metadata: run_metadata: 30 rows where experiment.library_layout = "SINGLE", technology = "unknown" and tissue_curation

30 rows where experiment.library_layout = "SINGLE", technology = "unknown" and tissue_curation_coarse = "Endocrine System"

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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
10002	10002	ERR6806875	ERX6430468	ERS5060069	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22		Adult zebrafish whole pancreas RNA seq replicate2 raw reads	Zebrafish Whole Pancreas RNA seq replicate2	SAMEA7301510	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301510\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Whole Pancreas RNA seq replicate2\|common name:zebrafish\|sample name:Zebrafish Whole Pancreas RNA seq replicate2\|tissue type:whole pancreas									Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:330 6	Exocrine2	1	Total RNA extracted with TRIZOL from zebrafish whole pancreas and preprared for sequencing with the TruSeq kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Exocrine_Old_1.fastq.gz	fastq	1715678250.0	34313565.0	ena RUN I3S 23 09 2021 16:43:09:330 6	0:50 1:0	A:423211245;C:429948631;G:413857387;T:448546996;N:113991	50	0	423211245	429948631	413857387	448546996	113991	ERX6430468	ERS5060069	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.94581	0.03181	0.80026	0.48102	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Pancreas	Endocrine System
10003	10003	ERR6806874	ERX6430467	ERS5060068	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22		Adult zebrafish whole pancreas RNA seq replicate1 raw reads	Zebrafish Whole Pancreas RNA seq replicate1	SAMEA7301509	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301509\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Whole Pancreas RNA seq replicate1\|common name:zebrafish\|sample name:Zebrafish Whole Pancreas RNA seq replicate1\|tissue type:whole pancreas									Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:330 5	Exocrine1	1	Total RNA extracted with TRIZOL from zebrafish whole pancreas and preprared for sequencing with the TruSeq kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Exocrine_Young_1.fastq.gz	fastq	1751070500.0	35021410.0	ena RUN I3S 23 09 2021 16:43:09:330 5	0:50 1:0	A:412303526;C:454121976;G:438481251;T:446048184;N:115563	50	0	412303526	454121976	438481251	446048184	115563	ERX6430467	ERS5060068	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.93968	0.02618	0.8003	0.58539	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Pancreas	Endocrine System
10004	10004	ERR6806873	ERX6430466	ERS5060036	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22		Adult zebrafish endocrine pancreas RNA seq replicate4 raw reads	Zebrafish Endocrine Pancreas RNA seq replicate4	SAMEA7301477	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301477\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Endocrine Pancreas RNA seq replicate4\|common name:zebrafish\|sample name:Zebrafish Endocrine Pancreas RNA seq replicate4\|tissue type:endocrine pancreas principal islet									Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:330 4	Endocrine4	1	Total RNA extracted with TRIZOL from zebrafish primary pancreatic islet and preprared for sequencing with the TruSeq kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Endocrine_Old_2.fastq.gz	fastq	1710560600.0	34211212.0	ena RUN I3S 23 09 2021 16:43:09:330 4	0:50 1:0	A:441527784;C:412091003;G:396100295;T:460728135;N:113383	50	0	441527784	412091003	396100295	460728135	113383	ERX6430466	ERS5060036	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.95616	0.04334	0.84585	0.17182	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Pancreas	Endocrine System
10005	10005	ERR6806872	ERX6430465	ERS5060035	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22		Adult zebrafish endocrine pancreas RNA seq replicate3 raw reads	Zebrafish Endocrine Pancreas RNA seq replicate3	SAMEA7301476	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301476\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Endocrine Pancreas RNA seq replicate3\|common name:zebrafish\|sample name:Zebrafish Endocrine Pancreas RNA seq replicate3\|tissue type:endocrine pancreas principal islet									Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:330 3	Endocrine3	1	Total RNA extracted with TRIZOL from zebrafish primary pancreatic islet and preprared for sequencing with the TruSeq kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Endocrine_Old_1.fastq.gz	fastq	1979582750.0	39591655.0	ena RUN I3S 23 09 2021 16:43:09:330 3	0:50 1:0	A:483713055;C:499972514;G:479484600;T:516281513;N:131068	50	0	483713055	499972514	479484600	516281513	131068	ERX6430465	ERS5060035	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.93722	0.04096	0.7559	0.52069	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Pancreas	Endocrine System
10006	10006	ERR6806871	ERX6430464	ERS5060034	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22		Adult zebrafish endocrine pancreas principal islet RNA seq raw reads replicate2	Zebrafish Endocrine Pancreas RNA seq replicate2	SAMEA7301475	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301475\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Endocrine Pancreas RNA seq replicate2\|common name:zebrafish\|sample name:Zebrafish Endocrine Pancreas RNA seq replicate2\|tissue type:endocrine pancreas principal islet									Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:329 2	Endocrine2	1	Total RNA extracted with TRIZOL from zebrafish primary pancreatic islet and preprared for sequencing with the TruSeq kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Endocrine_Young_2.fastq.gz	fastq	1846315600.0	36926312.0	ena RUN I3S 23 09 2021 16:43:09:329 2	0:50 1:0	A:466245839;C:453675875;G:433502059;T:492768958;N:122869	50	0	466245839	453675875	433502059	492768958	122869	ERX6430464	ERS5060034	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.93566	0.06945	0.74065	0.47497	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Pancreas	Endocrine System
10007	10007	ERR6806870	ERX6430463	ERS5060033	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22		Adult zebrafish endocrine pancreas principal islet RNA seq raw reads replicate1	Zebrafish Endocrine Pancreas RNA seq replicate1	SAMEA7301474	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301474\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Endocrine Pancreas RNA seq replicate1\|common name:zebrafish\|sample name:Zebrafish Endocrine Pancreas RNA seq replicate1\|tissue type:endocrine pancreas principal islet									Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:329 1	Endocrine1	1	Total RNA extracted with TRIZOL from zebrafish primary pancreatic islet and preprared for sequencing with the TruSeq kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Endocrine_Young_1.fastq.gz	fastq	1331184450.0	26623689.0	ena RUN I3S 23 09 2021 16:43:09:329 1	0:50 1:0	A:336761837;C:326693218;G:311881921;T:355763246;N:84228	50	0	336761837	326693218	311881921	355763246	84228	ERX6430463	ERS5060033	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.93154	0.07422	0.73064	0.53917	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Pancreas	Endocrine System
39917	39917	SRR2353210	SRX1225282	SRS1065171	SRP063624	PRJNA295427	Expression profiling of centroacinar cells from adult zebrafish pancreas	GSE72963	Transcriptome Analysis	We sequenced mRNA from two preparations of isolated Notch responsive ductal pancreas cells and compared transcript expression to all other non Notch responsive cells from each sample to charactarize zebrafish centroacinar cells. Overall design: Determination of gene expression levels in centroacinar cells and non centroacinar cells from adult pancreas.		pubmed:26153247		non CAC rep 2	GSM1875475		source name:pancreas non CAC\|tissue:pancreas\|developmental stage:adult\|strain:AB\|cell type:isolated non centroacinar cells	non CAC rep 2	Reads were processed and mapped to Zv9/danRer7 using RSEM EBseq was used to determine differential expression and significance values Genome build: Zv9/danRer7 Supplementary files format and content: tab delimited text files using corrected and uncorrected foldchange values	pancreas non CAC		Pancreas was dissected on ice and dissociated. CACs and non CACs were sorted by FACS and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used for the construction of sequencing libraries. Libraries were constructed using standard Illumina protocols		tissue:pancreas\|developmental stage:adult\|strain:AB\|cell type:isolated non centroacinar cells	GSM1875475	GSM1875475: non CAC rep 2; Danio rerio; RNA Seq	GSM1875475		1	Pancreas was dissected on ice and dissociated. CACs and non CACs were sorted by FACS and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used for the construction of sequencing libraries. Libraries were constructed using standard Illumina protocols	GEO Accession:GSM1875475	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer II	SRP063624			H0J49ADXXs_2_2_merged.fastq.bz2	fastq	8206500750.0	109420010.0	GSM1875475 r1	0:75	A:2316013641;C:1680081024;G:1838151157;T:2362455717;N:9799211	75		2316013641	1680081024	1838151157	2362455717	9799211	SRX1225282	SRS1065171	SRA297337	GEO	Institute of Genetic Medicine, Johns Hopkins University	1	0.5785	0.17732	0.77469	0.62483	75	B	usable mapping rate	illumina	early_illumina	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2015-09-11	Adult	Adult	Pancreas	Endocrine System
39918	39918	SRR2353209	SRX1225281	SRS1065172	SRP063624	PRJNA295427	Expression profiling of centroacinar cells from adult zebrafish pancreas	GSE72963	Transcriptome Analysis	We sequenced mRNA from two preparations of isolated Notch responsive ductal pancreas cells and compared transcript expression to all other non Notch responsive cells from each sample to charactarize zebrafish centroacinar cells. Overall design: Determination of gene expression levels in centroacinar cells and non centroacinar cells from adult pancreas.		pubmed:26153247		CAC rep 2	GSM1875474		source name:pancreas CAC\|tissue:pancreas\|developmental stage:adult\|strain:AB\|cell type:isolated centroacinar cells	CAC rep 2	Reads were processed and mapped to Zv9/danRer7 using RSEM EBseq was used to determine differential expression and significance values Genome build: Zv9/danRer7 Supplementary files format and content: tab delimited text files using corrected and uncorrected foldchange values	pancreas CAC		Pancreas was dissected on ice and dissociated. CACs and non CACs were sorted by FACS and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used for the construction of sequencing libraries. Libraries were constructed using standard Illumina protocols		tissue:pancreas\|developmental stage:adult\|strain:AB\|cell type:isolated centroacinar cells	GSM1875474	GSM1875474: CAC rep 2; Danio rerio; RNA Seq	GSM1875474		1	Pancreas was dissected on ice and dissociated. CACs and non CACs were sorted by FACS and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used for the construction of sequencing libraries. Libraries were constructed using standard Illumina protocols	GEO Accession:GSM1875474	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer II	SRP063624			H0J49ADXXs_2_1_merged.fastq.bz2	fastq	8206500750.0	109420010.0	GSM1875474 r1	0:75	A:2399854503;C:1714800726;G:1801618139;T:2289278152;N:949230	75		2399854503	1714800726	1801618139	2289278152	949230	SRX1225281	SRS1065172	SRA297337	GEO	Institute of Genetic Medicine, Johns Hopkins University	1	0.66738	0.21282	0.75694	0.6409	75	B	usable mapping rate	illumina	early_illumina	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2015-09-11	Adult	Adult	Pancreas	Endocrine System
39919	39919	SRR2353208	SRX1225280	SRS1065173	SRP063624	PRJNA295427	Expression profiling of centroacinar cells from adult zebrafish pancreas	GSE72963	Transcriptome Analysis	We sequenced mRNA from two preparations of isolated Notch responsive ductal pancreas cells and compared transcript expression to all other non Notch responsive cells from each sample to charactarize zebrafish centroacinar cells. Overall design: Determination of gene expression levels in centroacinar cells and non centroacinar cells from adult pancreas.		pubmed:26153247		non CAC rep 1	GSM1875473		source name:pancreas non CAC\|tissue:pancreas\|developmental stage:adult\|strain:AB\|cell type:isolated non centroacinar cells	non CAC rep 1	Reads were processed and mapped to Zv9/danRer7 using RSEM EBseq was used to determine differential expression and significance values Genome build: Zv9/danRer7 Supplementary files format and content: tab delimited text files using corrected and uncorrected foldchange values	pancreas non CAC		Pancreas was dissected on ice and dissociated. CACs and non CACs were sorted by FACS and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used for the construction of sequencing libraries. Libraries were constructed using standard Illumina protocols		tissue:pancreas\|developmental stage:adult\|strain:AB\|cell type:isolated non centroacinar cells	GSM1875473	GSM1875473: non CAC rep 1; Danio rerio; RNA Seq	GSM1875473		1	Pancreas was dissected on ice and dissociated. CACs and non CACs were sorted by FACS and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used for the construction of sequencing libraries. Libraries were constructed using standard Illumina protocols	GEO Accession:GSM1875473	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer II	SRP063624			H0J49ADXXs_1_2_merged.fastq.bz2	fastq	8167909125.0	108905455.0	GSM1875473 r1	0:75	A:2352532315;C:1630885687;G:1811590860;T:2358426654;N:14473609	75		2352532315	1630885687	1811590860	2358426654	14473609	SRX1225280	SRS1065173	SRA297337	GEO	Institute of Genetic Medicine, Johns Hopkins University	1	0.56456	0.17736	0.74525	0.57983	75	B	usable mapping rate	illumina	early_illumina	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2015-09-11	Adult	Adult	Pancreas	Endocrine System
39920	39920	SRR2353207	SRX1225279	SRS1065174	SRP063624	PRJNA295427	Expression profiling of centroacinar cells from adult zebrafish pancreas	GSE72963	Transcriptome Analysis	We sequenced mRNA from two preparations of isolated Notch responsive ductal pancreas cells and compared transcript expression to all other non Notch responsive cells from each sample to charactarize zebrafish centroacinar cells. Overall design: Determination of gene expression levels in centroacinar cells and non centroacinar cells from adult pancreas.		pubmed:26153247		CAC rep 1	GSM1875472		source name:pancreas CAC\|tissue:pancreas\|developmental stage:adult\|strain:AB\|cell type:isolated centroacinar cells	CAC rep 1	Reads were processed and mapped to Zv9/danRer7 using RSEM EBseq was used to determine differential expression and significance values Genome build: Zv9/danRer7 Supplementary files format and content: tab delimited text files using corrected and uncorrected foldchange values	pancreas CAC		Pancreas was dissected on ice and dissociated. CACs and non CACs were sorted by FACS and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used for the construction of sequencing libraries. Libraries were constructed using standard Illumina protocols		tissue:pancreas\|developmental stage:adult\|strain:AB\|cell type:isolated centroacinar cells	GSM1875472	GSM1875472: CAC rep 1; Danio rerio; RNA Seq	GSM1875472		1	Pancreas was dissected on ice and dissociated. CACs and non CACs were sorted by FACS and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used for the construction of sequencing libraries. Libraries were constructed using standard Illumina protocols	GEO Accession:GSM1875472	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer II	SRP063624			H0J49ADXXs_1_1_merged.fastq.bz2	fastq	8167909125.0	108905455.0	GSM1875472 r1	0:75	A:2418955841;C:1674627530;G:1764871153;T:2308386909;N:1067692	75		2418955841	1674627530	1764871153	2308386909	1067692	SRX1225279	SRS1065174	SRA297337	GEO	Institute of Genetic Medicine, Johns Hopkins University	1	0.66215	0.21771	0.72437	0.57789	75	B	usable mapping rate	illumina	early_illumina	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2015-09-11	Adult	Adult	Pancreas	Endocrine System
44043	44043	SRR6237746	SRX3345984	SRS2646512	SRP123109	PRJNA416462	Transcriptome of zebrafish neurohypophyseal astroglia pituicytes	GSE106371	Transcriptome Analysis	The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections endothelial blood vessels and astroglial like cells termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface which allows the release of neurohormones from the brain to the periphery. However the molecular blueprint of pituicytes specific genes is still unknown. We have labelled and isolated zebrafish pituicytes cells and have identified their molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing in 5 biological replicates using Illumina HiSeq 2500 v4 instrument		pubmed:30449506		Sample Plate2 A6 AMCA	GSM2836694		source name:hypophysis\|strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Neg\|cell type:non pituicytes	Sample Plate2 A6 AMCA	cutadapt used to trim poly A and poly T low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters: s no t exon m intersection strict i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2	hypophysis	Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al. Gene Expr Patterns 2009.	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	Adult zebrafish were raised and bred according to standard protocols.	strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Neg\|cell type:non pituicytes	GSM2836694	GSM2836694: Sample Plate2 A6 AMCA; Danio rerio; RNA Seq	GSM2836694		1	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	GEO Accession:GSM2836694	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP123109			Sample_Plate2_A6_AMCA_Neg.fastq.gz	fastq	1229895822.0	20184545.0	GSM2836694 r1	0:60.93 1:0	A:354923207;C:259144918;G:256606445;T:359057403;N:163849	60	0	354923207	259144918	256606445	359057403	163849	SRX3345984	SRS2646512	SRA626615	GEO	Bioinformatics Unit, Biological Services, Weizmann Institute of Science	1	0.87646	0.26527	0.8257	0.55303	61	B	usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Israel	2017-10-31	Adult	Adult	Pituitary Gland	Endocrine System
44044	44044	SRR6237745	SRX3345983	SRS2646515	SRP123109	PRJNA416462	Transcriptome of zebrafish neurohypophyseal astroglia pituicytes	GSE106371	Transcriptome Analysis	The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections endothelial blood vessels and astroglial like cells termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface which allows the release of neurohormones from the brain to the periphery. However the molecular blueprint of pituicytes specific genes is still unknown. We have labelled and isolated zebrafish pituicytes cells and have identified their molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing in 5 biological replicates using Illumina HiSeq 2500 v4 instrument		pubmed:30449506		Sample Plate2 A5 AMCA	GSM2836693		source name:hypophysis\|strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Pos\|cell type:pituicytes	Sample Plate2 A5 AMCA	cutadapt used to trim poly A and poly T low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters: s no t exon m intersection strict i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2	hypophysis	Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al. Gene Expr Patterns 2009.	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	Adult zebrafish were raised and bred according to standard protocols.	strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Pos\|cell type:pituicytes	GSM2836693	GSM2836693: Sample Plate2 A5 AMCA; Danio rerio; RNA Seq	GSM2836693		1	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	GEO Accession:GSM2836693	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP123109			Sample_Plate2_A5_AMCA_Pos.fastq.gz	fastq	925676587.0	15189171.0	GSM2836693 r1	0:60.94 1:0	A:282028510;C:179853567;G:179383383;T:284281435;N:129692	60	0	282028510	179853567	179383383	284281435	129692	SRX3345983	SRS2646515	SRA626615	GEO	Bioinformatics Unit, Biological Services, Weizmann Institute of Science	1	0.90747	0.36422	0.74215	0.54419	61	B	usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Israel	2017-10-31	Adult	Adult	Pituitary Gland	Endocrine System
44045	44045	SRR6237744	SRX3345982	SRS2646511	SRP123109	PRJNA416462	Transcriptome of zebrafish neurohypophyseal astroglia pituicytes	GSE106371	Transcriptome Analysis	The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections endothelial blood vessels and astroglial like cells termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface which allows the release of neurohormones from the brain to the periphery. However the molecular blueprint of pituicytes specific genes is still unknown. We have labelled and isolated zebrafish pituicytes cells and have identified their molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing in 5 biological replicates using Illumina HiSeq 2500 v4 instrument		pubmed:30449506		Sample Plate2 A4 AMCA	GSM2836692		source name:hypophysis\|strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Neg\|cell type:non pituicytes	Sample Plate2 A4 AMCA	cutadapt used to trim poly A and poly T low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters: s no t exon m intersection strict i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2	hypophysis	Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al. Gene Expr Patterns 2009.	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	Adult zebrafish were raised and bred according to standard protocols.	strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Neg\|cell type:non pituicytes	GSM2836692	GSM2836692: Sample Plate2 A4 AMCA; Danio rerio; RNA Seq	GSM2836692		1	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	GEO Accession:GSM2836692	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP123109			Sample_Plate2_A4_AMCA_Neg.fastq.gz	fastq	1160014329.0	19037174.0	GSM2836692 r1	0:60.93 1:0	A:339245851;C:240318483;G:237965388;T:342331066;N:153541	60	0	339245851	240318483	237965388	342331066	153541	SRX3345982	SRS2646511	SRA626615	GEO	Bioinformatics Unit, Biological Services, Weizmann Institute of Science	1	0.89175	0.24416	0.82384	0.55389	61	B	usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Israel	2017-10-31	Adult	Adult	Pituitary Gland	Endocrine System
44046	44046	SRR6237743	SRX3345981	SRS2646513	SRP123109	PRJNA416462	Transcriptome of zebrafish neurohypophyseal astroglia pituicytes	GSE106371	Transcriptome Analysis	The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections endothelial blood vessels and astroglial like cells termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface which allows the release of neurohormones from the brain to the periphery. However the molecular blueprint of pituicytes specific genes is still unknown. We have labelled and isolated zebrafish pituicytes cells and have identified their molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing in 5 biological replicates using Illumina HiSeq 2500 v4 instrument		pubmed:30449506		Sample Plate2 A3 AMCA	GSM2836691		source name:hypophysis\|strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Pos\|cell type:pituicytes	Sample Plate2 A3 AMCA	cutadapt used to trim poly A and poly T low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters: s no t exon m intersection strict i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2	hypophysis	Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al. Gene Expr Patterns 2009.	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	Adult zebrafish were raised and bred according to standard protocols.	strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Pos\|cell type:pituicytes	GSM2836691	GSM2836691: Sample Plate2 A3 AMCA; Danio rerio; RNA Seq	GSM2836691		1	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	GEO Accession:GSM2836691	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP123109			Sample_Plate2_A3_AMCA_Pos.fastq.gz	fastq	855655864.0	14040472.0	GSM2836691 r1	0:60.94 1:0	A:257233140;C:169854422;G:169238352;T:259211059;N:118891	60	0	257233140	169854422	169238352	259211059	118891	SRX3345981	SRS2646513	SRA626615	GEO	Bioinformatics Unit, Biological Services, Weizmann Institute of Science	1	0.90605	0.30761	0.74067	0.55271	61	B	usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Israel	2017-10-31	Adult	Adult	Pituitary Gland	Endocrine System
44047	44047	SRR6237742	SRX3345980	SRS2646514	SRP123109	PRJNA416462	Transcriptome of zebrafish neurohypophyseal astroglia pituicytes	GSE106371	Transcriptome Analysis	The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections endothelial blood vessels and astroglial like cells termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface which allows the release of neurohormones from the brain to the periphery. However the molecular blueprint of pituicytes specific genes is still unknown. We have labelled and isolated zebrafish pituicytes cells and have identified their molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing in 5 biological replicates using Illumina HiSeq 2500 v4 instrument		pubmed:30449506		Sample Plate2 A2 AMCA	GSM2836690		source name:hypophysis\|strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Neg\|cell type:non pituicytes	Sample Plate2 A2 AMCA	cutadapt used to trim poly A and poly T low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters: s no t exon m intersection strict i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2	hypophysis	Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al. Gene Expr Patterns 2009.	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	Adult zebrafish were raised and bred according to standard protocols.	strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Neg\|cell type:non pituicytes	GSM2836690	GSM2836690: Sample Plate2 A2 AMCA; Danio rerio; RNA Seq	GSM2836690		1	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	GEO Accession:GSM2836690	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP123109			Sample_Plate2_A2_AMCA_Neg.fastq.gz	fastq	1168909471.0	19185392.0	GSM2836690 r1	0:60.93 1:0	A:326281148;C:256738933;G:252744782;T:332989234;N:155374	60	0	326281148	256738933	252744782	332989234	155374	SRX3345980	SRS2646514	SRA626615	GEO	Bioinformatics Unit, Biological Services, Weizmann Institute of Science	1	0.88849	0.1697	0.86602	0.52913	61	B	usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Israel	2017-10-31	Adult	Adult	Pituitary Gland	Endocrine System
44048	44048	SRR6237741	SRX3345979	SRS2646510	SRP123109	PRJNA416462	Transcriptome of zebrafish neurohypophyseal astroglia pituicytes	GSE106371	Transcriptome Analysis	The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections endothelial blood vessels and astroglial like cells termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface which allows the release of neurohormones from the brain to the periphery. However the molecular blueprint of pituicytes specific genes is still unknown. We have labelled and isolated zebrafish pituicytes cells and have identified their molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing in 5 biological replicates using Illumina HiSeq 2500 v4 instrument		pubmed:30449506		Sample Plate2 A1 AMCA	GSM2836689		source name:hypophysis\|strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Pos\|cell type:pituicytes	Sample Plate2 A1 AMCA	cutadapt used to trim poly A and poly T low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters: s no t exon m intersection strict i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2	hypophysis	Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al. Gene Expr Patterns 2009.	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	Adult zebrafish were raised and bred according to standard protocols.	strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Pos\|cell type:pituicytes	GSM2836689	GSM2836689: Sample Plate2 A1 AMCA; Danio rerio; RNA Seq	GSM2836689		1	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	GEO Accession:GSM2836689	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP123109			Sample_Plate2_A1_AMCA_Pos.fastq.gz	fastq	915106129.0	15016536.0	GSM2836689 r1	0:60.94 1:0	A:271804923;C:184830364;G:184695096;T:273646193;N:129553	60	0	271804923	184830364	184695096	273646193	129553	SRX3345979	SRS2646510	SRA626615	GEO	Bioinformatics Unit, Biological Services, Weizmann Institute of Science	1	0.909	0.28209	0.74582	0.54537	61	B	usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Israel	2017-10-31	Adult	Adult	Pituitary Gland	Endocrine System
44049	44049	SRR6237740	SRX3345978	SRS2646509	SRP123109	PRJNA416462	Transcriptome of zebrafish neurohypophyseal astroglia pituicytes	GSE106371	Transcriptome Analysis	The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections endothelial blood vessels and astroglial like cells termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface which allows the release of neurohormones from the brain to the periphery. However the molecular blueprint of pituicytes specific genes is still unknown. We have labelled and isolated zebrafish pituicytes cells and have identified their molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing in 5 biological replicates using Illumina HiSeq 2500 v4 instrument		pubmed:30449506		Sample Plate1 A8 AMCA	GSM2836688		source name:hypophysis\|strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Neg\|cell type:non pituicytes	Sample Plate1 A8 AMCA	cutadapt used to trim poly A and poly T low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters: s no t exon m intersection strict i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2	hypophysis	Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al. Gene Expr Patterns 2009.	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	Adult zebrafish were raised and bred according to standard protocols.	strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Neg\|cell type:non pituicytes	GSM2836688	GSM2836688: Sample Plate1 A8 AMCA; Danio rerio; RNA Seq	GSM2836688		1	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	GEO Accession:GSM2836688	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP123109			Sample_Plate1_A8_AMCA_Neg.fastq.gz	fastq	1174636209.0	19276749.0	GSM2836688 r1	0:60.94 1:0	A:346218731;C:240547553;G:237863913;T:349847274;N:158738	60	0	346218731	240547553	237863913	349847274	158738	SRX3345978	SRS2646509	SRA626615	GEO	Bioinformatics Unit, Biological Services, Weizmann Institute of Science	1	0.89653	0.29731	0.82388	0.57688	61	B	usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Israel	2017-10-31	Adult	Adult	Pituitary Gland	Endocrine System
44050	44050	SRR6237739	SRX3345977	SRS2646507	SRP123109	PRJNA416462	Transcriptome of zebrafish neurohypophyseal astroglia pituicytes	GSE106371	Transcriptome Analysis	The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections endothelial blood vessels and astroglial like cells termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface which allows the release of neurohormones from the brain to the periphery. However the molecular blueprint of pituicytes specific genes is still unknown. We have labelled and isolated zebrafish pituicytes cells and have identified their molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing in 5 biological replicates using Illumina HiSeq 2500 v4 instrument		pubmed:30449506		Sample Plate1 A7 AMCA	GSM2836687		source name:hypophysis\|strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Pos\|cell type:pituicytes	Sample Plate1 A7 AMCA	cutadapt used to trim poly A and poly T low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters: s no t exon m intersection strict i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2	hypophysis	Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al. Gene Expr Patterns 2009.	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	Adult zebrafish were raised and bred according to standard protocols.	strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Pos\|cell type:pituicytes	GSM2836687	GSM2836687: Sample Plate1 A7 AMCA; Danio rerio; RNA Seq	GSM2836687		1	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	GEO Accession:GSM2836687	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP123109			Sample_Plate1_A7_AMCA_Pos.fastq.gz	fastq	919004945.0	15079582.0	GSM2836687 r1	0:60.94 1:0	A:281188323;C:177657384;G:177254638;T:282775426;N:129174	60	0	281188323	177657384	177254638	282775426	129174	SRX3345977	SRS2646507	SRA626615	GEO	Bioinformatics Unit, Biological Services, Weizmann Institute of Science	1	0.8999	0.31855	0.7643	0.56856	61	B	usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Israel	2017-10-31	Adult	Adult	Pituitary Gland	Endocrine System
44051	44051	SRR6237738	SRX3345976	SRS2646506	SRP123109	PRJNA416462	Transcriptome of zebrafish neurohypophyseal astroglia pituicytes	GSE106371	Transcriptome Analysis	The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections endothelial blood vessels and astroglial like cells termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface which allows the release of neurohormones from the brain to the periphery. However the molecular blueprint of pituicytes specific genes is still unknown. We have labelled and isolated zebrafish pituicytes cells and have identified their molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing in 5 biological replicates using Illumina HiSeq 2500 v4 instrument		pubmed:30449506		Sample Plate1 A6 AMCA	GSM2836686		source name:hypophysis\|strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Neg\|cell type:non pituicytes	Sample Plate1 A6 AMCA	cutadapt used to trim poly A and poly T low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters: s no t exon m intersection strict i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2	hypophysis	Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al. Gene Expr Patterns 2009.	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	Adult zebrafish were raised and bred according to standard protocols.	strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Neg\|cell type:non pituicytes	GSM2836686	GSM2836686: Sample Plate1 A6 AMCA; Danio rerio; RNA Seq	GSM2836686		1	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	GEO Accession:GSM2836686	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP123109			Sample_Plate1_A6_AMCA_Neg.fastq.gz	fastq	1217567270.0	19981819.0	GSM2836686 r1	0:60.93 1:0	A:366468588;C:242252329;G:239380324;T:369298417;N:167612	60	0	366468588	242252329	239380324	369298417	167612	SRX3345976	SRS2646506	SRA626615	GEO	Bioinformatics Unit, Biological Services, Weizmann Institute of Science	1	0.87327	0.29592	0.86026	0.61414	61	B	usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Israel	2017-10-31	Adult	Adult	Pituitary Gland	Endocrine System
44052	44052	SRR6237737	SRX3345975	SRS2646508	SRP123109	PRJNA416462	Transcriptome of zebrafish neurohypophyseal astroglia pituicytes	GSE106371	Transcriptome Analysis	The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections endothelial blood vessels and astroglial like cells termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface which allows the release of neurohormones from the brain to the periphery. However the molecular blueprint of pituicytes specific genes is still unknown. We have labelled and isolated zebrafish pituicytes cells and have identified their molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing in 5 biological replicates using Illumina HiSeq 2500 v4 instrument		pubmed:30449506		Sample Plate1 A5 AMCA	GSM2836685		source name:hypophysis\|strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Pos\|cell type:pituicytes	Sample Plate1 A5 AMCA	cutadapt used to trim poly A and poly T low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters: s no t exon m intersection strict i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2	hypophysis	Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al. Gene Expr Patterns 2009.	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	Adult zebrafish were raised and bred according to standard protocols.	strain:TL\|tissue:hypophysis\|age:12 month\|Sex:male\|b ala lys ne amca labelling:Pos\|cell type:pituicytes	GSM2836685	GSM2836685: Sample Plate1 A5 AMCA; Danio rerio; RNA Seq	GSM2836685		1	Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting. Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO 0.8mM CaCl2 Pen 50 U/mL + Strep 0.05/mL FBS 1% and filtered with a 40 μm cell strainer BD Transduction Laboratories San Jose CA. Propidium iodide was added to label dead cells. High speed FACS was performed using an SORP FACSAria machine BD Bioscience San Jose CA with 70µm nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control non AMCA AMCA cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing v3 Takara Bio USA Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at 80°C. Two independent FACS experiments were performed yielding six samples 3 AMCA+ and 3 AMCA from 3 groups and four samples 2 AMCA+ and 2 AMCA from 2 groups. Samples were thawed reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing v3 kit. Amplification was performed with 15 cycles. Following the amplification clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X. About 3ng of sheared amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multip…	GEO Accession:GSM2836685	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP123109			Sample_Plate1_A5_AMCA_Pos.fastq.gz	fastq	995781320.0	16339491.0	GSM2836685 r1	0:60.94 1:0	A:304872127;C:192446811;G:191928153;T:306392280;N:141949	60	0	304872127	192446811	191928153	306392280	141949	SRX3345975	SRS2646508	SRA626615	GEO	Bioinformatics Unit, Biological Services, Weizmann Institute of Science	1	0.90464	0.36217	0.74836	0.56177	61	B	usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Israel	2017-10-31	Adult	Adult	Pituitary Gland	Endocrine System
50713	50713	SRR8255922	SRX5073702	SRS4087528	SRP171016	PRJNA507363	Modelling pancreatic beta cell inflammation in zebrafish identifies a natural product for human beta cell protection	GSE123036	Transcriptome Analysis	To assess the effect of chronic inflammation on the beta cells transcriptome we conducted RNA sequencing from 3 mpf zebrafish transgenic line Tgins:IL1B animals and WT siblings The total RNA from FACS sorted Beta cells was isolated using Quick RNA MicroPrep kit R1050 Zymo Research and following the manufacturer instructions. The sequencing was made on llumina HiSeq2500 in 2x75bp paired end mode. method Results:Two replicates for controls and two for IL1B expressing beta cells were sequenced. About 40 million sequence reads per sample were mapped to the Zebrafish genome. We identify around 19 thousand genes per sample. Approximately 6% of the genes were differentially expressed. 1 245 genes with a FDR of 5 showed a fold change =0.7 and adjusted p value <0.05. Conclusions: Hierarchical clustering by Pearson correlation of differentially expressed genes uncovered the expression of alpha cell related genes in beta cells. This provides a possible impairment of beta cell identity reflected in RNA expression profiles. Overall design: Beta cell mRNA profiles of 3 mpf wild type WT and Tgins:IL1B; cryaa:mCherry Zebrafihs were generated by deep sequencing in duplicate using llumina HiSeq2500.		pubmed:30679186		Il1B rep2	GSM3494234		source name:Pancreatic beta cells\|genotype/variation:Tgins:IL1B; Tgins:mKO\|tissue:Pancreatic beta cells\|age:3 mpf\|genotype:Interleukin 1B expression in beta cells	Il1B rep2	Illumina NextSeq Control/RTA2 software was used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zebrafish genome GRCz10 using GSNAP from Ensembl gene annotation version 87 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Pancreatic beta cells		Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation islets were collected in PBS chilled on ice. post one washing with ice cold PBS islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 with 0.1% Pluronic F 68 ThermoFisher 24040032 at 37˚C in a benchtop shaker set at 350 rpm for 50 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4˚C. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+ Mg2++0.1% Pluronic F 68. To remove debris the solution was passed over a 30 mm cell filter Miltenyi Biotec 130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype/variation:Tgins:IL1B; Tgins:mKO\|tissue:Pancreatic beta cells\|age:3 mpf\|genotype:Interleukin 1B expression in beta cells	GSM3494234	GSM3494234: Il1B rep2; Danio rerio; RNA Seq	GSM3494234		1	Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation islets were collected in PBS chilled on ice. post one washing with ice cold PBS islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 with 0.1% Pluronic F 68 ThermoFisher 24040032 at 37˚C in a benchtop shaker set at 350 rpm for 50 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4˚C. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+ Mg2++0.1% Pluronic F 68. To remove debris the solution was passed over a 30 mm cell filter Miltenyi Biotec 130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3494234	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP171016			L19371_Track-47496_R1.fastq.gz	fastq	3282305632.0	43188232.0	GSM3494234 r1	0:76 1:0	A:961171458;C:699797228;G:707162172;T:914140351;N:34423	76	0	961171458	699797228	707162172	914140351	34423	SRX5073702	SRS4087528	SRA815642	GEO	Ninov, CRTD	1	0.88789	0.19663	0.77461	0.56289	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2018-11-28	Adult	Adult	Pancreas	Endocrine System
50714	50714	SRR8255921	SRX5073701	SRS4087527	SRP171016	PRJNA507363	Modelling pancreatic beta cell inflammation in zebrafish identifies a natural product for human beta cell protection	GSE123036	Transcriptome Analysis	To assess the effect of chronic inflammation on the beta cells transcriptome we conducted RNA sequencing from 3 mpf zebrafish transgenic line Tgins:IL1B animals and WT siblings The total RNA from FACS sorted Beta cells was isolated using Quick RNA MicroPrep kit R1050 Zymo Research and following the manufacturer instructions. The sequencing was made on llumina HiSeq2500 in 2x75bp paired end mode. method Results:Two replicates for controls and two for IL1B expressing beta cells were sequenced. About 40 million sequence reads per sample were mapped to the Zebrafish genome. We identify around 19 thousand genes per sample. Approximately 6% of the genes were differentially expressed. 1 245 genes with a FDR of 5 showed a fold change =0.7 and adjusted p value <0.05. Conclusions: Hierarchical clustering by Pearson correlation of differentially expressed genes uncovered the expression of alpha cell related genes in beta cells. This provides a possible impairment of beta cell identity reflected in RNA expression profiles. Overall design: Beta cell mRNA profiles of 3 mpf wild type WT and Tgins:IL1B; cryaa:mCherry Zebrafihs were generated by deep sequencing in duplicate using llumina HiSeq2500.		pubmed:30679186		Il1B rep1	GSM3494233		source name:Pancreatic beta cells\|genotype/variation:Tgins:IL1B; Tgins:mKO\|tissue:Pancreatic beta cells\|age:3 mpf\|genotype:Interleukin 1B expression in beta cells	Il1B rep1	Illumina NextSeq Control/RTA2 software was used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zebrafish genome GRCz10 using GSNAP from Ensembl gene annotation version 87 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Pancreatic beta cells		Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation islets were collected in PBS chilled on ice. post one washing with ice cold PBS islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 with 0.1% Pluronic F 68 ThermoFisher 24040032 at 37˚C in a benchtop shaker set at 350 rpm for 50 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4˚C. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+ Mg2++0.1% Pluronic F 68. To remove debris the solution was passed over a 30 mm cell filter Miltenyi Biotec 130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype/variation:Tgins:IL1B; Tgins:mKO\|tissue:Pancreatic beta cells\|age:3 mpf\|genotype:Interleukin 1B expression in beta cells	GSM3494233	GSM3494233: Il1B rep1; Danio rerio; RNA Seq	GSM3494233		1	Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation islets were collected in PBS chilled on ice. post one washing with ice cold PBS islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 with 0.1% Pluronic F 68 ThermoFisher 24040032 at 37˚C in a benchtop shaker set at 350 rpm for 50 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4˚C. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+ Mg2++0.1% Pluronic F 68. To remove debris the solution was passed over a 30 mm cell filter Miltenyi Biotec 130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3494233	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP171016			L19370_Track-47495_R1.fastq.gz	fastq	3117378488.0	41018138.0	GSM3494233 r1	0:76 1:0	A:900337994;C:672684479;G:688186415;T:856137569;N:32031	76	0	900337994	672684479	688186415	856137569	32031	SRX5073701	SRS4087527	SRA815642	GEO	Ninov, CRTD	1	0.88054	0.16457	0.7735	0.55887	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2018-11-28	Adult	Adult	Pancreas	Endocrine System
50715	50715	SRR8255920	SRX5073700	SRS4087526	SRP171016	PRJNA507363	Modelling pancreatic beta cell inflammation in zebrafish identifies a natural product for human beta cell protection	GSE123036	Transcriptome Analysis	To assess the effect of chronic inflammation on the beta cells transcriptome we conducted RNA sequencing from 3 mpf zebrafish transgenic line Tgins:IL1B animals and WT siblings The total RNA from FACS sorted Beta cells was isolated using Quick RNA MicroPrep kit R1050 Zymo Research and following the manufacturer instructions. The sequencing was made on llumina HiSeq2500 in 2x75bp paired end mode. method Results:Two replicates for controls and two for IL1B expressing beta cells were sequenced. About 40 million sequence reads per sample were mapped to the Zebrafish genome. We identify around 19 thousand genes per sample. Approximately 6% of the genes were differentially expressed. 1 245 genes with a FDR of 5 showed a fold change =0.7 and adjusted p value <0.05. Conclusions: Hierarchical clustering by Pearson correlation of differentially expressed genes uncovered the expression of alpha cell related genes in beta cells. This provides a possible impairment of beta cell identity reflected in RNA expression profiles. Overall design: Beta cell mRNA profiles of 3 mpf wild type WT and Tgins:IL1B; cryaa:mCherry Zebrafihs were generated by deep sequencing in duplicate using llumina HiSeq2500.		pubmed:30679186		Con rep2	GSM3494232		source name:Pancreatic beta cells\|genotype/variation:Tgins:mKO\|tissue:Pancreatic beta cells\|age:3 mpf\|genotype:wild type	Con rep2	Illumina NextSeq Control/RTA2 software was used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zebrafish genome GRCz10 using GSNAP from Ensembl gene annotation version 87 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Pancreatic beta cells		Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation islets were collected in PBS chilled on ice. post one washing with ice cold PBS islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 with 0.1% Pluronic F 68 ThermoFisher 24040032 at 37˚C in a benchtop shaker set at 350 rpm for 50 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4˚C. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+ Mg2++0.1% Pluronic F 68. To remove debris the solution was passed over a 30 mm cell filter Miltenyi Biotec 130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype/variation:Tgins:mKO\|tissue:Pancreatic beta cells\|age:3 mpf\|genotype:wild type	GSM3494232	GSM3494232: Con rep2; Danio rerio; RNA Seq	GSM3494232		1	Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation islets were collected in PBS chilled on ice. post one washing with ice cold PBS islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 with 0.1% Pluronic F 68 ThermoFisher 24040032 at 37˚C in a benchtop shaker set at 350 rpm for 50 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4˚C. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+ Mg2++0.1% Pluronic F 68. To remove debris the solution was passed over a 30 mm cell filter Miltenyi Biotec 130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3494232	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP171016			L19373_Track-47629_R1.fastq.gz	fastq	3896547512.0	51270362.0	GSM3494232 r1	0:76	A:1137736314;C:843105511;G:852627922;T:1062822946;N:254819	76		1137736314	843105511	852627922	1062822946	254819	SRX5073700	SRS4087526	SRA815642	GEO	Ninov, CRTD	1	0.86977	0.16515	0.77078	0.40368	76	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2018-11-28	Adult	Adult	Pancreas	Endocrine System
50716	50716	SRR8255919	SRX5073699	SRS4087525	SRP171016	PRJNA507363	Modelling pancreatic beta cell inflammation in zebrafish identifies a natural product for human beta cell protection	GSE123036	Transcriptome Analysis	To assess the effect of chronic inflammation on the beta cells transcriptome we conducted RNA sequencing from 3 mpf zebrafish transgenic line Tgins:IL1B animals and WT siblings The total RNA from FACS sorted Beta cells was isolated using Quick RNA MicroPrep kit R1050 Zymo Research and following the manufacturer instructions. The sequencing was made on llumina HiSeq2500 in 2x75bp paired end mode. method Results:Two replicates for controls and two for IL1B expressing beta cells were sequenced. About 40 million sequence reads per sample were mapped to the Zebrafish genome. We identify around 19 thousand genes per sample. Approximately 6% of the genes were differentially expressed. 1 245 genes with a FDR of 5 showed a fold change =0.7 and adjusted p value <0.05. Conclusions: Hierarchical clustering by Pearson correlation of differentially expressed genes uncovered the expression of alpha cell related genes in beta cells. This provides a possible impairment of beta cell identity reflected in RNA expression profiles. Overall design: Beta cell mRNA profiles of 3 mpf wild type WT and Tgins:IL1B; cryaa:mCherry Zebrafihs were generated by deep sequencing in duplicate using llumina HiSeq2500.		pubmed:30679186		Con rep1	GSM3494231		source name:Pancreatic beta cells\|genotype/variation:Tgins:mKO\|tissue:Pancreatic beta cells\|age:3 mpf\|genotype:wild type	Con rep1	Illumina NextSeq Control/RTA2 software was used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zebrafish genome GRCz10 using GSNAP from Ensembl gene annotation version 87 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Pancreatic beta cells		Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation islets were collected in PBS chilled on ice. post one washing with ice cold PBS islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 with 0.1% Pluronic F 68 ThermoFisher 24040032 at 37˚C in a benchtop shaker set at 350 rpm for 50 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4˚C. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+ Mg2++0.1% Pluronic F 68. To remove debris the solution was passed over a 30 mm cell filter Miltenyi Biotec 130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype/variation:Tgins:mKO\|tissue:Pancreatic beta cells\|age:3 mpf\|genotype:wild type	GSM3494231	GSM3494231: Con rep1; Danio rerio; RNA Seq	GSM3494231		1	Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation islets were collected in PBS chilled on ice. post one washing with ice cold PBS islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 with 0.1% Pluronic F 68 ThermoFisher 24040032 at 37˚C in a benchtop shaker set at 350 rpm for 50 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4˚C. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+ Mg2++0.1% Pluronic F 68. To remove debris the solution was passed over a 30 mm cell filter Miltenyi Biotec 130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3494231	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP171016			L19372_Track-47628_R1.fastq.gz	fastq	3743010792.0	49250142.0	GSM3494231 r1	0:76	A:1081119100;C:816543927;G:821868656;T:1023236057;N:243052	76		1081119100	816543927	821868656	1023236057	243052	SRX5073699	SRS4087525	SRA815642	GEO	Ninov, CRTD	1	0.87612	0.16984	0.7684	0.57882	76	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2018-11-28	Adult	Adult	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");;