metadata: run_metadata: 240 rows where experiment.library_selection = "size fractionation" and tissue

240 rows where experiment.library_selection = "size fractionation" and tissue_curation = "Whole Organism"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	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
25283	25283	SRR25764121	SRX21486801	SRS18719093	SRP457111	PRJNA1009808	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]	GSE241754	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326		WT bud 10 hpf tRNA seq rep2	GSM7734782		source name:Gastrula\|strain:TLAB strain\|tissue:Gastrula\|developmental stage:Bud 10 hpf\|genotype:WT\|geo loc name:missing\|collection date:missing	WT bud 10 hpf tRNA seq rep2	Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts	Gastrula	unperturbed growth conditions in E3 medium for zebrafish embryos.	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq	Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.	strain:TLAB strain\|tissue:Gastrula\|developmental stage:Bud 10 hpf\|genotype:WT	GSM7734782	GSM7734782: WT bud 10 hpf tRNA seq rep2; Danio rerio; ncRNA Seq	GSM7734782 r1	GSM7734782	1	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP457111			WT_tRNA_bud_2.fastq.gz	fastq	278145656.0	4215107.0	GSM7734782 r1	0:65.99	A:52499947;C:77161357;G:79314034;T:69169753;N:565	65		52499947	77161357	79314034	69169753	565	SRX21486801	SRS18719093	SRA1700461	Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry	Max Planck Institute of Biochemistry	1	0.31888		0.01661		0.92348		0.40156		75		B		usable mapping rate	illumina	nextseq	5prime	size_fractionation	unknown	bulk	unknown	unknown	Germany	2023-08-28	Gastrula	Embryo	Whole Organism	All anatomical structures
25284	25284	SRR25764122	SRX21486800	SRS18719092	SRP457111	PRJNA1009808	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]	GSE241754	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326		WT bud 10 hpf tRNA seq rep1	GSM7734781		source name:Gastrula\|strain:TLAB strain\|tissue:Gastrula\|developmental stage:Bud 10 hpf\|genotype:WT\|geo loc name:missing\|collection date:missing	WT bud 10 hpf tRNA seq rep1	Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts	Gastrula	unperturbed growth conditions in E3 medium for zebrafish embryos.	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq	Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.	strain:TLAB strain\|tissue:Gastrula\|developmental stage:Bud 10 hpf\|genotype:WT	GSM7734781	GSM7734781: WT bud 10 hpf tRNA seq rep1; Danio rerio; ncRNA Seq	GSM7734781 r1	GSM7734781	1	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP457111			WT_tRNA_bud_1.fastq.gz	fastq	385514625.0	5770392.0	GSM7734781 r1	0:66.81	A:73305393;C:107155246;G:109793285;T:95259823;N:878	66		73305393	107155246	109793285	95259823	878	SRX21486800	SRS18719092	SRA1700461	Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry	Max Planck Institute of Biochemistry	1	0.33213		0.01782		0.92354		0.42724		39		B		usable mapping rate	illumina	nextseq	5prime	size_fractionation	unknown	bulk	unknown	unknown	Germany	2023-08-28	Gastrula	Embryo	Whole Organism	All anatomical structures
25285	25285	SRR25764123	SRX21486799	SRS18719098	SRP457111	PRJNA1009808	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]	GSE241754	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326		WT shield 6 hpf tRNA seq rep2	GSM7734780		source name:Gastrula\|strain:TLAB strain\|tissue:Gastrula\|developmental stage:Shield 6 hpf\|genotype:WT\|geo loc name:missing\|collection date:missing	WT shield 6 hpf tRNA seq rep2	Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts	Gastrula	unperturbed growth conditions in E3 medium for zebrafish embryos.	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq	Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.	strain:TLAB strain\|tissue:Gastrula\|developmental stage:Shield 6 hpf\|genotype:WT	GSM7734780	GSM7734780: WT shield 6 hpf tRNA seq rep2; Danio rerio; ncRNA Seq	GSM7734780 r1	GSM7734780	1	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP457111			WT_tRNA_shield_2.fastq.gz	fastq	469031736.0	7421688.0	GSM7734780 r1	0:63.20	A:90257219;C:130440728;G:130549302;T:117783411;N:1076	63		90257219	130440728	130549302	117783411	1076	SRX21486799	SRS18719098	SRA1700461	Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry	Max Planck Institute of Biochemistry	1	0.29535		0.02113		0.91528		0.43824		37		B		usable mapping rate	illumina	nextseq	5prime	size_fractionation	unknown	bulk	unknown	unknown	Germany	2023-08-28	Gastrula	Embryo	Whole Organism	All anatomical structures
25286	25286	SRR25764124	SRX21486798	SRS18719100	SRP457111	PRJNA1009808	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]	GSE241754	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326		WT shield 6 hpf tRNA seq rep1	GSM7734779		source name:Gastrula\|strain:TLAB strain\|tissue:Gastrula\|developmental stage:Shield 6 hpf\|genotype:WT\|geo loc name:missing\|collection date:missing	WT shield 6 hpf tRNA seq rep1	Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts	Gastrula	unperturbed growth conditions in E3 medium for zebrafish embryos.	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq	Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.	strain:TLAB strain\|tissue:Gastrula\|developmental stage:Shield 6 hpf\|genotype:WT	GSM7734779	GSM7734779: WT shield 6 hpf tRNA seq rep1; Danio rerio; ncRNA Seq	GSM7734779 r1	GSM7734779	1	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP457111			WT_tRNA_shield_1.fastq.gz	fastq	487207771.0	7521930.0	GSM7734779 r1	0:64.77	A:94654510;C:134893975;G:135716906;T:121941280;N:1100	64		94654510	134893975	135716906	121941280	1100	SRX21486798	SRS18719100	SRA1700461	Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry	Max Planck Institute of Biochemistry	1	0.30664		0.02274		0.91297		0.46012		79		B		usable mapping rate	illumina	nextseq	5prime	size_fractionation	unknown	bulk	unknown	unknown	Germany	2023-08-28	Gastrula	Embryo	Whole Organism	All anatomical structures
25287	25287	SRR25764125	SRX21486797	SRS18719094	SRP457111	PRJNA1009808	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]	GSE241754	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326		WT sphere 4 hpf tRNA seq rep2	GSM7734778		source name:Blastula\|strain:TLAB strain\|tissue:Blastula\|developmental stage:Sphere 4 hpf\|genotype:WT\|geo loc name:missing\|collection date:missing	WT sphere 4 hpf tRNA seq rep2	Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts	Blastula	unperturbed growth conditions in E3 medium for zebrafish embryos.	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq	Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.	strain:TLAB strain\|tissue:Blastula\|developmental stage:Sphere 4 hpf\|genotype:WT	GSM7734778	GSM7734778: WT sphere 4 hpf tRNA seq rep2; Danio rerio; ncRNA Seq	GSM7734778 r1	GSM7734778	1	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP457111			WT_tRNA_sphere_2.fastq.gz	fastq	196089572.0	2998867.0	GSM7734778 r1	0:65.39	A:39134451;C:53803100;G:53602781;T:49548779;N:461	65		39134451	53803100	53602781	49548779	461	SRX21486797	SRS18719094	SRA1700461	Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry	Max Planck Institute of Biochemistry	1	0.28808		0.01959		0.91553		0.47742		78		B		usable mapping rate	illumina	nextseq	5prime	size_fractionation	unknown	bulk	unknown	unknown	Germany	2023-08-28	Blastula	Embryo	Whole Organism	All anatomical structures
25288	25288	SRR25764126	SRX21486796	SRS18719096	SRP457111	PRJNA1009808	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]	GSE241754	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326		WT sphere 4 hpf tRNA seq rep1	GSM7734777		source name:Blastula\|strain:TLAB strain\|tissue:Blastula\|developmental stage:Sphere 4 hpf\|genotype:WT\|geo loc name:missing\|collection date:missing	WT sphere 4 hpf tRNA seq rep1	Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts	Blastula	unperturbed growth conditions in E3 medium for zebrafish embryos.	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq	Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.	strain:TLAB strain\|tissue:Blastula\|developmental stage:Sphere 4 hpf\|genotype:WT	GSM7734777	GSM7734777: WT sphere 4 hpf tRNA seq rep1; Danio rerio; ncRNA Seq	GSM7734777 r1	GSM7734777	1	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP457111			WT_tRNA_sphere_1.fastq.gz	fastq	273027894.0	4080366.0	GSM7734777 r1	0:66.91	A:54678043;C:74713512;G:74872888;T:68762883;N:568	66		54678043	74713512	74872888	68762883	568	SRX21486796	SRS18719096	SRA1700461	Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry	Max Planck Institute of Biochemistry	1	0.30124		0.01877		0.9163		0.49987		79		B		usable mapping rate	illumina	nextseq	5prime	size_fractionation	unknown	bulk	unknown	unknown	Germany	2023-08-28	Blastula	Embryo	Whole Organism	All anatomical structures
25289	25289	SRR25764127	SRX21486795	SRS18719097	SRP457111	PRJNA1009808	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]	GSE241754	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326		WT 1000 cell 3 hpf tRNA seq rep2	GSM7734776		source name:Blastula\|strain:TLAB strain\|tissue:Blastula\|developmental stage:1000 cell 3 hpf\|genotype:WT\|geo loc name:missing\|collection date:missing	WT 1000 cell 3 hpf tRNA seq rep2	Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts	Blastula	unperturbed growth conditions in E3 medium for zebrafish embryos.	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq	Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.	strain:TLAB strain\|tissue:Blastula\|developmental stage:1000 cell 3 hpf\|genotype:WT	GSM7734776	GSM7734776: WT 1000 cell 3 hpf tRNA seq rep2; Danio rerio; ncRNA Seq	GSM7734776 r1	GSM7734776	1	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP457111			WT_tRNA_1Kcell_2.fastq.gz	fastq	240973473.0	3918764.0	GSM7734776 r1	0:61.49	A:48091658;C:66684510;G:65183534;T:61013184;N:587	61		48091658	66684510	65183534	61013184	587	SRX21486795	SRS18719097	SRA1700461	Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry	Max Planck Institute of Biochemistry	1	0.26629		0.02297		0.92305		0.48525		79		B		usable mapping rate	illumina	nextseq	5prime	size_fractionation	unknown	bulk	unknown	unknown	Germany	2023-08-28	Blastula	Embryo	Whole Organism	All anatomical structures
25290	25290	SRR25764128	SRX21486794	SRS18719095	SRP457111	PRJNA1009808	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]	GSE241754	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326		WT 1000 cell 3 hpf tRNA seq rep1	GSM7734775		source name:Blastula\|strain:TLAB strain\|tissue:Blastula\|developmental stage:1000 cell 3 hpf\|genotype:WT\|geo loc name:missing\|collection date:missing	WT 1000 cell 3 hpf tRNA seq rep1	Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts	Blastula	unperturbed growth conditions in E3 medium for zebrafish embryos.	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq	Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.	strain:TLAB strain\|tissue:Blastula\|developmental stage:1000 cell 3 hpf\|genotype:WT	GSM7734775	GSM7734775: WT 1000 cell 3 hpf tRNA seq rep1; Danio rerio; ncRNA Seq	GSM7734775 r1	GSM7734775	1	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP457111			WT_tRNA_1Kcell_1.fastq.gz	fastq	153597915.0	2445091.0	GSM7734775 r1	0:62.82	A:30905842;C:42377268;G:41639937;T:38674503;N:365	62		30905842	42377268	41639937	38674503	365	SRX21486794	SRS18719095	SRA1700461	Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry	Max Planck Institute of Biochemistry	1	0.27317		0.02516		0.92454		0.49385		77		B		usable mapping rate	illumina	nextseq	5prime	size_fractionation	unknown	bulk	unknown	unknown	Germany	2023-08-28	Blastula	Embryo	Whole Organism	All anatomical structures
25291	25291	SRR25764129	SRX21486793	SRS18719091	SRP457111	PRJNA1009808	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]	GSE241754	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326		WT 256 cell 2.5 hpf tRNA seq rep2	GSM7734774		source name:Blastula\|strain:TLAB strain\|tissue:Blastula\|developmental stage:256 cell 2.5 hpf\|genotype:WT\|geo loc name:missing\|collection date:missing	WT 256 cell 2.5 hpf tRNA seq rep2	Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts	Blastula	unperturbed growth conditions in E3 medium for zebrafish embryos.	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq	Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.	strain:TLAB strain\|tissue:Blastula\|developmental stage:256 cell 2.5 hpf\|genotype:WT	GSM7734774	GSM7734774: WT 256 cell 2.5 hpf tRNA seq rep2; Danio rerio; ncRNA Seq	GSM7734774 r1	GSM7734774	1	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP457111			WT_tRNA_256cell_2.fastq.gz	fastq	844659062.0	13660310.0	GSM7734774 r1	0:61.83	A:165996817;C:234451560;G:230230791;T:213977958;N:1936	61		165996817	234451560	230230791	213977958	1936	SRX21486793	SRS18719091	SRA1700461	Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry	Max Planck Institute of Biochemistry	1	0.26001		0.01993		0.92594		0.45714		61		B		usable mapping rate	illumina	nextseq	5prime	size_fractionation	unknown	bulk	unknown	unknown	Germany	2023-08-28	Blastula	Embryo	Whole Organism	All anatomical structures
25292	25292	SRR25764130	SRX21486792	SRS18719088	SRP457111	PRJNA1009808	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]	GSE241754	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326		WT 256 cell 2.5 hpf tRNA seq rep1	GSM7734773		source name:Blastula\|strain:TLAB strain\|tissue:Blastula\|developmental stage:256 cell 2.5 hpf\|genotype:WT\|geo loc name:missing\|collection date:missing	WT 256 cell 2.5 hpf tRNA seq rep1	Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts	Blastula	unperturbed growth conditions in E3 medium for zebrafish embryos.	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq	Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.	strain:TLAB strain\|tissue:Blastula\|developmental stage:256 cell 2.5 hpf\|genotype:WT	GSM7734773	GSM7734773: WT 256 cell 2.5 hpf tRNA seq rep1; Danio rerio; ncRNA Seq	GSM7734773 r1	GSM7734773	1	50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP457111			WT_tRNA_256cell_1.fastq.gz	fastq	215968508.0	3436266.0	GSM7734773 r1	0:62.85	A:43791388;C:59547637;G:58130851;T:54498124;N:508	62		43791388	59547637	58130851	54498124	508	SRX21486792	SRS18719088	SRA1700461	Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry	Max Planck Institute of Biochemistry	1	0.27383		0.02205		0.92748		0.46217		71		B		usable mapping rate	illumina	nextseq	5prime	size_fractionation	unknown	bulk	unknown	unknown	Germany	2023-08-28	Blastula	Embryo	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
29739	29739	SRR27467672	SRX23139234	SRS20090275	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Dome mock R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 5 hpf mock rep2	EV04009	EV04009	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV04009.R1.fastq.gz	fastq	609590940.0	4354221.0	EV04009.R1.fastq.gz	0:140	A:155062144;C:147628702;G:168099121;T:138772205;N:28768	140		155062144	147628702	168099121	138772205	28768	SRX23139234	SRS20090275	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Blastula	Embryo	Whole Organism	All anatomical structures
29740	29740	SRR27467673	SRX23139233	SRS20090278	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						1K cell BS R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 3 hpf BS rep2	EV04008	EV04008	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV04008.R1.fastq.gz	fastq	675505180.0	4825037.0	EV04008.R1.fastq.gz	0:140	A:178823976;C:121648962;G:198428643;T:176572292;N:31307	140		178823976	121648962	198428643	176572292	31307	SRX23139233	SRS20090278	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Blastula	Embryo	Whole Organism	All anatomical structures
29741	29741	SRR27467674	SRX23139232	SRS20090272	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						1K cell DM R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 3 hpf DM rep2	EV04007	EV04007	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV04007.R1.fastq.gz	fastq	702064440.0	5014746.0	EV04007.R1.fastq.gz	0:140	A:176719694;C:166467163;G:207893965;T:150951950;N:31668	140		176719694	166467163	207893965	150951950	31668	SRX23139232	SRS20090272	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	2e-05		0.0		0.99997		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Blastula	Embryo	Whole Organism	All anatomical structures
29742	29742	SRR27467675	SRX23139231	SRS20090271	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						1K cell mock R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 3 hpf mock rep2	EV04006	EV04006	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV04006.R1.fastq.gz	fastq	664790700.0	4748505.0	EV04006.R1.fastq.gz	0:140	A:172014219;C:146545691;G:200358431;T:145840649;N:31710	140		172014219	146545691	200358431	145840649	31710	SRX23139231	SRS20090271	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	3e-05		0.0		0.99993		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Blastula	Embryo	Whole Organism	All anatomical structures
29743	29743	SRR27467676	SRX23139230	SRS20090273	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						4 cell DM R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:1 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 1 hpf DM rep2	EV04004	EV04004	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV04004.R1.fastq.gz	fastq	895671560.0	6397654.0	EV04004.R1.fastq.gz	0:140	A:206443066;C:147067097;G:365386937;T:176734600;N:39860	140		206443066	147067097	365386937	176734600	39860	SRX23139230	SRS20090273	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Cleavage	Embryo	Whole Organism	All anatomical structures
29744	29744	SRR27467677	SRX23139229	SRS20090274	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						4 cell mock R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:1 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 1 hpf mock rep2	EV04003	EV04003	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV04003.R1.fastq.gz	fastq	664112120.0	4743658.0	EV04003.R1.fastq.gz	0:140	A:163711695;C:142612940;G:211194350;T:146562626;N:30509	140		163711695	142612940	211194350	146562626	30509	SRX23139229	SRS20090274	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	2e-05		0.0		0.99997		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Cleavage	Embryo	Whole Organism	All anatomical structures
29747	29747	SRR27467680	SRX23139226	SRS20090267	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						24h BS R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 24 hpf BS rep2	EV03009	EV03009	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV03009.R1.fastq.gz	fastq	168931280.0	2222780.0	EV03009.R1.fastq.gz	0:76	A:49803604;C:36479774;G:37758990;T:44874154;N:14758	76		49803604	36479774	37758990	44874154	14758	SRX23139226	SRS20090267	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00034		0.0002		0.99965		0.5		76		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Pharyngula	Embryo	Whole Organism	All anatomical structures
29748	29748	SRR27467681	SRX23139225	SRS20090266	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						24h DM R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 24 hpf DM rep2	EV03008	EV03008	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV03008.R1.fastq.gz	fastq	200878792.0	2643142.0	EV03008.R1.fastq.gz	0:76	A:46955288;C:54746275;G:55887832;T:43270561;N:18836	76		46955288	54746275	55887832	43270561	18836	SRX23139225	SRS20090266	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.29408		0.00737		0.91823		0.54549		76		B		usable mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Pharyngula	Embryo	Whole Organism	All anatomical structures
29749	29749	SRR27467682	SRX23139224	SRS20090269	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						24h mock R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 24 hpf mock rep2	EV03007	EV03007	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV03007.R1.fastq.gz	fastq	175642840.0	2311090.0	EV03007.R1.fastq.gz	0:76	A:44745275;C:48908904;G:44862157;T:37111895;N:14609	76		44745275	48908904	44862157	37111895	14609	SRX23139224	SRS20090269	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.06887		0.00273		0.96623		0.48721		76		B		usable mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Pharyngula	Embryo	Whole Organism	All anatomical structures
29750	29750	SRR27467683	SRX23139223	SRS20090265	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Bud BS R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 10 hpf BS rep2	EV04014	EV04014	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV04014.R1.fastq.gz	fastq	774901260.0	5535009.0	EV04014.R1.fastq.gz	0:140	A:193865579;C:138861953;G:251102013;T:191036071;N:35644	140		193865579	138861953	251102013	191036071	35644	SRX23139223	SRS20090265	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Gastrula	Embryo	Whole Organism	All anatomical structures
29751	29751	SRR27467684	SRX23139222	SRS20090264	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Bud DM R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 10 hpf DM rep2	EV04013	EV04013	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV04013.R1.fastq.gz	fastq	666372840.0	4759806.0	EV04013.R1.fastq.gz	0:140	A:172923134;C:142243998;G:211584978;T:139591020;N:29710	140		172923134	142243998	211584978	139591020	29710	SRX23139222	SRS20090264	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	3e-05		0.0		0.99991		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Gastrula	Embryo	Whole Organism	All anatomical structures
29752	29752	SRR27467685	SRX23139221	SRS20090262	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Bud mock R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 10 hpf mock rep2	EV04012	EV04012	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV04012.R1.fastq.gz	fastq	628769540.0	4491211.0	EV04012.R1.fastq.gz	0:140	A:160925901;C:143204697;G:183224867;T:141385307;N:28768	140		160925901	143204697	183224867	141385307	28768	SRX23139221	SRS20090262	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	1e-05		0.0		0.99997		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Gastrula	Embryo	Whole Organism	All anatomical structures
29753	29753	SRR27467686	SRX23139220	SRS20090263	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Dome BS R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 5 hpf BS rep2	EV04011	EV04011	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV04011.R1.fastq.gz	fastq	720913200.0	5149380.0	EV04011.R1.fastq.gz	0:140	A:185414155;C:126110104;G:238649631;T:170706590;N:32720	140		185414155	126110104	238649631	170706590	32720	SRX23139220	SRS20090263	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Blastula	Embryo	Whole Organism	All anatomical structures
29754	29754	SRR27467687	SRX23139219	SRS20090259	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Dome DM R2		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 5 hpf DM rep2	EV04010	EV04010	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV04010.R1.fastq.gz	fastq	443650200.0	3168930.0	EV04010.R1.fastq.gz	0:140	A:114663509;C:102512276;G:135709753;T:90744641;N:20021	140		114663509	102512276	135709753	90744641	20021	SRX23139219	SRS20090259	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	1e-05		0.0		0.99997		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Blastula	Embryo	Whole Organism	All anatomical structures
29757	29757	SRR27437477	SRX23109820	SRS20064574	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						1K cell mock R3		strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 3 hpf mock rep3	EV07007	EV07007	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV07007.R1.fastq.gz	fastq	479994620.0	3428533.0	EV07007.R1.fastq.gz	0:140	A:124628886;C:116843590;G:123136721;T:115372734;N:12689	140		124628886	116843590	123136721	115372734	12689	SRX23109820	SRS20064574	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	6e-05		1e-05		0.99989		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Blastula	Embryo	Whole Organism	All anatomical structures
29758	29758	SRR27437478	SRX23109819	SRS20064573	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						4 cell BS R3		strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:1 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 1 hpf BS rep3	EV07006	EV07006	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV07006.R1.fastq.gz	fastq	2584527680.0	18460912.0	EV07006.R1.fastq.gz	0:140	A:685107500;C:367766834;G:717359848;T:814224206;N:69292	140		685107500	367766834	717359848	814224206	69292	SRX23109819	SRS20064573	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	2e-05		1e-05		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Cleavage	Embryo	Whole Organism	All anatomical structures
29759	29759	SRR27437479	SRX23109818	SRS20064571	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						4 cell DM R3		strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:1 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 1 hpf DM rep3	EV07005	EV07005	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV07005.R1.fastq.gz	fastq	713829480.0	5098782.0	EV07005.R1.fastq.gz	0:140	A:183575304;C:168886779;G:213156258;T:148191838;N:19301	140		183575304	168886779	213156258	148191838	19301	SRX23109818	SRS20064571	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	5e-05		0.0		0.99989		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Cleavage	Embryo	Whole Organism	All anatomical structures
29760	29760	SRR27437480	SRX23109817	SRS20064572	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						4 cell mock R3		strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:1 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 1 hpf mock rep3	EV07004	EV07004	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV07004.R1.fastq.gz	fastq	517336680.0	3695262.0	EV07004.R1.fastq.gz	0:140	A:136783049;C:131207858;G:139873280;T:109458276;N:14217	140		136783049	131207858	139873280	109458276	14217	SRX23109817	SRS20064572	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	7e-05		0.0		0.99981		0.7		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Cleavage	Embryo	Whole Organism	All anatomical structures
29764	29764	SRR27437484	SRX23109813	SRS20064567	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						24h BS R3		strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 24 hpf BS rep3	EV07018	EV07018	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV07018.R1.fastq.gz	fastq	887731180.0	6340937.0	EV07018.R1.fastq.gz	0:140	A:204102176;C:148262233;G:350287017;T:185056779;N:22975	140		204102176	148262233	350287017	185056779	22975	SRX23109813	SRS20064567	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Pharyngula	Embryo	Whole Organism	All anatomical structures
29766	29766	SRR27437486	SRX23109811	SRS20064565	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						24h DM R3		strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 24 hpf DM rep3	EV07017	EV07017	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV07017.R1.fastq.gz	fastq	466089960.0	3329214.0	EV07017.R1.fastq.gz	0:140	A:117818387;C:108651920;G:144753443;T:94853810;N:12400	140		117818387	108651920	144753443	94853810	12400	SRX23109811	SRS20064565	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Pharyngula	Embryo	Whole Organism	All anatomical structures
29767	29767	SRR27437487	SRX23109810	SRS20064563	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						24h mock R3		strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 24 hpf mock rep3	EV07016	EV07016	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV07016.R1.fastq.gz	fastq	638674120.0	4561958.0	EV07016.R1.fastq.gz	0:140	A:159572532;C:147135537;G:186885553;T:145063254;N:17244	140		159572532	147135537	186885553	145063254	17244	SRX23109810	SRS20064563	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	4e-05		0.0		0.99993		0.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Pharyngula	Embryo	Whole Organism	All anatomical structures
29768	29768	SRR27437488	SRX23109809	SRS20064564	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Bud BS R3		strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 10 hpf BS rep3	EV07015	EV07015	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV07015.R1.fastq.gz	fastq	598389400.0	4274210.0	EV07015.R1.fastq.gz	0:140	A:150315140;C:106310211;G:186765596;T:154982225;N:16228	140		150315140	106310211	186765596	154982225	16228	SRX23109809	SRS20064564	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Gastrula	Embryo	Whole Organism	All anatomical structures
29769	29769	SRR27437489	SRX23109808	SRS20064562	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Bud DM R3		strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 10 hpf DM rep3	EV07014	EV07014	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV07014.R1.fastq.gz	fastq	739056780.0	5278977.0	EV07014.R1.fastq.gz	0:140	A:197948890;C:178761090;G:200265458;T:162060992;N:20350	140		197948890	178761090	200265458	162060992	20350	SRX23109808	SRS20064562	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	3e-05		0.0		0.99995		0.5		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Gastrula	Embryo	Whole Organism	All anatomical structures
29770	29770	SRR27437490	SRX23109807	SRS20064561	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Bud mock R3		strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 10 hpf mock rep3	EV07013	EV07013	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV07013.R1.fastq.gz	fastq	844338040.0	6030986.0	EV07013.R1.fastq.gz	0:140	A:217780710;C:182517044;G:251974206;T:192043675;N:22405	140		217780710	182517044	251974206	192043675	22405	SRX23109807	SRS20064561	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	4e-05		0.0		0.99993		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Gastrula	Embryo	Whole Organism	All anatomical structures
29771	29771	SRR27437491	SRX23109806	SRS20064560	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Dome BS R3		strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 5 hpf BS rep3	EV07011	EV07011	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV07011.R1.fastq.gz	fastq	893528580.0	6382347.0	EV07011.R1.fastq.gz	0:140	A:240101890;C:155985797;G:262065322;T:235351334;N:24237	140		240101890	155985797	262065322	235351334	24237	SRX23109806	SRS20064560	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Blastula	Embryo	Whole Organism	All anatomical structures
29772	29772	SRR27437492	SRX23109805	SRS20064559	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Dome DM R3		strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 5 hpf DM rep3	EV07012	EV07012	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV07012.R1.fastq.gz	fastq	797662600.0	5697590.0	EV07012.R1.fastq.gz	0:140	A:201908589;C:182656132;G:249672167;T:163404182;N:21530	140		201908589	182656132	249672167	163404182	21530	SRX23109805	SRS20064559	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	3e-05		0.0		0.99991		0.75		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Blastula	Embryo	Whole Organism	All anatomical structures
29773	29773	SRR27437493	SRX23109804	SRS20064558	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Dome mock R3		strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 5 hpf mock rep3	EV07010	EV07010	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV07010.R1.fastq.gz	fastq	467593280.0	3339952.0	EV07010.R1.fastq.gz	0:140	A:122604957;C:118747514;G:124074466;T:102153374;N:12969	140		122604957	118747514	124074466	102153374	12969	SRX23109804	SRS20064558	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	4e-05		0.0		0.99993		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Blastula	Embryo	Whole Organism	All anatomical structures
29774	29774	SRR27437494	SRX23109803	SRS20064557	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						1K cell BS R3		strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 3 hpf BS rep3	EV07008	EV07008	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV07008.R1.fastq.gz	fastq	705682040.0	5040586.0	EV07008.R1.fastq.gz	0:140	A:194506527;C:127442743;G:192893716;T:190818958;N:20096	140		194506527	127442743	192893716	190818958	20096	SRX23109803	SRS20064557	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Blastula	Embryo	Whole Organism	All anatomical structures
29775	29775	SRR27437495	SRX23109802	SRS20064556	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						1K cell DM R3		strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 3 hpf DM rep3	EV07009	EV07009	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV07009.R1.fastq.gz	fastq	380716280.0	2719402.0	EV07009.R1.fastq.gz	0:140	A:95351632;C:89558330;G:115625953;T:80169603;N:10762	140		95351632	89558330	115625953	80169603	10762	SRX23109802	SRS20064556	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	6e-05		1e-05		0.99991		0.75		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Blastula	Embryo	Whole Organism	All anatomical structures
29778	29778	SRR27435863	SRX23108233	SRS20063070	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						1K cell mock R4		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 3 hpf mock rep4	EV08010	EV08010	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV08010.R1.fastq.gz	fastq	678729520.0	4848068.0	EV08010.R1.fastq.gz	0:140	A:170672553;C:182320916;G:171865707;T:153824163;N:46181	140		170672553	182320916	171865707	153824163	46181	SRX23108233	SRS20063070	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0006		4e-05		0.99878		0.79069		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Blastula	Embryo	Whole Organism	All anatomical structures
29779	29779	SRR27435864	SRX23108232	SRS20063068	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						4 cell BS R4		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:1 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 1 hpf BS rep4	EV08009	EV08009	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV08009.R1.fastq.gz	fastq	756964460.0	5406889.0	EV08009.R1.fastq.gz	0:140	A:191381054;C:111783194;G:185694475;T:268052883;N:52854	140		191381054	111783194	185694475	268052883	52854	SRX23108232	SRS20063068	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	1e-05		0.0		0.99997		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Cleavage	Embryo	Whole Organism	All anatomical structures
29780	29780	SRR27435865	SRX23108231	SRS20063069	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						4 cell DM R4		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:1 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 1 hpf DM rep4	EV08008	EV08008	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV08008.R1.fastq.gz	fastq	751794680.0	5369962.0	EV08008.R1.fastq.gz	0:140	A:194845808;C:197389162;G:194749636;T:164756481;N:53593	140		194845808	197389162	194749636	164756481	53593	SRX23108231	SRS20063069	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00124		0.00029		0.99853		0.77083		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Cleavage	Embryo	Whole Organism	All anatomical structures
29781	29781	SRR27435866	SRX23108230	SRS20063066	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						4 cell mock R4		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:1 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 1 hpf mock rep4	EV08007	EV08007	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV08007.R1.fastq.gz	fastq	761961760.0	5442584.0	EV08007.R1.fastq.gz	0:140	A:194053323;C:191169414;G:194452160;T:182234253;N:52610	140		194053323	191169414	194452160	182234253	52610	SRX23108230	SRS20063066	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00242		0.00062		0.99803		0.81818		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Cleavage	Embryo	Whole Organism	All anatomical structures
29785	29785	SRR27435870	SRX23108226	SRS20063064	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						24h BS R4		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 24 hpf BS rep4	EV08021	EV08021	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV08021.R1.fastq.gz	fastq	747571860.0	5339799.0	EV08021.R1.fastq.gz	0:140	A:185666613;C:121868156;G:181153824;T:258830310;N:52957	140		185666613	121868156	181153824	258830310	52957	SRX23108226	SRS20063064	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Pharyngula	Embryo	Whole Organism	All anatomical structures
29787	29787	SRR27435872	SRX23108224	SRS20063061	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						24h DM R4		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 24 hpf DM rep4	EV08020	EV08020	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV08020.R1.fastq.gz	fastq	775090400.0	5536360.0	EV08020.R1.fastq.gz	0:140	A:198131068;C:205114604;G:198783890;T:173006366;N:54472	140		198131068	205114604	198783890	173006366	54472	SRX23108224	SRS20063061	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00056		4e-05		0.9989		0.71052		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Pharyngula	Embryo	Whole Organism	All anatomical structures
29788	29788	SRR27435873	SRX23108223	SRS20063060	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						24h mock R4		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 24 hpf mock rep4	EV08019	EV08019	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV08019.R1.fastq.gz	fastq	763233240.0	5451666.0	EV08019.R1.fastq.gz	0:140	A:189362337;C:199268270;G:198509945;T:176040551;N:52137	140		189362337	199268270	198509945	176040551	52137	SRX23108223	SRS20063060	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00036		6e-05		0.99939		0.85365		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Pharyngula	Embryo	Whole Organism	All anatomical structures
29789	29789	SRR27435874	SRX23108222	SRS20063057	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Bud BS R4		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 10 hpf BS rep4	EV08018	EV08018	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV08018.R1.fastq.gz	fastq	809203080.0	5780022.0	EV08018.R1.fastq.gz	0:140	A:209714496;C:130623600;G:197912909;T:270895413;N:56662	140		209714496	130623600	197912909	270895413	56662	SRX23108222	SRS20063057	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Gastrula	Embryo	Whole Organism	All anatomical structures
29790	29790	SRR27435875	SRX23108221	SRS20063059	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Bud DM R4		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 10 hpf DM rep4	EV08017	EV08017	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV08017.R1.fastq.gz	fastq	722137500.0	5158125.0	EV08017.R1.fastq.gz	0:140	A:176408094;C:195907583;G:188487109;T:161283055;N:51659	140		176408094	195907583	188487109	161283055	51659	SRX23108221	SRS20063059	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00053		3e-05		0.999		0.70422		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Gastrula	Embryo	Whole Organism	All anatomical structures
29791	29791	SRR27435876	SRX23108220	SRS20063058	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Bud mock R4		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 10 hpf mock rep4	EV08016	EV08016	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV08016.R1.fastq.gz	fastq	827605660.0	5911469.0	EV08016.R1.fastq.gz	0:140	A:204173663;C:224596562;G:206999037;T:191779555;N:56843	140		204173663	224596562	206999037	191779555	56843	SRX23108220	SRS20063058	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00037		2e-05		0.99908		0.7037		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Gastrula	Embryo	Whole Organism	All anatomical structures
29792	29792	SRR27435877	SRX23108219	SRS20063056	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Dome BS R4		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 5 hpf BS rep4	EV08015	EV08015	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV08015.R1.fastq.gz	fastq	804598200.0	5747130.0	EV08015.R1.fastq.gz	0:140	A:215467427;C:134937180;G:189531758;T:264604493;N:57342	140		215467427	134937180	189531758	264604493	57342	SRX23108219	SRS20063056	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	2e-05		0.0		0.99995		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Blastula	Embryo	Whole Organism	All anatomical structures
29793	29793	SRR27435878	SRX23108218	SRS20063055	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Dome DM R4		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 5 hpf DM rep4	EV08014	EV08014	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV08014.R1.fastq.gz	fastq	662443740.0	4731741.0	EV08014.R1.fastq.gz	0:140	A:164941700;C:167025964;G:177255084;T:153175163;N:45829	140		164941700	167025964	177255084	153175163	45829	SRX23108218	SRS20063055	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00069		0.0001		0.9992		0.83076		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Blastula	Embryo	Whole Organism	All anatomical structures
29794	29794	SRR27435879	SRX23108217	SRS20063052	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						Dome mock R4		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 5 hpf mock rep4	EV08013	EV08013	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV08013.R1.fastq.gz	fastq	794760540.0	5676861.0	EV08013.R1.fastq.gz	0:140	A:197361776;C:210230329;G:205734036;T:181380205;N:54194	140		197361776	210230329	205734036	181380205	54194	SRX23108217	SRS20063052	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00066		9e-05		0.99894		0.78378		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Blastula	Embryo	Whole Organism	All anatomical structures
29795	29795	SRR27435880	SRX23108216	SRS20063054	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						1K cell BS R4		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 3 hpf BS rep4	EV08012	EV08012	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV08012.R1.fastq.gz	fastq	722593200.0	5161380.0	EV08012.R1.fastq.gz	0:140	A:188475497;C:119550806;G:173208825;T:241306038;N:52034	140		188475497	119550806	173208825	241306038	52034	SRX23108216	SRS20063054	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Blastula	Embryo	Whole Organism	All anatomical structures
29796	29796	SRR27435881	SRX23108215	SRS20063053	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other						1K cell DM R4		strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: embryo 3 hpf DM rep4	EV08011	EV08011	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074			EV08011.R1.fastq.gz	fastq	753783380.0	5384167.0	EV08011.R1.fastq.gz	0:140	A:190029713;C:193734250;G:194752855;T:175212145;N:54417	140		190029713	193734250	194752855	175212145	54417	SRX23108215	SRS20063053	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00076		5e-05		0.99859		0.70873		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Blastula	Embryo	Whole Organism	All anatomical structures
36266	36266	SRR953577	SRX336218	SRS471213	SRP028895	PRJNA138095	Transcriptome wide analysis of small RNA expression in early zebrafish development	GSE27722	Transcriptome Analysis	During early vertebrate development a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription. The exact identity expression levels and function during early vertebrate development for most of these noncoding RNAs remains largely unknown. miRNAs microRNAs and piRNAs piwi interacting RNAs are two classes of small non coding RNAs that play important roles in gene regulation during early embryonic development. Here we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system. For miRNAs the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined. Significant sequence variation was observed at the five prime' and three prime' ends of miRNAs with a large number of extra nucleotides added in a non template directed manner. We also identified a large and diverse set of piRNAs expressed during early development far beyond that expected if piRNA expression is restricted to germ cells. Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Overall design: Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through put sequencing		pubmed:22408181		embryo 1dpf rep1	GSM686385		source name:the whole embryo\|strain:AB*WT\|developmental stage:1dpf\|tissue:the whole embryos	embryo 1dpf rep1	fasta: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm which allows one mismatch in the linker sequences. All the sequence with N inside was removed as well. The unique sequences were retained with the counts indicating thier abundance. The header of each sequence is composed of a unique sequence ID followed by a " x" and the reads counts. e.g. unique ID x counts. alignment: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm which allows one mismatch in the linker sequences. Small RNAs with perfect matches to the zebrafish genome Zv8 from Ensembl http://www.ensembl.org were retrieved using megaBLAST http://www.ncbi.nlm.nih.gov/blast/megablast.shtml and Bowtie http://bowtie bio.sourceforge.net/tutorial.shtml. To identify piRNAs consensus sequences from zebrafish repetitive elements were retrieved from Repbase http://www.girinst.org/repbase/index.html and Repeat Maskers using the UCSC genome browser http://genome.ucsc.edu. Small RNAs perfectly mapping to these consensus sequences and their genomic flanking regions were sorted into piRNA libraries with up to 3 genomic mapping positions for each unique RNA sequence. fasta files description: small RNA 15 30 nt alignment file description: piRNA map to repetitive elements	the whole embryo		Zebrafish embryos were collected at the 256 cell stage sphere stage shield stage and 1dpf. Total RNA was isolated from embryos using Trizol. RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified. cDNA libraries were generated using specific linkers and RT/PCR as previously described. Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.	Embryos were raised at 28Â°C in egg water 0.03% Instant Ocean marine salt mix for the initial several hours of development	strain:AB*WT\|developmental stage:1dpf\|tissue:the whole embryos	GSM686385	GSM686385: embryo 1dpf rep1; Danio rerio; ncRNA Seq	GSM686385		1	Zebrafish embryos were collected at the 256 cell stage sphere stage shield stage and 1dpf. Total RNA was isolated from embryos using Trizol. RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified. cDNA libraries were generated using specific linkers and RT/PCR as previously described. Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.	GEO Accession:GSM686385	ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II		SRP028895			GSM686385_1dpf_Raw.txt	fastq	293700240.0	8158340.0	GSM686385 r1	0:36	A:74642033;C:62153879;G:83836688;T:69542606;N:3525034	36		74642033	62153879	83836688	69542606	3525034	SRX336218	SRS471213	SRA098146	GEO	Lee Lab, Molecular Biology, Mass General Hospital	1	0.00386		0.00274		0.99758		0.53623		36		T		under 1.2% mapping rate	illumina	early_illumina	5prime	size_fractionation	unknown	bulk	unknown	unknown	United States	2011-03-07	Pharyngula	Embryo	Whole Organism	All anatomical structures
36267	36267	SRR953576	SRX336217	SRS471211	SRP028895	PRJNA138095	Transcriptome wide analysis of small RNA expression in early zebrafish development	GSE27722	Transcriptome Analysis	During early vertebrate development a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription. The exact identity expression levels and function during early vertebrate development for most of these noncoding RNAs remains largely unknown. miRNAs microRNAs and piRNAs piwi interacting RNAs are two classes of small non coding RNAs that play important roles in gene regulation during early embryonic development. Here we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system. For miRNAs the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined. Significant sequence variation was observed at the five prime' and three prime' ends of miRNAs with a large number of extra nucleotides added in a non template directed manner. We also identified a large and diverse set of piRNAs expressed during early development far beyond that expected if piRNA expression is restricted to germ cells. Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Overall design: Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through put sequencing		pubmed:22408181		embryo Shield rep1	GSM686384		source name:the whole embryo\|strain:AB*WT\|developmental stage:Shield\|tissue:the whole embryos	embryo Shield rep1	fasta: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm which allows one mismatch in the linker sequences. All the sequence with N inside was removed as well. The unique sequences were retained with the counts indicating thier abundance. The header of each sequence is composed of a unique sequence ID followed by a " x" and the reads counts. e.g. unique ID x counts. alignment: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm which allows one mismatch in the linker sequences. Small RNAs with perfect matches to the zebrafish genome Zv8 from Ensembl http://www.ensembl.org were retrieved using megaBLAST http://www.ncbi.nlm.nih.gov/blast/megablast.shtml and Bowtie http://bowtie bio.sourceforge.net/tutorial.shtml. To identify piRNAs consensus sequences from zebrafish repetitive elements were retrieved from Repbase http://www.girinst.org/repbase/index.html and Repeat Maskers using the UCSC genome browser http://genome.ucsc.edu. Small RNAs perfectly mapping to these consensus sequences and their genomic flanking regions were sorted into piRNA libraries with up to 3 genomic mapping positions for each unique RNA sequence. fasta files description: small RNA 15 30 nt alignment file description: piRNA map to repetitive elements	the whole embryo		Zebrafish embryos were collected at the 256 cell stage sphere stage shield stage and 1dpf. Total RNA was isolated from embryos using Trizol. RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified. cDNA libraries were generated using specific linkers and RT/PCR as previously described. Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.	Embryos were raised at 28Â°C in egg water 0.03% Instant Ocean marine salt mix for the initial several hours of development	strain:AB*WT\|developmental stage:Shield\|tissue:the whole embryos	GSM686384	GSM686384: embryo Shield rep1; Danio rerio; ncRNA Seq	GSM686384		1	Zebrafish embryos were collected at the 256 cell stage sphere stage shield stage and 1dpf. Total RNA was isolated from embryos using Trizol. RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified. cDNA libraries were generated using specific linkers and RT/PCR as previously described. Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.	GEO Accession:GSM686384	ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II		SRP028895			GSM686384_Shield_Raw.txt	fastq	115067916.0	3196331.0	GSM686384 r1	0:36	A:28435718;C:21893278;G:31779352;T:26635839;N:6323729	36		28435718	21893278	31779352	26635839	6323729	SRX336217	SRS471211	SRA098146	GEO	Lee Lab, Molecular Biology, Mass General Hospital	1	0.00278		0.00217		0.99933		0.60606		36		T		under 1.2% mapping rate	illumina	early_illumina	5prime	size_fractionation	unknown	bulk	unknown	unknown	United States	2011-03-07	Gastrula	Embryo	Whole Organism	All anatomical structures
36268	36268	SRR953575	SRX336216	SRS471212	SRP028895	PRJNA138095	Transcriptome wide analysis of small RNA expression in early zebrafish development	GSE27722	Transcriptome Analysis	During early vertebrate development a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription. The exact identity expression levels and function during early vertebrate development for most of these noncoding RNAs remains largely unknown. miRNAs microRNAs and piRNAs piwi interacting RNAs are two classes of small non coding RNAs that play important roles in gene regulation during early embryonic development. Here we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system. For miRNAs the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined. Significant sequence variation was observed at the five prime' and three prime' ends of miRNAs with a large number of extra nucleotides added in a non template directed manner. We also identified a large and diverse set of piRNAs expressed during early development far beyond that expected if piRNA expression is restricted to germ cells. Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Overall design: Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through put sequencing		pubmed:22408181		embryo sphere rep2	GSM686383		source name:the whole embryo\|strain:AB*WT\|developmental stage:sphere\|tissue:the whole embryos	embryo sphere rep2	fasta: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm which allows one mismatch in the linker sequences. All the sequence with N inside was removed as well. The unique sequences were retained with the counts indicating thier abundance. The header of each sequence is composed of a unique sequence ID followed by a " x" and the reads counts. e.g. unique ID x counts. alignment: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm which allows one mismatch in the linker sequences. Small RNAs with perfect matches to the zebrafish genome Zv8 from Ensembl http://www.ensembl.org were retrieved using megaBLAST http://www.ncbi.nlm.nih.gov/blast/megablast.shtml and Bowtie http://bowtie bio.sourceforge.net/tutorial.shtml. To identify piRNAs consensus sequences from zebrafish repetitive elements were retrieved from Repbase http://www.girinst.org/repbase/index.html and Repeat Maskers using the UCSC genome browser http://genome.ucsc.edu. Small RNAs perfectly mapping to these consensus sequences and their genomic flanking regions were sorted into piRNA libraries with up to 3 genomic mapping positions for each unique RNA sequence. fasta files description: small RNA 15 30 nt alignment file description: piRNA map to repetitive elements	the whole embryo		Zebrafish embryos were collected at the 256 cell stage sphere stage shield stage and 1dpf. Total RNA was isolated from embryos using Trizol. RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified. cDNA libraries were generated using specific linkers and RT/PCR as previously described. Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.	Embryos were raised at 28Â°C in egg water 0.03% Instant Ocean marine salt mix for the initial several hours of development	strain:AB*WT\|developmental stage:sphere\|tissue:the whole embryos	GSM686383	GSM686383: embryo sphere rep2; Danio rerio; ncRNA Seq	GSM686383		1	Zebrafish embryos were collected at the 256 cell stage sphere stage shield stage and 1dpf. Total RNA was isolated from embryos using Trizol. RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified. cDNA libraries were generated using specific linkers and RT/PCR as previously described. Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.	GEO Accession:GSM686383	ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II		SRP028895			GSM686383_Sphere_2_Raw.txt	fastq	369741456.0	10270596.0	GSM686383 r1	0:36	A:89854472;C:70044086;G:109552597;T:100266590;N:23711	36		89854472	70044086	109552597	100266590	23711	SRX336216	SRS471212	SRA098146	GEO	Lee Lab, Molecular Biology, Mass General Hospital	1	0.00421		0.00367		0.99924		0.51111		36		T		under 1.2% mapping rate	illumina	early_illumina	5prime	size_fractionation	unknown	bulk	unknown	unknown	United States	2011-03-07	Blastula	Embryo	Whole Organism	All anatomical structures
36269	36269	SRR953574	SRX336215	SRS471209	SRP028895	PRJNA138095	Transcriptome wide analysis of small RNA expression in early zebrafish development	GSE27722	Transcriptome Analysis	During early vertebrate development a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription. The exact identity expression levels and function during early vertebrate development for most of these noncoding RNAs remains largely unknown. miRNAs microRNAs and piRNAs piwi interacting RNAs are two classes of small non coding RNAs that play important roles in gene regulation during early embryonic development. Here we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system. For miRNAs the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined. Significant sequence variation was observed at the five prime' and three prime' ends of miRNAs with a large number of extra nucleotides added in a non template directed manner. We also identified a large and diverse set of piRNAs expressed during early development far beyond that expected if piRNA expression is restricted to germ cells. Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Overall design: Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through put sequencing		pubmed:22408181		embryo sphere rep1	GSM686382		source name:the whole embryo\|strain:AB*WT\|developmental stage:sphere\|tissue:the whole embryos	embryo sphere rep1	fasta: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm which allows one mismatch in the linker sequences. All the sequence with N inside was removed as well. The unique sequences were retained with the counts indicating thier abundance. The header of each sequence is composed of a unique sequence ID followed by a " x" and the reads counts. e.g. unique ID x counts. alignment: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm which allows one mismatch in the linker sequences. Small RNAs with perfect matches to the zebrafish genome Zv8 from Ensembl http://www.ensembl.org were retrieved using megaBLAST http://www.ncbi.nlm.nih.gov/blast/megablast.shtml and Bowtie http://bowtie bio.sourceforge.net/tutorial.shtml. To identify piRNAs consensus sequences from zebrafish repetitive elements were retrieved from Repbase http://www.girinst.org/repbase/index.html and Repeat Maskers using the UCSC genome browser http://genome.ucsc.edu. Small RNAs perfectly mapping to these consensus sequences and their genomic flanking regions were sorted into piRNA libraries with up to 3 genomic mapping positions for each unique RNA sequence. fasta files description: small RNA 15 30 nt alignment file description: piRNA map to repetitive elements	the whole embryo		Zebrafish embryos were collected at the 256 cell stage sphere stage shield stage and 1dpf. Total RNA was isolated from embryos using Trizol. RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified. cDNA libraries were generated using specific linkers and RT/PCR as previously described. Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.	Embryos were raised at 28Â°C in egg water 0.03% Instant Ocean marine salt mix for the initial several hours of development	strain:AB*WT\|developmental stage:sphere\|tissue:the whole embryos	GSM686382	GSM686382: embryo sphere rep1; Danio rerio; ncRNA Seq	GSM686382		1	Zebrafish embryos were collected at the 256 cell stage sphere stage shield stage and 1dpf. Total RNA was isolated from embryos using Trizol. RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified. cDNA libraries were generated using specific linkers and RT/PCR as previously described. Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.	GEO Accession:GSM686382	ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II		SRP028895			GSM686382_Sphere_1_Raw.txt	fastq	492502284.0	13680619.0	GSM686382 r1	0:36	A:114418890;C:99502519;G:142841794;T:135061742;N:677339	36		114418890	99502519	142841794	135061742	677339	SRX336215	SRS471209	SRA098146	GEO	Lee Lab, Molecular Biology, Mass General Hospital	1	0.00828		0.00636		0.9964		0.54822		36		T		under 1.2% mapping rate	illumina	early_illumina	5prime	size_fractionation	unknown	bulk	unknown	unknown	United States	2011-03-07	Blastula	Embryo	Whole Organism	All anatomical structures
36270	36270	SRR953573	SRX336214	SRS471210	SRP028895	PRJNA138095	Transcriptome wide analysis of small RNA expression in early zebrafish development	GSE27722	Transcriptome Analysis	During early vertebrate development a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription. The exact identity expression levels and function during early vertebrate development for most of these noncoding RNAs remains largely unknown. miRNAs microRNAs and piRNAs piwi interacting RNAs are two classes of small non coding RNAs that play important roles in gene regulation during early embryonic development. Here we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system. For miRNAs the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined. Significant sequence variation was observed at the five prime' and three prime' ends of miRNAs with a large number of extra nucleotides added in a non template directed manner. We also identified a large and diverse set of piRNAs expressed during early development far beyond that expected if piRNA expression is restricted to germ cells. Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Overall design: Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through put sequencing		pubmed:22408181		embryo 256 cell rep1	GSM686381		source name:the whole embryo\|strain:AB* WT\|developmental stage:256 cell\|tissue:the whole embryos	embryo 256 cell rep1	fasta: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm which allows one mismatch in the linker sequences. All the sequence with N inside was removed as well. The unique sequences were retained with the counts indicating thier abundance. The header of each sequence is composed of a unique sequence ID followed by a " x" and the reads counts. e.g. unique ID x counts. alignment: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm which allows one mismatch in the linker sequences. Small RNAs with perfect matches to the zebrafish genome Zv8 from Ensembl http://www.ensembl.org were retrieved using megaBLAST http://www.ncbi.nlm.nih.gov/blast/megablast.shtml and Bowtie http://bowtie bio.sourceforge.net/tutorial.shtml. To identify piRNAs consensus sequences from zebrafish repetitive elements were retrieved from Repbase http://www.girinst.org/repbase/index.html and Repeat Maskers using the UCSC genome browser http://genome.ucsc.edu. Small RNAs perfectly mapping to these consensus sequences and their genomic flanking regions were sorted into piRNA libraries with up to 3 genomic mapping positions for each unique RNA sequence. fasta files description: small RNA 15 30 nt alignment file description: piRNA map to repetitive elements	the whole embryo		Zebrafish embryos were collected at the 256 cell stage sphere stage shield stage and 1dpf. Total RNA was isolated from embryos using Trizol. RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified. cDNA libraries were generated using specific linkers and RT/PCR as previously described. Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.	Embryos were raised at 28Â°C in egg water 0.03% Instant Ocean marine salt mix for the initial several hours of development	strain:AB* WT\|developmental stage:256 cell\|tissue:the whole embryos	GSM686381	GSM686381: embryo 256 cell rep1; Danio rerio; ncRNA Seq	GSM686381		1	Zebrafish embryos were collected at the 256 cell stage sphere stage shield stage and 1dpf. Total RNA was isolated from embryos using Trizol. RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified. cDNA libraries were generated using specific linkers and RT/PCR as previously described. Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.	GEO Accession:GSM686381	ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II		SRP028895			GSM686381_256-cell_Raw.txt	fastq	177430716.0	4928631.0	GSM686381 r1	0:36	A:46047586;C:39494059;G:46591098;T:42305117;N:2992856	36		46047586	39494059	46591098	42305117	2992856	SRX336214	SRS471210	SRA098146	GEO	Lee Lab, Molecular Biology, Mass General Hospital	1	0.01914		0.01515		0.99164		0.52579		36		B		usable mapping rate	illumina	early_illumina	5prime	size_fractionation	unknown	bulk	unknown	unknown	United States	2011-03-07	Blastula	Embryo	Whole Organism	All anatomical structures
36278	36278	SRR352486	SRX100938	SRS266977	SRP008845	PRJNA146609	Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution	GSE32880	Other	Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs we used chromatin marks polyA site mapping and RNA Seq data to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs only 29 had detectable sequence similarity with putative mammalian orthologs typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3 H3K36me3 chromatin maps 3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome		pubmed:22196729		3P Seq Adult	GSM813764		source name:mixed gender adults\|tissue:whole adult\|developmental stage:mixed gender adults\|genotype:wt	3P Seq Adult	Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. GSE24924	mixed gender adults	For adult fish anesthetized fish were homogenized in the TissueRuptor Qiagen. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed and pellets were rinsed twice with PBS flash frozen in liquid nitrogen and stored at –80C.	3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html	Zebrafish embryos or adults grown under standard condition	tissue:whole adult\|developmental stage:mixed gender adults\|genotype:wt	GSM813764	GSM813764: 3P Seq Adult	GSM813764: 3P Seq Adult	GSM813764: 3P Seq Adult	1		GEO Accession:GSM813764	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP008845		read name barcode proc directive:ignore	3P_Seq_Adult.fastq	fastq	824962572.0	22915627.0	GSM813764 1	0:36	A:230176177;C:144743199;G:130818857;T:314618483;N:4605856	36		230176177	144743199	130818857	314618483	4605856	SRX100938	SRS266977	SRA047033	GEO	Whitehead Institute for Biomedical Research	1	0.64306		0.03985		0.78102		0.46237		36		B		usable mapping rate	illumina	early_illumina	3prime	size_fractionation	unknown	bulk	unknown	unknown	United States	2011-10-11	Adult	Adult	Whole Organism	All anatomical structures
36279	36279	SRR352485	SRX100937	SRS266976	SRP008845	PRJNA146609	Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution	GSE32880	Other	Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs we used chromatin marks polyA site mapping and RNA Seq data to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs only 29 had detectable sequence similarity with putative mammalian orthologs typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3 H3K36me3 chromatin maps 3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome		pubmed:22196729		3P Seq 72 hpf	GSM813763		tissue:whole embryo at 72 hpf embryo\|developmental stage:72 hpf	3P Seq 72 hpf	Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. GSE24924	whole embryo at 72 hpf	Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl 2.7 mM KCl 1.5 mM KH2PO4 8 mM Na2HP04 pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed and pellets were rinsed twice with PBS flash frozen in liquid nitrogen and stored at –80C.	3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html	Zebrafish embryos or adults grown under standard condition	tissue:whole embryo\|developmental stage:72 hpf	GSM813763	GSM813763: 3P Seq 72 hpf	GSM813763: 3P Seq 72 hpf	GSM813763: 3P Seq 72 hpf	1		GEO Accession:GSM813763	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP008845		read name barcode proc directive:ignore	3P_Seq_72hpf.fastq	fastq	875542968.0	24320638.0	GSM813763 1	0:36	A:246098313;C:139311840;G:129654215;T:353566279;N:6912321	36		246098313	139311840	129654215	353566279	6912321	SRX100937	SRS266976	SRA047033	GEO	Whitehead Institute for Biomedical Research	1	0.72092		0.09355		0.7601		0.4422		36		B		usable mapping rate	illumina	early_illumina	3prime	size_fractionation	unknown	bulk	unknown	unknown	United States	2011-10-11	Larval	Larval	Whole Organism	All anatomical structures
36280	36280	SRR352484	SRX100936	SRS266975	SRP008845	PRJNA146609	Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution	GSE32880	Other	Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs we used chromatin marks polyA site mapping and RNA Seq data to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs only 29 had detectable sequence similarity with putative mammalian orthologs typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3 H3K36me3 chromatin maps 3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome		pubmed:22196729		3P Seq 24 hpf	GSM813762		tissue:whole embryo at 24 hpf embryo\|developmental stage:24 hpf	3P Seq 24 hpf	Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. The BED file is as in Jan et al. GSE24924	whole embryo at 24 hpf	Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl 2.7 mM KCl 1.5 mM KH2PO4 8 mM Na2HP04 pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed and pellets were rinsed twice with PBS flash frozen in liquid nitrogen and stored at –80C.	3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html	Zebrafish embryos or adults grown under standard condition	tissue:whole embryo\|developmental stage:24 hpf	GSM813762	GSM813762: 3P Seq 24 hpf	GSM813762: 3P Seq 24 hpf	GSM813762: 3P Seq 24 hpf	1		GEO Accession:GSM813762	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP008845		read name barcode proc directive:ignore	3P_Seq_24hpf.fastq	fastq	951095592.0	26419322.0	GSM813762 1	0:36	A:261158914;C:169001356;G:163312440;T:350565754;N:7057128	36		261158914	169001356	163312440	350565754	7057128	SRX100936	SRS266975	SRA047033	GEO	Whitehead Institute for Biomedical Research												B		usable mapping rate	illumina	early_illumina	3prime	size_fractionation	unknown	bulk	unknown	unknown	United States	2011-10-11	Pharyngula	Embryo	Whole Organism	All anatomical structures
36281	36281	SRR352482	SRX100935	SRS266974	SRP008845	PRJNA146609	Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution	GSE32880	Other	Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs we used chromatin marks polyA site mapping and RNA Seq data to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs only 29 had detectable sequence similarity with putative mammalian orthologs typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3 H3K36me3 chromatin maps 3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome		pubmed:22196729		Strand specific RNA Seq 72 hpf	GSM813761		tissue:whole embryo at 72 hpf embryo\|developmental stage:72 hpf	Strand specific RNA Seq 72 hpf	Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie allowing for up to one mismatch and up to 4 genomic matches.	whole embryo at 72 hpf	Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl 2.7 mM KCl 1.5 mM KH2PO4 8 mM Na2HP04 pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed and pellets were rinsed twice with PBS flash frozen in liquid nitrogen and stored at –80C.	polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al 2010 GSE21992	Zebrafish embryos or adults grown under standard condition	tissue:whole embryo\|developmental stage:72 hpf	GSM813761	GSM813761: Strand specific RNA Seq 72 hpf	GSM813761: Strand specific RNA Seq 72 hpf	GSM813761: Strand specific RNA Seq 72 hpf	1		GEO Accession:GSM813761	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP008845		read name barcode proc directive:ignore	RNA_Seq_72hpf.1.fastq	fastq	734147136.0	20392976.0	GSM813761 1	0:36	A:175662892;C:172216317;G:208650086;T:171852136;N:5765705	36		175662892	172216317	208650086	171852136	5765705	SRX100935	SRS266974	SRA047033	GEO	Whitehead Institute for Biomedical Research	1	0.4603		0.10593		0.88274		0.59195		36		B		usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2011-10-11	Larval	Larval	Whole Organism	All anatomical structures
36282	36282	SRR352483	SRX100935	SRS266974	SRP008845	PRJNA146609	Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution	GSE32880	Other	Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs we used chromatin marks polyA site mapping and RNA Seq data to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs only 29 had detectable sequence similarity with putative mammalian orthologs typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3 H3K36me3 chromatin maps 3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome		pubmed:22196729		Strand specific RNA Seq 72 hpf	GSM813761		tissue:whole embryo at 72 hpf embryo\|developmental stage:72 hpf	Strand specific RNA Seq 72 hpf	Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie allowing for up to one mismatch and up to 4 genomic matches.	whole embryo at 72 hpf	Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl 2.7 mM KCl 1.5 mM KH2PO4 8 mM Na2HP04 pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed and pellets were rinsed twice with PBS flash frozen in liquid nitrogen and stored at –80C.	polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al 2010 GSE21992	Zebrafish embryos or adults grown under standard condition	tissue:whole embryo\|developmental stage:72 hpf	GSM813761	GSM813761: Strand specific RNA Seq 72 hpf	GSM813761: Strand specific RNA Seq 72 hpf	GSM813761: Strand specific RNA Seq 72 hpf	1		GEO Accession:GSM813761	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP008845		read name barcode proc directive:ignore	RNA_Seq_72hpf.2.fastq	fastq	924879168.0	25691088.0	GSM813761 2	0:36	A:218871678;C:217000200;G:266487098;T:214411336;N:8108856	36		218871678	217000200	266487098	214411336	8108856	SRX100935	SRS266974	SRA047033	GEO	Whitehead Institute for Biomedical Research	1	0.47296		0.10988		0.86397		0.59423		36		B		usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2011-10-11	Larval	Larval	Whole Organism	All anatomical structures
36283	36283	SRR352480	SRX100934	SRS266973	SRP008845	PRJNA146609	Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution	GSE32880	Other	Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs we used chromatin marks polyA site mapping and RNA Seq data to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs only 29 had detectable sequence similarity with putative mammalian orthologs typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3 H3K36me3 chromatin maps 3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome		pubmed:22196729		Strand specific RNA Seq 24 hpf	GSM813760		tissue:whole embryo at 24 hpf embryo\|developmental stage:24 hpf	Strand specific RNA Seq 24 hpf	Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie allowing for up to one mismatch and up to 4 genomic matches.	whole embryo at 24 hpf	Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl 2.7 mM KCl 1.5 mM KH2PO4 8 mM Na2HP04 pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed and pellets were rinsed twice with PBS flash frozen in liquid nitrogen and stored at –80C.	polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al 2010 GSE21992	Zebrafish embryos or adults grown under standard condition	tissue:whole embryo\|developmental stage:24 hpf	GSM813760	GSM813760: Strand specific RNA Seq 24 hpf	GSM813760: Strand specific RNA Seq 24 hpf	GSM813760: Strand specific RNA Seq 24 hpf	1		GEO Accession:GSM813760	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP008845		read name barcode proc directive:ignore	RNA_Seq_24hpf.1.fastq	fastq	759129588.0	21086933.0	GSM813760 1	0:36	A:169759696;C:187766678;G:221392768;T:174382883;N:5827563	36		169759696	187766678	221392768	174382883	5827563	SRX100934	SRS266973	SRA047033	GEO	Whitehead Institute for Biomedical Research	1	0.52959		0.10037		0.87014		0.61896		36		B		usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2011-10-11	Pharyngula	Embryo	Whole Organism	All anatomical structures
36284	36284	SRR352481	SRX100934	SRS266973	SRP008845	PRJNA146609	Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution	GSE32880	Other	Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs we used chromatin marks polyA site mapping and RNA Seq data to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs only 29 had detectable sequence similarity with putative mammalian orthologs typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3 H3K36me3 chromatin maps 3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome		pubmed:22196729		Strand specific RNA Seq 24 hpf	GSM813760		tissue:whole embryo at 24 hpf embryo\|developmental stage:24 hpf	Strand specific RNA Seq 24 hpf	Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie allowing for up to one mismatch and up to 4 genomic matches.	whole embryo at 24 hpf	Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl 2.7 mM KCl 1.5 mM KH2PO4 8 mM Na2HP04 pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed and pellets were rinsed twice with PBS flash frozen in liquid nitrogen and stored at –80C.	polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al 2010 GSE21992	Zebrafish embryos or adults grown under standard condition	tissue:whole embryo\|developmental stage:24 hpf	GSM813760	GSM813760: Strand specific RNA Seq 24 hpf	GSM813760: Strand specific RNA Seq 24 hpf	GSM813760: Strand specific RNA Seq 24 hpf	1		GEO Accession:GSM813760	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP008845		read name barcode proc directive:ignore	RNA_Seq_24hpf.2.fastq	fastq	916505136.0	25458476.0	GSM813760 2	0:36	A:203678661;C:227621613;G:269472018;T:207401580;N:8331264	36		203678661	227621613	269472018	207401580	8331264	SRX100934	SRS266973	SRA047033	GEO	Whitehead Institute for Biomedical Research	1	0.54008		0.10064		0.85425		0.61991		36		B		usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2011-10-11	Pharyngula	Embryo	Whole Organism	All anatomical structures
36731	36731	SRR836199	SRX272888	SRS417394	SRP021915	PRJNA200706	Ribosome Profiling over a Zebrafish Developmental Timecourse	GSE46512	Transcriptome Analysis	To experimentally validate the non coding status of annotated lncRNAs we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell 256 cell 1K cell Dome Shield Bud 28hpf and 5dpf		pubmed:23698349		20120724 RPF Seq 5dpf	GSM1131537		tissue:Whole embryos\|developmental stage:5 dpf molecule:ribosome footprinted RNA	20120724 RPF Seq 5dpf	Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2 N 1 L 20 k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels no novel junctions M g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs +13 for 29 31nt RPFs +13 for 29 31nt RPFs +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes	Whole embryos	Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen	Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011	400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995	developmental stage:5 dpf molecule:ribosome footprinted RNA	GSM1131537	GSM1131537: 20120724 RPF Seq 5dpf; Danio rerio; RNA Seq	GSM1131537 1		1	Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011	GEO Accession:GSM1131537	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP021915			20120724_RPF-Seq_5dpf.fastq.gz	fastq	5339394852.0	121349883.0	GSM1131537 r1	0:44	A:993131212;C:1552513636;G:1792926993;T:1000757523;N:65488	44		993131212	1552513636	1792926993	1000757523	65488	SRX272888	SRS417394	SRA075002	GEO	Schier, Dept of Molecular and Cellular Biology, Harvard University	1	0.04708		0.00988		0.99774		0.7502		44		B		usable mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	United States	2013-04-30	Larval	Larval	Whole Organism	All anatomical structures
36732	36732	SRR836198	SRX272887	SRS417393	SRP021915	PRJNA200706	Ribosome Profiling over a Zebrafish Developmental Timecourse	GSE46512	Transcriptome Analysis	To experimentally validate the non coding status of annotated lncRNAs we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell 256 cell 1K cell Dome Shield Bud 28hpf and 5dpf		pubmed:23698349		20120724 RPF Seq 28hpf	GSM1131536		tissue:Whole embryos\|developmental stage:28 hpf molecule:ribosome footprinted RNA	20120724 RPF Seq 28hpf	Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2 N 1 L 20 k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels no novel junctions M g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs +13 for 29 31nt RPFs +13 for 29 31nt RPFs +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes	Whole embryos	Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen	Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011	400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995	developmental stage:28 hpf molecule:ribosome footprinted RNA	GSM1131536	GSM1131536: 20120724 RPF Seq 28hpf; Danio rerio; RNA Seq	GSM1131536 1		1	Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011	GEO Accession:GSM1131536	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP021915			20120724_RPF-Seq_28hpf.fastq.gz	fastq	5844769480.0	132835670.0	GSM1131536 r1	0:44	A:967687923;C:1803414766;G:2048220630;T:1024594100;N:852061	44		967687923	1803414766	2048220630	1024594100	852061	SRX272887	SRS417393	SRA075002	GEO	Schier, Dept of Molecular and Cellular Biology, Harvard University	1	0.054		0.00377		0.99762		0.77752		44		B		usable mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	United States	2013-04-30	Pharyngula	Embryo	Whole Organism	All anatomical structures
36733	36733	SRR836197	SRX272886	SRS417392	SRP021915	PRJNA200706	Ribosome Profiling over a Zebrafish Developmental Timecourse	GSE46512	Transcriptome Analysis	To experimentally validate the non coding status of annotated lncRNAs we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell 256 cell 1K cell Dome Shield Bud 28hpf and 5dpf		pubmed:23698349		20120724 RPF Seq Bud	GSM1131535		tissue:Whole embryos\|developmental stage:Bud\|strain:TL/AB\|target molecule:ribosome footprinted RNA	20120724 RPF Seq Bud	Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2 N 1 L 20 k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels no novel junctions M g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs +13 for 29 31nt RPFs +13 for 29 31nt RPFs +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes	Whole embryos	Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen	Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011	400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995	developmental stage:Bud\|strain:TL/AB\|target molecule:ribosome footprinted RNA	GSM1131535	GSM1131535: 20120724 RPF Seq Bud; Danio rerio; RNA Seq	GSM1131535 1		1	Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011	GEO Accession:GSM1131535	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP021915			20120724_RPF-Seq_Bud.fastq.gz	fastq	5245678988.0	119219977.0	GSM1131535 r1	0:44	A:785136766;C:1705642298;G:1892015387;T:862815185;N:69352	44		785136766	1705642298	1892015387	862815185	69352	SRX272886	SRS417392	SRA075002	GEO	Schier, Dept of Molecular and Cellular Biology, Harvard University	1	0.0214		0.00105		0.99823		0.906		44		B		usable mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	United States	2013-04-30	Undetermined	Embryo	Whole Organism	All anatomical structures
36734	36734	SRR836196	SRX272885	SRS417391	SRP021915	PRJNA200706	Ribosome Profiling over a Zebrafish Developmental Timecourse	GSE46512	Transcriptome Analysis	To experimentally validate the non coding status of annotated lncRNAs we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell 256 cell 1K cell Dome Shield Bud 28hpf and 5dpf		pubmed:23698349		20120724 RPF Seq Shield	GSM1131534		tissue:Whole embryos\|developmental stage:Shield\|strain:TL/AB\|target molecule:ribosome footprinted RNA	20120724 RPF Seq Shield	Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2 N 1 L 20 k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels no novel junctions M g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs +13 for 29 31nt RPFs +13 for 29 31nt RPFs +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes	Whole embryos	Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen	Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011	400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995	developmental stage:Shield\|strain:TL/AB\|target molecule:ribosome footprinted RNA	GSM1131534	GSM1131534: 20120724 RPF Seq Shield; Danio rerio; RNA Seq	GSM1131534 1		1	Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011	GEO Accession:GSM1131534	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP021915			20120724_RPF-Seq_Shield.fastq.gz	fastq	5407148516.0	122889739.0	GSM1131534 r1	0:44	A:1112688703;C:1598204601;G:1639649897;T:1055648833;N:956482	44		1112688703	1598204601	1639649897	1055648833	956482	SRX272885	SRS417391	SRA075002	GEO	Schier, Dept of Molecular and Cellular Biology, Harvard University	1	0.01533		0.0016		0.99864		0.73416		44		B		usable mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	United States	2013-04-30	Gastrula	Embryo	Whole Organism	All anatomical structures
36735	36735	SRR836195	SRX272884	SRS417390	SRP021915	PRJNA200706	Ribosome Profiling over a Zebrafish Developmental Timecourse	GSE46512	Transcriptome Analysis	To experimentally validate the non coding status of annotated lncRNAs we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell 256 cell 1K cell Dome Shield Bud 28hpf and 5dpf		pubmed:23698349		20120724 RPF Seq Dome	GSM1131533		tissue:Whole embryos\|developmental stage:Dome\|strain:TL/AB\|target molecule:ribosome footprinted RNA	20120724 RPF Seq Dome	Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2 N 1 L 20 k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels no novel junctions M g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs +13 for 29 31nt RPFs +13 for 29 31nt RPFs +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes	Whole embryos	Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen	Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011	400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995	developmental stage:Dome\|strain:TL/AB\|target molecule:ribosome footprinted RNA	GSM1131533	GSM1131533: 20120724 RPF Seq Dome; Danio rerio; RNA Seq	GSM1131533 1		1	Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011	GEO Accession:GSM1131533	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP021915			20120724_RPF-Seq_Dome.fastq.gz	fastq	5455941832.0	123998678.0	GSM1131533 r1	0:44	A:1174530251;C:1596486361;G:1605087499;T:1077423125;N:2414596	44		1174530251	1596486361	1605087499	1077423125	2414596	SRX272884	SRS417390	SRA075002	GEO	Schier, Dept of Molecular and Cellular Biology, Harvard University	1	0.00739		0.0007		0.99898		0.86907		44		T		under 1.2% mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	United States	2013-04-30	Blastula	Embryo	Whole Organism	All anatomical structures
36736	36736	SRR836194	SRX272883	SRS417389	SRP021915	PRJNA200706	Ribosome Profiling over a Zebrafish Developmental Timecourse	GSE46512	Transcriptome Analysis	To experimentally validate the non coding status of annotated lncRNAs we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell 256 cell 1K cell Dome Shield Bud 28hpf and 5dpf		pubmed:23698349		20120724 RPF Seq 1KCell	GSM1131532		tissue:Whole embryos\|developmental stage:1k cells\|strain:TL/AB\|target molecule:ribosome footprinted RNA	20120724 RPF Seq 1KCell	Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2 N 1 L 20 k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels no novel junctions M g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs +13 for 29 31nt RPFs +13 for 29 31nt RPFs +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes	Whole embryos	Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen	Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011	400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995	developmental stage:1k cells\|strain:TL/AB\|target molecule:ribosome footprinted RNA	GSM1131532	GSM1131532: 20120724 RPF Seq 1KCell; Danio rerio; RNA Seq	GSM1131532 1		1	Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011	GEO Accession:GSM1131532	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP021915			20120724_RPF-Seq_1KCell.fastq.gz	fastq	6177670620.0	140401605.0	GSM1131532 r1	0:44	A:1115906097;C:1874096579;G:1974799887;T:1211772717;N:1095340	44		1115906097	1874096579	1974799887	1211772717	1095340	SRX272883	SRS417389	SRA075002	GEO	Schier, Dept of Molecular and Cellular Biology, Harvard University	1	0.02237		0.00392		0.99847		0.87194		44		B		usable mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	United States	2013-04-30	Blastula	Embryo	Whole Organism	All anatomical structures
36737	36737	SRR836193	SRX272882	SRS417388	SRP021915	PRJNA200706	Ribosome Profiling over a Zebrafish Developmental Timecourse	GSE46512	Transcriptome Analysis	To experimentally validate the non coding status of annotated lncRNAs we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell 256 cell 1K cell Dome Shield Bud 28hpf and 5dpf		pubmed:23698349		20120724 RPF Seq 256Cell	GSM1131531		tissue:Whole embryos\|developmental stage:256 cells\|strain:TL/AB\|target molecule:ribosome footprinted RNA	20120724 RPF Seq 256Cell	Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2 N 1 L 20 k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels no novel junctions M g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs +13 for 29 31nt RPFs +13 for 29 31nt RPFs +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes	Whole embryos	Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen	Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011	400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995	developmental stage:256 cells\|strain:TL/AB\|target molecule:ribosome footprinted RNA	GSM1131531	GSM1131531: 20120724 RPF Seq 256Cell; Danio rerio; RNA Seq	GSM1131531 1		1	Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011	GEO Accession:GSM1131531	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP021915			20120724_RPF-Seq_256Cell.fastq.gz	fastq	5883566700.0	133717425.0	GSM1131531 r1	0:44	A:1010263447;C:1822722383;G:1960819573;T:1088614485;N:1146812	44		1010263447	1822722383	1960819573	1088614485	1146812	SRX272882	SRS417388	SRA075002	GEO	Schier, Dept of Molecular and Cellular Biology, Harvard University	1	0.02862		0.0036		0.99837		0.90559		44		B		usable mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	United States	2013-04-30	Blastula	Embryo	Whole Organism	All anatomical structures
36738	36738	SRR836192	SRX272881	SRS417387	SRP021915	PRJNA200706	Ribosome Profiling over a Zebrafish Developmental Timecourse	GSE46512	Transcriptome Analysis	To experimentally validate the non coding status of annotated lncRNAs we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell 256 cell 1K cell Dome Shield Bud 28hpf and 5dpf		pubmed:23698349		20120724 RPF Seq 2 4Cell	GSM1131530		tissue:Whole embryos\|developmental stage:2 4 cells\|strain:TL/AB\|target molecule:ribosome footprinted RNA	20120724 RPF Seq 2 4Cell	Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2 N 1 L 20 k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels no novel junctions M g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs +13 for 29 31nt RPFs +13 for 29 31nt RPFs +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes	Whole embryos	Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen	Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011	400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995	developmental stage:2 4 cells\|strain:TL/AB\|target molecule:ribosome footprinted RNA	GSM1131530	GSM1131530: 20120724 RPF Seq 2 4Cell; Danio rerio; RNA Seq	GSM1131530 1		1	Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011	GEO Accession:GSM1131530	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP021915			20120724_RPF-Seq_2-4Cell.fastq.gz	fastq	1568173420.0	35640305.0	GSM1131530 r1	0:44	A:256220962;C:489258424;G:538563811;T:283859833;N:270390	44		256220962	489258424	538563811	283859833	270390	SRX272881	SRS417387	SRA075002	GEO	Schier, Dept of Molecular and Cellular Biology, Harvard University	1	0.0297		0.00558		0.99821		0.89066		44		B		usable mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	United States	2013-04-30	Cleavage	Embryo	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
41244	41244	SRR3953261	SRX1977497	SRS1585138	SRP079896	PRJNA335352	Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment	GSE84845	Transcriptome Analysis	Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control a dozen of validated zebrafish miRNAs including dre miR 142a 3p dre miR 142b 5p dre miR 144 3p dre miR 146a dre miR 190a dre miR 219 5p dre miR 301b 3p dre miR 459 5p rno miR 33 5p dre miR 735 3p and dre miR 735 5p significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank vehicle and 2 different concentrations of BDE47 treatments.		pubmed:28072866		500 μg/l BDE47 treatment miRNA	GSM2252184		source name:6 dpf larvae\|strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	500 μg/l BDE47 treatment miRNA	Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.	6 dpf larvae		Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.		strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	GSM2252184	GSM2252184: 500 μg/l BDE47 treatment miRNA; Danio rerio; miRNA Seq	GSM2252184		1	Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2252184	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP079896			Sample_500_1_filtered.fastq.gz	fastq	427211416.0	18037304.0	GSM2252184 r1	0:23.68 1:0	A:104654735;C:95575450;G:107353019;T:119612667;N:15545	23	0	104654735	95575450	107353019	119612667	15545	SRX1977497	SRS1585138	SRA444471	GEO	Tongji University	1	0.85356		0.06282		0.88609		0.63407		21		B		usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	China	2016-07-26	Larval	Larval	Whole Organism	All anatomical structures
41245	41245	SRR3953260	SRX1977496	SRS1585141	SRP079896	PRJNA335352	Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment	GSE84845	Transcriptome Analysis	Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control a dozen of validated zebrafish miRNAs including dre miR 142a 3p dre miR 142b 5p dre miR 144 3p dre miR 146a dre miR 190a dre miR 219 5p dre miR 301b 3p dre miR 459 5p rno miR 33 5p dre miR 735 3p and dre miR 735 5p significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank vehicle and 2 different concentrations of BDE47 treatments.		pubmed:28072866		5 μg/l BDE47 treatment miRNA	GSM2252183		source name:6 dpf larvae\|strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	5 μg/l BDE47 treatment miRNA	Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.	6 dpf larvae		Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.		strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	GSM2252183	GSM2252183: 5 μg/l BDE47 treatment miRNA; Danio rerio; miRNA Seq	GSM2252183		1	Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2252183	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP079896			Sample_5_1_filtered.fastq.gz	fastq	450698842.0	19202408.0	GSM2252183 r1	0:23.47 1:0	A:112159775;C:101086362;G:111723361;T:125713845;N:15499	23	0	112159775	101086362	111723361	125713845	15499	SRX1977496	SRS1585141	SRA444471	GEO	Tongji University	1	0.84838		0.06014		0.88637		0.6441		23		B		usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	China	2016-07-26	Larval	Larval	Whole Organism	All anatomical structures
41246	41246	SRR3953259	SRX1977495	SRS1585136	SRP079896	PRJNA335352	Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment	GSE84845	Transcriptome Analysis	Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control a dozen of validated zebrafish miRNAs including dre miR 142a 3p dre miR 142b 5p dre miR 144 3p dre miR 146a dre miR 190a dre miR 219 5p dre miR 301b 3p dre miR 459 5p rno miR 33 5p dre miR 735 3p and dre miR 735 5p significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank vehicle and 2 different concentrations of BDE47 treatments.		pubmed:28072866		s DMSO vehicle miRNA	GSM2252182		source name:6 dpf larvae\|strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	s DMSO vehicle miRNA	Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.	6 dpf larvae		Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.		strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	GSM2252182	GSM2252182: s DMSO vehicle miRNA; Danio rerio; miRNA Seq	GSM2252182		1	Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2252182	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP079896			Sample_s_1_filtered.fq.gz	fastq	383701320.0	16988819.0	GSM2252182 r1	0:22.59 1:0	A:97700155;C:85144858;G:93319367;T:107531046;N:5894	22	0	97700155	85144858	93319367	107531046	5894	SRX1977495	SRS1585136	SRA444471	GEO	Tongji University	1	0.86023		0.05501		0.89534		0.59715		22		B		usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	China	2016-07-26	Larval	Larval	Whole Organism	All anatomical structures
41247	41247	SRR3953258	SRX1977494	SRS1585137	SRP079896	PRJNA335352	Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment	GSE84845	Transcriptome Analysis	Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control a dozen of validated zebrafish miRNAs including dre miR 142a 3p dre miR 142b 5p dre miR 144 3p dre miR 146a dre miR 190a dre miR 219 5p dre miR 301b 3p dre miR 459 5p rno miR 33 5p dre miR 735 3p and dre miR 735 5p significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank vehicle and 2 different concentrations of BDE47 treatments.		pubmed:28072866		c Wildtype miRNA	GSM2252181		source name:6 dpf larvae\|strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	c Wildtype miRNA	Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.	6 dpf larvae		Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.		strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	GSM2252181	GSM2252181: c Wildtype miRNA; Danio rerio; miRNA Seq	GSM2252181		1	Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2252181	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP079896			Sample_c_1_filtered.fastq.gz	fastq	413922462.0	17365113.0	GSM2252181 r1	0:23.84 1:0	A:102173642;C:93233248;G:103684592;T:114815345;N:15635	23	0	102173642	93233248	103684592	114815345	15635	SRX1977494	SRS1585137	SRA444471	GEO	Tongji University	1	0.85083		0.06831		0.88152		0.63274		27		B		usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	China	2016-07-26	Larval	Larval	Whole Organism	All anatomical structures
53033	53033	SRR9674344	SRX6434730	SRS5089289	SRP214428	PRJNA554249	the role of SMN complex in tissue regeneration	GSE134187	Transcriptome Analysis	we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.				rnpc3 WT 1 [miRNA seq]	GSM3938561		source name:Wildtype siblings of rnpc3 mutants repeat 1\|strain background:TAB 5\|genotype/variation:Wildtype siblings of rnpc3 mutants\|Stage:7 dpf\|tissue:whole fish embryos	rnpc3 WT 1 [miRNA seq]	Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or "hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary" miRNA abundance is measured by RSEM "rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output" for mRNA Seq "rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance	Wildtype siblings of rnpc3 mutants repeat 1		Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols		strain background:TAB 5\|genotype/variation:Wildtype siblings of rnpc3 mutants\|Stage:7 dpf\|tissue:whole fish embryos	GSM3938561	GSM3938561: rnpc3 WT 1 [miRNA seq]; Danio rerio; miRNA Seq	GSM3938561		1	Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3938561	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP214428			mir_Rpc3_1Ctrl.fastq.gz	fastq	1129597674.0	22148974.0	GSM3938561 r1	0:51	A:255811479;C:280511308;G:313965625;T:279284342;N:24920	51		255811479	280511308	313965625	279284342	24920	SRX6434730	SRS5089289	SRA920248	GEO	Burgess, NHGRI, NIH	1	0.00979		0.00166		0.99588		0.63728		51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	bulk	bulk	United States	2019-07-12	Larval	Larval	Whole Organism	All anatomical structures
53034	53034	SRR9674343	SRX6434729	SRS5089288	SRP214428	PRJNA554249	the role of SMN complex in tissue regeneration	GSE134187	Transcriptome Analysis	we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.				smn1 WT 1 [miRNA seq]	GSM3938560		source name:Wildtype siblings of smn1 mutants repeat 1\|strain background:TAB 5\|genotype/variation:Wildtype siblings of smn1 mutants\|Stage:7 dpf\|tissue:whole fish embryos	smn1 WT 1 [miRNA seq]	Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or "hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary" miRNA abundance is measured by RSEM "rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output" for mRNA Seq "rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance	Wildtype siblings of smn1 mutants repeat 1		Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols		strain background:TAB 5\|genotype/variation:Wildtype siblings of smn1 mutants\|Stage:7 dpf\|tissue:whole fish embryos	GSM3938560	GSM3938560: smn1 WT 1 [miRNA seq]; Danio rerio; miRNA Seq	GSM3938560		1	Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3938560	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP214428			mir_Smn1_1Ctrl.fastq.gz	fastq	1381751976.0	27093176.0	GSM3938560 r1	0:51	A:323091185;C:348663819;G:380517013;T:329446099;N:33860	51		323091185	348663819	380517013	329446099	33860	SRX6434729	SRS5089288	SRA920248	GEO	Burgess, NHGRI, NIH	1	0.00712		0.00142		0.99642		0.66315		51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	bulk	bulk	United States	2019-07-12	Larval	Larval	Whole Organism	All anatomical structures
53035	53035	SRR9674342	SRX6434728	SRS5089287	SRP214428	PRJNA554249	the role of SMN complex in tissue regeneration	GSE134187	Transcriptome Analysis	we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.				gemin5 WT 1 [miRNA seq]	GSM3938559		source name:Wildtype siblings of germin5 mutants repeat 1\|strain background:TAB 5\|genotype/variation:Wildtype siblings of germin5 mutants\|Stage:7 dpf\|tissue:whole fish embryos	gemin5 WT 1 [miRNA seq]	Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or "hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary" miRNA abundance is measured by RSEM "rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output" for mRNA Seq "rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance	Wildtype siblings of germin5 mutants repeat 1		Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols		strain background:TAB 5\|genotype/variation:Wildtype siblings of germin5 mutants\|Stage:7 dpf\|tissue:whole fish embryos	GSM3938559	GSM3938559: gemin5 WT 1 [miRNA seq]; Danio rerio; miRNA Seq	GSM3938559		1	Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3938559	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP214428			mir_Gmn5_1Ctrl.fastq.gz	fastq	1347630171.0	26424121.0	GSM3938559 r1	0:51	A:307019777;C:335315873;G:378259746;T:327002846;N:31929	51		307019777	335315873	378259746	327002846	31929	SRX6434728	SRS5089287	SRA920248	GEO	Burgess, NHGRI, NIH	1	0.00723		0.00127		0.99582		0.63934		51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	bulk	bulk	United States	2019-07-12	Larval	Larval	Whole Organism	All anatomical structures
53036	53036	SRR9674341	SRX6434727	SRS5089286	SRP214428	PRJNA554249	the role of SMN complex in tissue regeneration	GSE134187	Transcriptome Analysis	we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.				smn1 hom 3 [miRNA seq]	GSM3938558		source name:Homozygous smn1 mutants repeat 3\|strain background:TAB 5\|genotype/variation:Homozygous smn1 mutants\|Stage:7 dpf\|tissue:whole fish embryos	smn1 hom 3 [miRNA seq]	Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or "hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary" miRNA abundance is measured by RSEM "rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output" for mRNA Seq "rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance	Homozygous smn1 mutants repeat 3		Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols		strain background:TAB 5\|genotype/variation:Homozygous smn1 mutants\|Stage:7 dpf\|tissue:whole fish embryos	GSM3938558	GSM3938558: smn1 hom 3 [miRNA seq]; Danio rerio; miRNA Seq	GSM3938558		1	Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3938558	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP214428			mir_Smn1_3hom.fastq.gz	fastq	1269172638.0	24885738.0	GSM3938558 r1	0:51	A:290351922;C:320656517;G:354834895;T:303300306;N:28998	51		290351922	320656517	354834895	303300306	28998	SRX6434727	SRS5089286	SRA920248	GEO	Burgess, NHGRI, NIH	1	0.0061		0.00111		0.9962		0.5917		51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	bulk	bulk	United States	2019-07-12	Larval	Larval	Whole Organism	All anatomical structures
53037	53037	SRR9674340	SRX6434726	SRS5089285	SRP214428	PRJNA554249	the role of SMN complex in tissue regeneration	GSE134187	Transcriptome Analysis	we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.				smn1 hom 2 [miRNA seq]	GSM3938557		source name:Homozygous smn1 mutants repeat 2\|strain background:TAB 5\|genotype/variation:Homozygous smn1 mutants\|Stage:7 dpf\|tissue:whole fish embryos	smn1 hom 2 [miRNA seq]	Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or "hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary" miRNA abundance is measured by RSEM "rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output" for mRNA Seq "rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance	Homozygous smn1 mutants repeat 2		Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols		strain background:TAB 5\|genotype/variation:Homozygous smn1 mutants\|Stage:7 dpf\|tissue:whole fish embryos	GSM3938557	GSM3938557: smn1 hom 2 [miRNA seq]; Danio rerio; miRNA Seq	GSM3938557		1	Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3938557	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP214428			mir_Smn1_2hom.fastq.gz	fastq	1625802786.0	31878486.0	GSM3938557 r1	0:51	A:376836190;C:399950981;G:453572869;T:395403783;N:38963	51		376836190	399950981	453572869	395403783	38963	SRX6434726	SRS5089285	SRA920248	GEO	Burgess, NHGRI, NIH	1	0.00609		0.00111		0.99638		0.63347		51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	bulk	bulk	United States	2019-07-12	Larval	Larval	Whole Organism	All anatomical structures
53038	53038	SRR9674339	SRX6434725	SRS5089284	SRP214428	PRJNA554249	the role of SMN complex in tissue regeneration	GSE134187	Transcriptome Analysis	we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.				smn1 hom 1 [miRNA seq]	GSM3938556		source name:Homozygous smn1 mutants repeat 1\|strain background:TAB 5\|genotype/variation:Homozygous smn1 mutants\|Stage:7 dpf\|tissue:whole fish embryos	smn1 hom 1 [miRNA seq]	Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or "hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary" miRNA abundance is measured by RSEM "rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output" for mRNA Seq "rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance	Homozygous smn1 mutants repeat 1		Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols		strain background:TAB 5\|genotype/variation:Homozygous smn1 mutants\|Stage:7 dpf\|tissue:whole fish embryos	GSM3938556	GSM3938556: smn1 hom 1 [miRNA seq]; Danio rerio; miRNA Seq	GSM3938556		1	Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3938556	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP214428			mir_Smn1_1hom.fastq.gz	fastq	1553527320.0	30461320.0	GSM3938556 r1	0:51	A:360279409;C:388795394;G:432335873;T:372080058;N:36586	51		360279409	388795394	432335873	372080058	36586	SRX6434725	SRS5089284	SRA920248	GEO	Burgess, NHGRI, NIH	1	0.00691		0.00137		0.99638		0.61909		51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	bulk	bulk	United States	2019-07-12	Larval	Larval	Whole Organism	All anatomical structures
53039	53039	SRR9674338	SRX6434724	SRS5089283	SRP214428	PRJNA554249	the role of SMN complex in tissue regeneration	GSE134187	Transcriptome Analysis	we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.				gemin5 hom 3 [miRNA seq]	GSM3938555		source name:Homozygous gemin5 mutants repeat 3\|strain background:TAB 5\|genotype/variation:Homozygous gemin5 mutants\|Stage:7 dpf\|tissue:whole fish embryos	gemin5 hom 3 [miRNA seq]	Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or "hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary" miRNA abundance is measured by RSEM "rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output" for mRNA Seq "rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance	Homozygous gemin5 mutants repeat 3		Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols		strain background:TAB 5\|genotype/variation:Homozygous gemin5 mutants\|Stage:7 dpf\|tissue:whole fish embryos	GSM3938555	GSM3938555: gemin5 hom 3 [miRNA seq]; Danio rerio; miRNA Seq	GSM3938555		1	Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3938555	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP214428			mir_Gmn5_3hom.fastq.gz	fastq	1162857936.0	22801136.0	GSM3938555 r1	0:51	A:267576310;C:282684680;G:327841913;T:284728561;N:26472	51		267576310	282684680	327841913	284728561	26472	SRX6434724	SRS5089283	SRA920248	GEO	Burgess, NHGRI, NIH	1	0.00597		0.00114		0.99618		0.62386		51		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	bulk	bulk	United States	2019-07-12	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");;