metadata: run_metadata: 10 rows where devstage_curation = "Larval" and tissue

10 rows where devstage_curation = "Larval" and tissue_curation = "Pancreas"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	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.study_ref	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
51051	51051	SRR8456909	SRX5263565	SRS4264370	SRP180299	PRJNA515911	Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish	GSE125354	Transcriptome Analysis	Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish Overall design: RNA seq of beta cells isolated from either wildtype or alms1 mutant zebrafish	pubmed:31324766	alms1MUT 2	GSM3569389	tissue:beta cells\|cell marker:FACS isolated mCherry+ cells\|cell type:beta cell enriched\|genotype:alms1 / \|age:5 dpf	alms1MUT 2	trimmed to remove low quality bases at ends mapping to ref genome using CLC Genomics Workbench v 10.0.1 calculated total gene hit counts and RPKM values Genome build: GRCz10 Supplementary files format and content: tab delineated text files of gene expression for each sample set	beta cells	single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices.	5 dpf zebrafish animals of either Tgins:mCherry or alms1 mutants carrying Tgins:mCherry	cell marker:FACS isolated mCherry+ cells\|cell type:beta cell enriched\|genotype:alms1 / \|age:5 dpf	GSM3569389	GSM3569389: alms1MUT 2; Danio rerio; RNA Seq	GSM3569389		1	single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices.	GEO Accession:GSM3569389	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP180299	alms1MUT-2_S204_R1_001.fastq.gz alms1MUT-2_S204_R2_001.fastq.gz	fastq fastq	34706891262.0	114923481.0	GSM3569389 r1	0:151 1:151	A:9976818172;C:7360068941;G:7101573916;T:10265591911;N:2838322	151	151	9976818172	7360068941	7101573916	10265591911	2838322	SRX5263565	SRS4264370	SRA836454	GEO	Medicine, University of Maryland School of Medicine	2	0.87723	0.87816	0.52783	0.53313	0.6729	0.69288	0.50497	0.5044	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	United States	2019-01-18	Larval	Larval	Pancreas	Endocrine System
51052	51052	SRR8456908	SRX5263564	SRS4264369	SRP180299	PRJNA515911	Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish	GSE125354	Transcriptome Analysis	Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish Overall design: RNA seq of beta cells isolated from either wildtype or alms1 mutant zebrafish	pubmed:31324766	alms1MUT 1	GSM3569388	tissue:beta cells\|cell marker:FACS isolated mCherry+ cells\|cell type:beta cell enriched\|genotype:alms1 / \|age:5 dpf	alms1MUT 1	trimmed to remove low quality bases at ends mapping to ref genome using CLC Genomics Workbench v 10.0.1 calculated total gene hit counts and RPKM values Genome build: GRCz10 Supplementary files format and content: tab delineated text files of gene expression for each sample set	beta cells	single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices.	5 dpf zebrafish animals of either Tgins:mCherry or alms1 mutants carrying Tgins:mCherry	cell marker:FACS isolated mCherry+ cells\|cell type:beta cell enriched\|genotype:alms1 / \|age:5 dpf	GSM3569388	GSM3569388: alms1MUT 1; Danio rerio; RNA Seq	GSM3569388		1	single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices.	GEO Accession:GSM3569388	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP180299	alms1MUT-1_S203_R1_001.fastq.gz alms1MUT-1_S203_R2_001.fastq.gz	fastq fastq	31132041158.0	103086229.0	GSM3569388 r1	0:151 1:151	A:8977930028;C:6567587111;G:6338188683;T:9245824930;N:2510406	151	151	8977930028	6567587111	6338188683	9245824930	2510406	SRX5263564	SRS4264369	SRA836454	GEO	Medicine, University of Maryland School of Medicine	2	0.87391	0.87469	0.49807	0.50313	0.68947	0.70449	0.51756	0.50827	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	United States	2019-01-18	Larval	Larval	Pancreas	Endocrine System
51053	51053	SRR8456907	SRX5263563	SRS4264368	SRP180299	PRJNA515911	Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish	GSE125354	Transcriptome Analysis	Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish Overall design: RNA seq of beta cells isolated from either wildtype or alms1 mutant zebrafish	pubmed:31324766	WT 2	GSM3569387	tissue:beta cells\|cell marker:FACS isolated mCherry+ cells\|cell type:beta cell enriched\|genotype:wildtype\|age:5 dpf	WT 2	trimmed to remove low quality bases at ends mapping to ref genome using CLC Genomics Workbench v 10.0.1 calculated total gene hit counts and RPKM values Genome build: GRCz10 Supplementary files format and content: tab delineated text files of gene expression for each sample set	beta cells	single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices.	5 dpf zebrafish animals of either Tgins:mCherry or alms1 mutants carrying Tgins:mCherry	cell marker:FACS isolated mCherry+ cells\|cell type:beta cell enriched\|genotype:wildtype\|age:5 dpf	GSM3569387	GSM3569387: WT 2; Danio rerio; RNA Seq	GSM3569387		1	single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices.	GEO Accession:GSM3569387	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP180299	WT-2_S202_R1_001.fastq.gz WT-2_S202_R2_001.fastq.gz	fastq fastq	33558516632.0	111120916.0	GSM3569387 r1	0:151 1:151	A:9387420547;C:7359835200;G:7201488528;T:9607046373;N:2725984	151	151	9387420547	7359835200	7201488528	9607046373	2725984	SRX5263563	SRS4264368	SRA836454	GEO	Medicine, University of Maryland School of Medicine	2	0.90113	0.9024	0.21941	0.22244	0.69572	0.70621	0.51483	0.51186	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	United States	2019-01-18	Larval	Larval	Pancreas	Endocrine System
51054	51054	SRR8456906	SRX5263562	SRS4264367	SRP180299	PRJNA515911	Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish	GSE125354	Transcriptome Analysis	Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish Overall design: RNA seq of beta cells isolated from either wildtype or alms1 mutant zebrafish	pubmed:31324766	WT 1	GSM3569386	tissue:beta cells\|cell marker:FACS isolated mCherry+ cells\|cell type:beta cell enriched\|genotype:wildtype\|age:5 dpf	WT 1	trimmed to remove low quality bases at ends mapping to ref genome using CLC Genomics Workbench v 10.0.1 calculated total gene hit counts and RPKM values Genome build: GRCz10 Supplementary files format and content: tab delineated text files of gene expression for each sample set	beta cells	single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices.	5 dpf zebrafish animals of either Tgins:mCherry or alms1 mutants carrying Tgins:mCherry	cell marker:FACS isolated mCherry+ cells\|cell type:beta cell enriched\|genotype:wildtype\|age:5 dpf	GSM3569386	GSM3569386: WT 1; Danio rerio; RNA Seq	GSM3569386		1	single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices.	GEO Accession:GSM3569386	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP180299	WT-1_S201_R1_001.fastq.gz WT-1_S201_R2_001.fastq.gz	fastq fastq	35627069558.0	117970429.0	GSM3569386 r1	0:151 1:151	A:9789934413;C:8039430934;G:7849037733;T:9945758380;N:2908098	151	151	9789934413	8039430934	7849037733	9945758380	2908098	SRX5263562	SRS4264367	SRA836454	GEO	Medicine, University of Maryland School of Medicine	2	0.91881	0.91874	0.23468	0.24084	0.66616	0.67969	0.46826	0.46848	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	United States	2019-01-18	Larval	Larval	Pancreas	Endocrine System
64122	64122	SRR14272168	SRX10633820	SRS8730202	SRP315319	PRJNA722925	Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation	PRJNA722925	Other	Diabetes can be caused by an insufficiency in beta cell mass. Here we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets the increased beta cell differentiation originated from ductal cells. Mechanistically comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine carnitine and serine pathways. Overall our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.		Pancreas islets Pancreas islet 6dpf B2	Pancreas islets Islet 6d B2 AGN000787	strain:TU/AB\|age:not applicable\|dev stage:Day 6\|sex:pooled male and female\|tissue:pancreas\|molecule:mRNA\|selection:pA\|sample ref:AGS000684\|replicate ref:AGN000787\|replicate order:2\|BioSampleModel:Model organism or animal								Pancreas islets Pancreas islet 6dpf B2	AGR001074	AGR001074	mRNA			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP315319	AGR001074_R1.fastq.gz	fastq	467368080.0	6149580.0	AGR001074 R1.fastq.gz	0:76 1:0	A:144866246;C:90980862;G:90828673;T:140671264;N:21035	76	0	144866246	90980862	90828673	140671264	21035	SRX10633820	SRS8730202	SRA1220217	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.86223		0.47625		0.68556		0.52132		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2021-04-19	Larval	Larval	Pancreas	Endocrine System
64123	64123	SRR14272169	SRX10633819	SRS8730201	SRP315319	PRJNA722925	Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation	PRJNA722925	Other	Diabetes can be caused by an insufficiency in beta cell mass. Here we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets the increased beta cell differentiation originated from ductal cells. Mechanistically comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine carnitine and serine pathways. Overall our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.		Pancreas islets Pancreas islet 6dpf B1	Pancreas islets Islet 6d B1 AGN000786	strain:TU/AB\|age:not applicable\|dev stage:Day 6\|sex:pooled male and female\|tissue:pancreas\|molecule:mRNA\|selection:pA\|sample ref:AGS000684\|replicate ref:AGN000786\|replicate order:1\|BioSampleModel:Model organism or animal								Pancreas islets Pancreas islet 6dpf B1	AGR001073	AGR001073	mRNA			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP315319	AGR001073_R1.fastq.gz	fastq	592506792.0	7796142.0	AGR001073 R1.fastq.gz	0:76 1:0	A:179281934;C:120318002;G:119990438;T:172891644;N:24774	76	0	179281934	120318002	119990438	172891644	24774	SRX10633819	SRS8730201	SRA1220217	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.84252		0.35277		0.69219		0.54723		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2021-04-19	Larval	Larval	Pancreas	Endocrine System
64128	64128	SRR14272174	SRX10633814	SRS8730196	SRP315319	PRJNA722925	Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation	PRJNA722925	Other	Diabetes can be caused by an insufficiency in beta cell mass. Here we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets the increased beta cell differentiation originated from ductal cells. Mechanistically comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine carnitine and serine pathways. Overall our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.		Pancreas islets Pancreas islet 4dpf somatostatin transgene sst2:RFP beta cell ablation B2	Pancreas islets Islet SST b cell abt 4d B2 AGN000782	strain:TU/AB\|age:not applicable\|dev stage:Day 4\|sex:pooled male and female\|tissue:pancreas\|treatment:metronidazole\|molecule:mRNA\|selection:pA\|sample ref:AGS000680\|replicate ref:AGN000782\|replicate order:2\|BioSampleModel:Model organism or animal								Pancreas islets Pancreas islet 4dpf somatostatin transgene sst2:RFP beta cell ablation B2	AGR001070	AGR001070	mRNA			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP315319	AGR001070_R1.fastq.gz	fastq	481320616.0	6333166.0	AGR001070 R1.fastq.gz	0:76 1:0	A:151409804;C:91026556;G:90673968;T:148189727;N:20561	76	0	151409804	91026556	90673968	148189727	20561	SRX10633814	SRS8730196	SRA1220217	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.82954		0.59765		0.75538		0.53049		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2021-04-19	Larval	Larval	Pancreas	Endocrine System
64129	64129	SRR14272175	SRX10633813	SRS8730195	SRP315319	PRJNA722925	Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation	PRJNA722925	Other	Diabetes can be caused by an insufficiency in beta cell mass. Here we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets the increased beta cell differentiation originated from ductal cells. Mechanistically comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine carnitine and serine pathways. Overall our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.		Pancreas islets Pancreas islet 4dpf somatostatin transgene sst2:RFP beta cell ablation B1	Pancreas islets Islet SST b cell abt 4d B1 AGN000781	strain:TU/AB\|age:not applicable\|dev stage:Day 4\|sex:pooled male and female\|tissue:pancreas\|treatment:metronidazole\|molecule:mRNA\|selection:pA\|sample ref:AGS000680\|replicate ref:AGN000781\|replicate order:1\|BioSampleModel:Model organism or animal								Pancreas islets Pancreas islet 4dpf somatostatin transgene sst2:RFP beta cell ablation B1	AGR001069	AGR001069	mRNA			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP315319	AGR001069_R1.fastq.gz	fastq	379230956.0	4989881.0	AGR001069 R1.fastq.gz	0:76 1:0	A:116227158;C:75587948;G:75371178;T:112027929;N:16743	76	0	116227158	75587948	75371178	112027929	16743	SRX10633813	SRS8730195	SRA1220217	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.87385		0.38949		0.69242		0.47061		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2021-04-19	Larval	Larval	Pancreas	Endocrine System
64133	64133	SRR14272179	SRX10633809	SRS8730192	SRP315319	PRJNA722925	Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation	PRJNA722925	Other	Diabetes can be caused by an insufficiency in beta cell mass. Here we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets the increased beta cell differentiation originated from ductal cells. Mechanistically comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine carnitine and serine pathways. Overall our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.		Pancreas islets Pancreas islet 4dpf somatostatin transgene sst2:RFP B2	Pancreas islets Islet SST 4d B2 AGN000780	strain:TU/AB\|age:not applicable\|dev stage:Day 4\|sex:pooled male and female\|tissue:pancreas\|molecule:mRNA\|selection:pA\|sample ref:AGS000678\|replicate ref:AGN000780\|replicate order:2\|BioSampleModel:Model organism or animal								Pancreas islets Pancreas islet 4dpf somatostatin transgene sst2:RFP B2	AGR001068	AGR001068	mRNA			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP315319	AGR001068_R1.fastq.gz	fastq	1025641204.0	13495279.0	AGR001068 R1.fastq.gz	0:76 1:0	A:313399325;C:201992871;G:202026959;T:308179140;N:42909	76	0	313399325	201992871	202026959	308179140	42909	SRX10633809	SRS8730192	SRA1220217	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.8692		0.47406		0.68081		0.54006		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2021-04-19	Larval	Larval	Pancreas	Endocrine System
64134	64134	SRR14272180	SRX10633808	SRS8730191	SRP315319	PRJNA722925	Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation	PRJNA722925	Other	Diabetes can be caused by an insufficiency in beta cell mass. Here we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets the increased beta cell differentiation originated from ductal cells. Mechanistically comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine carnitine and serine pathways. Overall our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.		Pancreas islets Pancreas islet 4dpf somatostatin transgene sst2:RFP B1	Pancreas islets Islet SST 4d B1 AGN000779	strain:TU/AB\|age:not applicable\|dev stage:Day 4\|sex:pooled male and female\|tissue:pancreas\|molecule:mRNA\|selection:pA\|sample ref:AGS000678\|replicate ref:AGN000779\|replicate order:1\|BioSampleModel:Model organism or animal								Pancreas islets Pancreas islet 4dpf somatostatin transgene sst2:RFP B1	AGR001067	AGR001067	mRNA			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP315319	AGR001067_R1.fastq.gz	fastq	645391392.0	8491992.0	AGR001067 R1.fastq.gz	0:76 1:0	A:198297729;C:127050955;G:126777924;T:193238145;N:26639	76	0	198297729	127050955	126777924	193238145	26639	SRX10633808	SRS8730191	SRA1220217	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.85746		0.50636		0.68286		0.48271		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2021-04-19	Larval	Larval	Pancreas	Endocrine System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;