment	CX1 for transcriptome 1	CX1		strain:AB\|cultivar:WT\|ecotype:China: Jiangsu\|age:7 dpf\|dev stage:Larvae\|collection date:2022 11\|geo loc name:China: Jiangsu suzhou\|sex:pooled male and female\|tissue:larvae\|lat lon:31.32 N 120.65 E\|treatment:Treatment Group\|BioSampleModel:Model organism or animal								ALST1 for transcriptome 1	CX1 for transcriptome 1	CX1 for transcriptome 1	CX1 for transcriptome 1			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Ten		SRP465070			Unknown_AY803-03T0004_good_1.fq.gz Unknown_AY803-03T0004_good_2.fq.gz	fastq fastq	6478923586.0	21662443.0	Unknown AY803 03T0004 good 1.fq.gz	0:149.54 1:149.54	A:1712718473;C:1518937459;G:1523570227;T:1723510437;N:186990	149	149	1712718473	1518937459	1523570227	1723510437	186990	SRX22027738	SRS19100853	SRA1727563	Soochow University\|School of biology & basic medical sciences	Soochow University	2	0.89423	0.9176	0.08944	0.09254	0.6575	0.65458	0.4693	0.46842	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-10-11	Larval	Larval	Whole Organism	All anatomical structures
28493	28493	SRR26319604	SRX22027737	SRS19100856	SRP465070	PRJNA1025141	Danio rerio Raw sequence reads	PRJNA1025141	Other	Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.		Control	con3 for transcriptome 3	con3		strain:AB\|cultivar:Wild type\|ecotype:China: Jiangsu suzhou\|age:7 dpf\|dev stage:Larvae phase\|collection date:2022 11\|geo loc name:China: Jiangsu suzhou\|sex:pooled male and female\|tissue:larvae\|lat lon:31.32 N 120.64 E\|treatment:Control Group\|BioSampleModel:Model organism or animal								con3 for transcriptome 3	con3 for transcriptome 3	con3 for transcriptome 3	con3 for transcriptome 3			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Ten		SRP465070			Unknown_AY803-03T0003_good_2.fq.gz Unknown_AY803-03T0003_good_1.fq.gz	fastq fastq	6341537566.0	21218597.0	Unknown AY803 03T0003 good 1.fq.gz	0:149.43 1:149.43	A:1679811754;C:1483631833;G:1489430825;T:1688482904;N:180250	149	149	1679811754	1483631833	1489430825	1688482904	180250	SRX22027737	SRS19100856	SRA1727563	Soochow University\|School of biology & basic medical sciences	Soochow University	2	0.88245	0.91856	0.09069	0.09654	0.66253	0.65817	0.46245	0.46336	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-10-11	Larval	Larval	Whole Organism	All anatomical structures
28494	28494	SRR26319605	SRX22027736	SRS19100855	SRP465070	PRJNA1025141	Danio rerio Raw sequence reads	PRJNA1025141	Other	Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.		Control	con2 for transcriptome 2	con2		strain:AB\|cultivar:Wild type\|ecotype:China: Jiangsu suzhou\|age:7 dpf\|dev stage:Larvae phase\|collection date:2022 11\|geo loc name:China: Jiangsu suzhou\|sex:pooled male and female\|tissue:larvae\|lat lon:31.32 N 120.63 E\|treatment:Control Group\|BioSampleModel:Model organism or animal								con2 for transcriptome 2	con2 for transcriptome 2	con2 for transcriptome 2	con2 for transcriptome 2			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Ten		SRP465070			Unknown_AY803-03T0002_good_2.fq.gz Unknown_AY803-03T0002_good_1.fq.gz	fastq fastq	5709771178.0	19100144.0	Unknown AY803 03T0002 good 1.fq.gz	0:149.47 1:149.47	A:1505730979;C:1342843084;G:1346105868;T:1514941964;N:149283	149	149	1505730979	1342843084	1346105868	1514941964	149283	SRX22027736	SRS19100855	SRA1727563	Soochow University\|School of biology & basic medical sciences	Soochow University	2	0.8924	0.91903	0.09155	0.09604	0.65902	0.65593	0.4634	0.46028	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-10-11	Larval	Larval	Whole Organism	All anatomical structures
28495	28495	SRR26319606	SRX22027735	SRS19100852	SRP465070	PRJNA1025141	Danio rerio Raw sequence reads	PRJNA1025141	Other	Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.		Control	con1 for transcriptome 1	con1		strain:AB\|cultivar:Wild type\|ecotype:China: Jiangsu suzhou\|age:7 dpf\|dev stage:Larvae phase\|collection date:2022 11\|geo loc name:China: Jiangsu suzhou\|sex:pooled male and female\|tissue:larvae\|lat lon:31.32 N 120.62 E\|treatment:Control Group\|BioSampleModel:Model organism or animal								con1 for transcriptome 1	con1 for transcriptome 1	con1 for transcriptome 1	con1 for transcriptome 1			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Ten		SRP465070			Unknown_AY803-03T0001_good_1.fq.gz Unknown_AY803-03T0001_good_2.fq.gz	fastq fastq	6544586118.0	21872265.0	Unknown AY803 03T0001 good 1.fq.gz	0:149.61 1:149.61	A:1731179229;C:1528367346;G:1541103688;T:1743735521;N:200334	149	149	1731179229	1528367346	1541103688	1743735521	200334	SRX22027735	SRS19100852	SRA1727563	Soochow University\|School of biology & basic medical sciences	Soochow University	2	0.87588	0.92739	0.08683	0.09494	0.65711	0.6504	0.46774	0.47072	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-10-11	Larval	Larval	Whole Organism	All anatomical structures
40707	40707	SRR3502888	SRX1760541	SRS1436386	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.			Zebrafish tRNA at 6hpf	tRNA AB 6h		strain:TUAB\|age:6hpf\|dev stage:Shield\|sex:pooled male and female\|tissue:Whole animal\|collected by:Ariel Bazzini\|genotype:WT\|BioSampleModel:Model organism or animal								Zebrafish tRNAs at 6hpf	tRNA 6hpf zebrafish	TGIRT tRNA Library	1			OTHER	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296			AB-tRNA_S9_R1_001.fastq.gz AB-tRNA_S9_R2_001.fastq.gz	fastq fastq	7860522000.0	26201740.0	tRNA zebrafish 6hpf	0:150 1:150	A:1945184302;C:2012637521;G:2171934357;T:1730625218;N:140602	150	150	1945184302	2012637521	2171934357	1730625218	140602	SRX1760541	SRS1436386	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.04186	0.04313	0.00633	0.00639	0.96834	0.96913	0.53967	0.5329	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2016-06-17	Gastrula	Embryo	Whole Organism	All anatomical structures
49332	49332	SRR7888761	SRX4726390	SRS3810123	SRP162319	PRJNA492406	Profiles analysis reveals circRNAs involving zebrafish physiological development	GSE120289	Transcriptome Analysis	Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.			72h	GSM3397729		source name:Embryo\|tissue:Embryo\|age:72 hpf\|developmental stage:incubation\|strain:Tubingenz\|genotype:WT	72h	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.	Embryo	Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development.	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina	tissue:Embryo\|age:72 hpf\|developmental stage:incubation\|strain:Tubingenz\|genotype:WT	GSM3397729	GSM3397729: 72h; Danio rerio; ncRNA Seq	GSM3397729		1	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina	GEO Accession:GSM3397729	ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP162319			72h_1.fq.gz 72h_2.fq.gz	fastq fastq	12097159200.0	40323864.0	GSM3397729 r1	0:150 1:150	A:2809307023;C:3169515166;G:3184429517;T:2931448896;N:2458598	150	150	2809307023	3169515166	3184429517	2931448896	2458598	SRX4726390	SRS3810123	SRA781248	GEO	Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital	2	0.90426	0.90717	0.27165	0.26439	0.70739	0.72397	0.60155	0.60561	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2018-09-21	Larval	Larval	Embryo Imprecise	All anatomical structures
49333	49333	SRR7888760	SRX4726389	SRS3810122	SRP162319	PRJNA492406	Profiles analysis reveals circRNAs involving zebrafish physiological development	GSE120289	Transcriptome Analysis	Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.			48h	GSM3397728		source name:Embryo\|tissue:Embryo\|age:48 hpf\|developmental stage:throat\|strain:Tubingenz\|genotype:WT	48h	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.	Embryo	Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development.	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina	tissue:Embryo\|age:48 hpf\|developmental stage:throat\|strain:Tubingenz\|genotype:WT	GSM3397728	GSM3397728: 48h; Danio rerio; ncRNA Seq	GSM3397728		1	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina	GEO Accession:GSM3397728	ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP162319			48h_2.fq.gz 48h_1.fq.gz	fastq fastq	13525174500.0	45083915.0	GSM3397728 r1	0:150 1:150	A:2352542664;C:4312268007;G:4256218842;T:2601416951;N:2728036	150	150	2352542664	4312268007	4256218842	2601416951	2728036	SRX4726389	SRS3810122	SRA781248	GEO	Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital	2	0.91614	0.91412	0.12891	0.12218	0.76751	0.77948	0.71008	0.73648	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2018-09-21	Hatching	Embryo	Embryo Imprecise	All anatomical structures
49334	49334	SRR7888759	SRX4726388	SRS3810120	SRP162319	PRJNA492406	Profiles analysis reveals circRNAs involving zebrafish physiological development	GSE120289	Transcriptome Analysis	Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.			24h	GSM3397727		source name:Embryo\|tissue:Embryo\|age:24 hpf\|developmental stage:segmentation\|strain:Tubingenz\|genotype:WT	24h	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.	Embryo	Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development.	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina	tissue:Embryo\|age:24 hpf\|developmental stage:segmentation\|strain:Tubingenz\|genotype:WT	GSM3397727	GSM3397727: 24h; Danio rerio; ncRNA Seq	GSM3397727		1	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina	GEO Accession:GSM3397727	ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP162319			24h_1.fq.gz 24h_2.fq.gz	fastq fastq	14333175000.0	47777250.0	GSM3397727 r1	0:150 1:150	A:2728754113;C:4276840070;G:4344116037;T:2980570245;N:2894535	150	150	2728754113	4276840070	4344116037	2980570245	2894535	SRX4726388	SRS3810120	SRA781248	GEO	Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital	2	0.89719	0.89478	0.18044	0.18119	0.76942	0.7876	0.75758	0.75366	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2018-09-21	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
49335	49335	SRR7888758	SRX4726387	SRS3810121	SRP162319	PRJNA492406	Profiles analysis reveals circRNAs involving zebrafish physiological development	GSE120289	Transcriptome Analysis	Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.			8h	GSM3397726		source name:Embryo\|tissue:Embryo\|age:8 hpf\|developmental stage:gastrula\|strain:Tubingenz\|genotype:WT	8h	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.	Embryo	Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development.	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina	tissue:Embryo\|age:8 hpf\|developmental stage:gastrula\|strain:Tubingenz\|genotype:WT	GSM3397726	GSM3397726: 8h; Danio rerio; ncRNA Seq	GSM3397726		1	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina	GEO Accession:GSM3397726	ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP162319			8h_2.fq.gz 8h_1.fq.gz	fastq fastq	15434085600.0	51446952.0	GSM3397726 r1	0:150 1:150	A:2318158791;C:5134519748;G:5292209580;T:2686084369;N:3113112	150	150	2318158791	5134519748	5292209580	2686084369	3113112	SRX4726387	SRS3810121	SRA781248	GEO	Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital	2	0.95788	0.95584	0.07233	0.07686	0.81889	0.82946	0.81383	0.80143	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2018-09-21	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
49336	49336	SRR7888757	SRX4726386	SRS3810119	SRP162319	PRJNA492406	Profiles analysis reveals circRNAs involving zebrafish physiological development	GSE120289	Transcriptome Analysis	Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.			4.5h	GSM3397725		source name:Embryo\|tissue:Embryo\|age:4.5 hpf\|developmental stage:blastula\|strain:Tubingenz\|genotype:WT	4.5h	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.	Embryo	Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development.	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina	tissue:Embryo\|age:4.5 hpf\|developmental stage:blastula\|strain:Tubingenz\|genotype:WT	GSM3397725	GSM3397725: 4.5h; Danio rerio; ncRNA Seq	GSM3397725		1	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina	GEO Accession:GSM3397725	ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP162319			4_5h_2.fq.gz 4_5h_1.fq.gz	fastq fastq	12988242600.0	43294142.0	GSM3397725 r1	0:150 1:150	A:2232301074;C:3998769528;G:4233380689;T:2521224783;N:2566526	150	150	2232301074	3998769528	4233380689	2521224783	2566526	SRX4726386	SRS3810119	SRA781248	GEO	Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital	2	0.96961	0.96817	0.05627	0.05463	0.77068	0.78198	0.74899	0.75759	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2018-09-21	Blastula	Embryo	Embryo Imprecise	All anatomical structures
75414	75414	SRR24517729	SRX20302027	SRS17627883	SRP437283	PRJNA971676	zebrafish kiss genes knockouts deep sequencing	PRJNA971676	Other	Mammals possess only one Kisspeptin gene but in teleost like zebrafish there are two copies. While knockout of Kiss1 results in infertility in mammals knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.			RNA seq of zebrafish:5dpf larvae kiss1kiss2DKO Replicate2	zebrafish AO149 01T0008		strain:AB\|age:5dpf\|dev stage:larvae\|sex:not determined\|tissue:whole organism\|collection date:2020\|genotype:kiss1 and kiss2 double knockout\|geo loc name:China: Suzhou\|sample type:whole organism\|Replicate:2\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish: larvae	RNA Seq for zebrafish kiss1kiss2DKO larvae 2	RNA Seq for zebrafish kiss1kiss2DKO larvae 2	RNA Seq zebrafish kiss1kiss2DKO larvae 2			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP437283			Unknown_AO149-01T0008_good_1.fq.gz Unknown_AO149-01T0008_good_2.fq.gz	fastq fastq	6912158300.0	23173882.0	Unknown AO149 01T0008 good 1.fq.gz	0:149.14 1:149.14	A:1796529490;C:1649628994;G:1669079817;T:1796880198;N:39801	149	149	1796529490	1649628994	1669079817	1796880198	39801	SRX20302027	SRS17627883	SRA1636880	Soochow University\|Medical College	Soochow University	2	0.95632	0.95592	0.06085	0.06019	0.66515	0.66563	0.47686	0.47575	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-05-11	Larval	Larval	Whole Organism	All anatomical structures
75415	75415	SRR24517730	SRX20302026	SRS17627882	SRP437283	PRJNA971676	zebrafish kiss genes knockouts deep sequencing	PRJNA971676	Other	Mammals possess only one Kisspeptin gene but in teleost like zebrafish there are two copies. While knockout of Kiss1 results in infertility in mammals knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.			RNA seq of zebrafish:5dpf larvae kiss1kiss2DKO Replicate1	zebrafish AO149 01T0007		strain:AB\|age:5dpf\|dev stage:larvae\|sex:not determined\|tissue:whole organism\|collection date:2020\|genotype:kiss1 and kiss2 double knockout\|geo loc name:China: Suzhou\|sample type:whole organism\|Replicate:1\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish: larvae	RNA Seq for zebrafish kiss1kiss2DKO larvae 1	RNA Seq for zebrafish kiss1kiss2DKO larvae 1	RNA Seq zebrafish kiss1kiss2DKO larvae 1			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP437283			Unknown_AO149-01T0007_good_1.fq.gz Unknown_AO149-01T0007_good_2.fq.gz	fastq fastq	8005311792.0	26909041.0	Unknown AO149 01T0007 good 1.fq.gz	0:148.75 1:148.75	A:2077441584;C:1913582326;G:1934120275;T:2080121870;N:45737	148	148	2077441584	1913582326	1934120275	2080121870	45737	SRX20302026	SRS17627882	SRA1636880	Soochow University\|Medical College	Soochow University	2	0.9522	0.95194	0.06345	0.06296	0.65691	0.65744	0.48074	0.48185	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-05-11	Larval	Larval	Whole Organism	All anatomical structures
75416	75416	SRR24517731	SRX20302025	SRS17627881	SRP437283	PRJNA971676	zebrafish kiss genes knockouts deep sequencing	PRJNA971676	Other	Mammals possess only one Kisspeptin gene but in teleost like zebrafish there are two copies. While knockout of Kiss1 results in infertility in mammals knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.			RNA seq of zebrafish:5dpf larvae kiss2KO Replicate2	zebrafish AO149 01T0006		strain:AB\|age:5dpf\|dev stage:larvae\|sex:not determined\|tissue:whole organism\|collection date:2020\|genotype:kiss2 knockout\|geo loc name:China: Suzhou\|sample type:whole organism\|Replicate:2\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish: larvae	RNA Seq for zebrafish kiss2KO larvae 2	RNA Seq for zebrafish kiss2KO larvae 2	RNA Seq zebrafish kiss2KO larvae 2			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP437283			Unknown_AO149-01T0006_good_1.fq.gz Unknown_AO149-01T0006_good_2.fq.gz	fastq fastq	7638089446.0	25894588.0	Unknown AO149 01T0006 good 1.fq.gz	0:147.48 1:147.48	A:2051138070;C:1759130157;G:1773591862;T:2054190526;N:38831	147	147	2051138070	1759130157	1773591862	2054190526	38831	SRX20302025	SRS17627881	SRA1636880	Soochow University\|Medical College	Soochow University	2	0.94967	0.94887	0.08556	0.08576	0.64898	0.64954	0.47984	0.48067	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-05-11	Larval	Larval	Whole Organism	All anatomical structures
75417	75417	SRR24517732	SRX20302024	SRS17627879	SRP437283	PRJNA971676	zebrafish kiss genes knockouts deep sequencing	PRJNA971676	Other	Mammals possess only one Kisspeptin gene but in teleost like zebrafish there are two copies. While knockout of Kiss1 results in infertility in mammals knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.			RNA seq of zebrafish:5dpf larvae kiss2KO Replicate1	zebrafish AO149 01T0005		strain:AB\|age:5dpf\|dev stage:larvae\|sex:not determined\|tissue:whole organism\|collection date:2020\|genotype:kiss2 knockout\|geo loc name:China: Suzhou\|sample type:whole organism\|Replicate:1\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish: larvae	RNA Seq for zebrafish kiss2KO larvae 1	RNA Seq for zebrafish kiss2KO larvae 1	RNA Seq zebrafish kiss2KO larvae 1			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP437283			Unknown_AO149-01T0005_good_1.fq.gz Unknown_AO149-01T0005_good_2.fq.gz	fastq fastq	7054134954.0	23687508.0	Unknown AO149 01T0005 good 1.fq.gz	0:148.90 1:148.90	A:1848389593;C:1667928954;G:1687707295;T:1850068763;N:40349	148	148	1848389593	1667928954	1687707295	1850068763	40349	SRX20302024	SRS17627879	SRA1636880	Soochow University\|Medical College	Soochow University	2	0.94976	0.95007	0.07472	0.07458	0.65299	0.65324	0.48045	0.47909	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-05-11	Larval	Larval	Whole Organism	All anatomical structures
75418	75418	SRR24517733	SRX20302023	SRS17627880	SRP437283	PRJNA971676	zebrafish kiss genes knockouts deep sequencing	PRJNA971676	Other	Mammals possess only one Kisspeptin gene but in teleost like zebrafish there are two copies. While knockout of Kiss1 results in infertility in mammals knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.			RNA seq of zebrafish:5dpf larvae kiss1KO Replicate2	zebrafish AO149 01T0004		strain:AB\|age:5dpf\|dev stage:larvae\|sex:not determined\|tissue:whole organism\|collection date:2020\|genotype:kiss1 knockout\|geo loc name:China: Suzhou\|sample type:whole organism\|Replicate:2\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish: larvae	RNA Seq for zebrafish kiss1KO larvae 2	RNA Seq for zebrafish kiss1KO larvae 2	RNA Seq zebrafish kiss1KO larvae 2			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP437283			Unknown_AO149-01T0004_good_1.fq.gz Unknown_AO149-01T0004_good_2.fq.gz	fastq fastq	5814495346.0	19499621.0	Unknown AO149 01T0004 good 1.fq.gz	0:149.09 1:149.09	A:1528388873;C:1369910846;G:1386794007;T:1529368087;N:33533	149	149	1528388873	1369910846	1386794007	1529368087	33533	SRX20302023	SRS17627880	SRA1636880	Soochow University\|Medical College	Soochow University	2	0.94765	0.94711	0.07972	0.07979	0.65283	0.65397	0.48362	0.48203	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-05-11	Larval	Larval	Whole Organism	All anatomical structures
75419	75419	SRR24517734	SRX20302022	SRS17627877	SRP437283	PRJNA971676	zebrafish kiss genes knockouts deep sequencing	PRJNA971676	Other	Mammals possess only one Kisspeptin gene but in teleost like zebrafish there are two copies. While knockout of Kiss1 results in infertility in mammals knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.			RNA seq of zebrafish:5dpf larvae kiss1KO Replicate1	zebrafish AO149 01T0003		strain:AB\|age:5dpf\|dev stage:larvae\|sex:not determined\|tissue:whole organism\|collection date:2020\|genotype:kiss1 knockout\|geo loc name:China: Suzhou\|sample type:whole organism\|Replicate:1\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish: larvae	RNA Seq for zebrafish kiss1KO larvae 1	RNA Seq for zebrafish kiss1KO larvae 1	RNA Seq zebrafish kiss1KO larvae 1			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP437283			Unknown_AO149-01T0003_good_1.fq.gz Unknown_AO149-01T0003_good_2.fq.gz	fastq fastq	6174484352.0	20748774.0	Unknown AO149 01T0003 good 1.fq.gz	0:148.79 1:148.79	A:1629263285;C:1446858897;G:1467609266;T:1630717493;N:35411	148	148	1629263285	1446858897	1467609266	1630717493	35411	SRX20302022	SRS17627877	SRA1636880	Soochow University\|Medical College	Soochow University	2	0.94831	0.94853	0.07898	0.07866	0.65295	0.65419	0.47605	0.47682	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-05-11	Larval	Larval	Whole Organism	All anatomical structures
75420	75420	SRR24517735	SRX20302021	SRS17627878	SRP437283	PRJNA971676	zebrafish kiss genes knockouts deep sequencing	PRJNA971676	Other	Mammals possess only one Kisspeptin gene but in teleost like zebrafish there are two copies. While knockout of Kiss1 results in infertility in mammals knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.			RNA seq of zebrafish:5dpf larvae wt Replicate2	zebrafish AO149 01T0002		strain:AB\|age:5dpf\|dev stage:larvae\|sex:not determined\|tissue:whole organism\|collection date:2020\|genotype:WT\|geo loc name:China: Suzhou\|sample type:whole organism\|Replicate:2\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish: larvae	RNA Seq for zebrafish WT larvae 2	RNA Seq for zebrafish WT larvae 2	RNA Seq zebrafish WT larvae 2			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP437283			Unknown_AO149-01T0002_good_1.fq.gz Unknown_AO149-01T0002_good_2.fq.gz	fastq fastq	6059983436.0	20361363.0	Unknown AO149 01T0002 good 1.fq.gz	0:148.81 1:148.81	A:1608075382;C:1408291949;G:1433236990;T:1610344312;N:34803	148	148	1608075382	1408291949	1433236990	1610344312	34803	SRX20302021	SRS17627878	SRA1636880	Soochow University\|Medical College	Soochow University	2	0.9529	0.95334	0.07296	0.07315	0.65435	0.65247	0.49743	0.47334	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-05-11	Larval	Larval	Whole Organism	All anatomical structures
75421	75421	SRR24517736	SRX20302020	SRS17627876	SRP437283	PRJNA971676	zebrafish kiss genes knockouts deep sequencing	PRJNA971676	Other	Mammals possess only one Kisspeptin gene but in teleost like zebrafish there are two copies. While knockout of Kiss1 results in infertility in mammals knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.			RNA seq of zebrafish:5dpf larvae wt Replicate1	zebrafish AO149 01T0001		strain:AB\|age:5dpf\|dev stage:larvae\|sex:not determined\|tissue:whole organism\|collection date:2020\|genotype:WT\|geo loc name:China: Suzhou\|sample type:whole organism\|Replicate:1\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish: larvae	RNA Seq for zebrafish WT larvae 1	RNA Seq for zebrafish WT larvae 1	RNA Seq zebrafish WT larvae 1			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP437283			Unknown_AO149-01T0001_good_1.fq.gz Unknown_AO149-01T0001_good_2.fq.gz	fastq fastq	6809997812.0	22853255.0	Unknown AO149 01T0001 good 1.fq.gz	0:148.99 1:148.99	A:1813360438;C:1582845212;G:1601287701;T:1812465242;N:39219	148	148	1813360438	1582845212	1601287701	1812465242	39219	SRX20302020	SRS17627876	SRA1636880	Soochow University\|Medical College	Soochow University	2	0.94825	0.94824	0.087	0.08724	0.64695	0.64715	0.49206	0.493	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-05-11	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");;