metadata: run_metadata: 37 rows where experiment.library_selection = "cDNA", technology = "smartseq" and tissue

37 rows where experiment.library_selection = "cDNA", technology = "smartseq" and tissue_curation = "Gut"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
59044	59044	SRR11585444	SRX8152997	SRS6515547	SRP257811	PRJNA627266	Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks	GSE149081	Transcriptome Analysis	Background: Endocrine cells of the digestive system including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium play an important role in metabolism. Although EECs and PECs are located in distinct organs they share many features and several common genes control their differentiation. In this study we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap. pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes leading to an increase of ghrelin and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion: This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall desi…	pubmed:32867764;pubmed:35286299	EEC MUT 3	GSM4490224	source name:Enteroendocrine cells EECs\|strain:AB\|tissue:Enteroendocrine cells\|age:4 dpf\|genotype:Pax6b /	EEC MUT 3	Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al. 2013 and gene expression was measured from the mapped reads by using built in STAR module quantMode GeneCounts. Genome build: GRCz11 release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample	Enteroendocrine cells EECs	The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al. 2008b TgBACpdx1:EGFPbns13 Helker et al. 2019 TG 8.5nkx2.2a:GFPia2 Pauls et al. 2007 pax6bsa0086 and pax6bsunrise Verbruggen et al. 2010.	Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications the first in the “yield mode” and the second in “the purity mode” using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al. 2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos the pax6sa0086 line Verbruggen et al. 2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086 transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C according the the Smart seq2 protocol Picelli et al. 2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivi…	Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al. 1995.	strain:AB\|tissue:Enteroendocrine cells\|age:4 dpf\|genotype:Pax6b /	GSM4490224	GSM4490224: EEC MUT 3; Danio rerio; RNA Seq	GSM4490224	1	Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications the first in the “yield mode” and the second in “the purity mode” using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al. 2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos the pax6sa0086 line Verbruggen et al. 2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086 transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C according the the Smart seq2 protocol Picelli et al. 2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivi…	GEO Accession:GSM4490224	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP257811	NGS14-B816_Y_TAAGGCGA_L006_R1_001.fastq.gz NGS14-B816_Y_TAAGGCGA_L006_R2_001.fastq.gz	fastq fastq	7305946100.0	36168050.0	GSM4490224 r1	0:101 1:101	A:2038766865;C:1613931139;G:1509805073;T:2128443712;N:14999311	101	101	2038766865	1613931139	1509805073	2128443712	14999311	SRX8152997	SRS6515547	SRA1067841	GEO	GIGA, University of Liège	2	0.8749	0.87565	0.15943	0.16056	0.75365	0.75402	0.54284	0.54869	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	Belgium	2020-04-21	Larval	Larval	Gut	Digestive System
59045	59045	SRR11585443	SRX8152996	SRS6515546	SRP257811	PRJNA627266	Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks	GSE149081	Transcriptome Analysis	Background: Endocrine cells of the digestive system including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium play an important role in metabolism. Although EECs and PECs are located in distinct organs they share many features and several common genes control their differentiation. In this study we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap. pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes leading to an increase of ghrelin and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion: This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall desi…	pubmed:32867764;pubmed:35286299	EEC MUT 2	GSM4490223	source name:Enteroendocrine cells EECs\|strain:AB\|tissue:Enteroendocrine cells\|age:4 dpf\|genotype:Pax6b /	EEC MUT 2	Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al. 2013 and gene expression was measured from the mapped reads by using built in STAR module quantMode GeneCounts. Genome build: GRCz11 release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample	Enteroendocrine cells EECs	The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al. 2008b TgBACpdx1:EGFPbns13 Helker et al. 2019 TG 8.5nkx2.2a:GFPia2 Pauls et al. 2007 pax6bsa0086 and pax6bsunrise Verbruggen et al. 2010.	Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications the first in the “yield mode” and the second in “the purity mode” using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al. 2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos the pax6sa0086 line Verbruggen et al. 2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086 transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C according the the Smart seq2 protocol Picelli et al. 2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivi…	Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al. 1995.	strain:AB\|tissue:Enteroendocrine cells\|age:4 dpf\|genotype:Pax6b /	GSM4490223	GSM4490223: EEC MUT 2; Danio rerio; RNA Seq	GSM4490223	1	Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications the first in the “yield mode” and the second in “the purity mode” using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al. 2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos the pax6sa0086 line Verbruggen et al. 2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086 transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C according the the Smart seq2 protocol Picelli et al. 2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivi…	GEO Accession:GSM4490223	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP257811	NGS14-B812_7_CGTACTAG_L008_R2_001.fastq.gz NGS14-B812_7_CGTACTAG_L008_R1_001.fastq.gz	fastq fastq	11918410666.0	59002033.0	GSM4490223 r1	0:101 1:101	A:3329793292;C:2614866685;G:2397465569;T:3556331253;N:19953867	101	101	3329793292	2614866685	2397465569	3556331253	19953867	SRX8152996	SRS6515546	SRA1067841	GEO	GIGA, University of Liège	2	0.86265	0.86065	0.18072	0.18105	0.7637	0.76646	0.48622	0.58912	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	Belgium	2020-04-21	Larval	Larval	Gut	Digestive System
59046	59046	SRR11585442	SRX8152995	SRS6515545	SRP257811	PRJNA627266	Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks	GSE149081	Transcriptome Analysis	Background: Endocrine cells of the digestive system including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium play an important role in metabolism. Although EECs and PECs are located in distinct organs they share many features and several common genes control their differentiation. In this study we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap. pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes leading to an increase of ghrelin and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion: This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall desi…	pubmed:32867764;pubmed:35286299	EEC MUT 1	GSM4490222	source name:Enteroendocrine cells EECs\|strain:AB\|tissue:Enteroendocrine cells\|age:4 dpf\|genotype:Pax6b /	EEC MUT 1	Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al. 2013 and gene expression was measured from the mapped reads by using built in STAR module quantMode GeneCounts. Genome build: GRCz11 release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample	Enteroendocrine cells EECs	The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al. 2008b TgBACpdx1:EGFPbns13 Helker et al. 2019 TG 8.5nkx2.2a:GFPia2 Pauls et al. 2007 pax6bsa0086 and pax6bsunrise Verbruggen et al. 2010.	Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications the first in the “yield mode” and the second in “the purity mode” using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al. 2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos the pax6sa0086 line Verbruggen et al. 2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086 transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C according the the Smart seq2 protocol Picelli et al. 2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivi…	Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al. 1995.	strain:AB\|tissue:Enteroendocrine cells\|age:4 dpf\|genotype:Pax6b /	GSM4490222	GSM4490222: EEC MUT 1; Danio rerio; RNA Seq	GSM4490222	1	Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications the first in the “yield mode” and the second in “the purity mode” using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al. 2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos the pax6sa0086 line Verbruggen et al. 2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086 transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C according the the Smart seq2 protocol Picelli et al. 2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivi…	GEO Accession:GSM4490222	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP257811	NGS14-B811_4_TAAGGCGA_L008_R1_001.fastq.gz NGS14-B811_4_TAAGGCGA_L008_R2_001.fastq.gz	fastq fastq	17357075836.0	85926118.0	GSM4490222 r1	0:101 1:101	A:4885184535;C:3776696530;G:3534374130;T:5131850822;N:28969819	101	101	4885184535	3776696530	3534374130	5131850822	28969819	SRX8152995	SRS6515545	SRA1067841	GEO	GIGA, University of Liège	2	0.86595	0.86596	0.17082	0.17065	0.75469	0.7569	0.57569	0.57998	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	Belgium	2020-04-21	Larval	Larval	Gut	Digestive System
59047	59047	SRR11585441	SRX8152994	SRS6515544	SRP257811	PRJNA627266	Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks	GSE149081	Transcriptome Analysis	Background: Endocrine cells of the digestive system including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium play an important role in metabolism. Although EECs and PECs are located in distinct organs they share many features and several common genes control their differentiation. In this study we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap. pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes leading to an increase of ghrelin and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion: This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall desi…	pubmed:32867764;pubmed:35286299	EEC WT 4	GSM4490221	source name:Enteroendocrine cells EECs\|strain:AB\|tissue:Enteroendocrine cells\|age:4 dpf\|genotype:Wild type	EEC WT 4	Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al. 2013 and gene expression was measured from the mapped reads by using built in STAR module quantMode GeneCounts. Genome build: GRCz11 release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample	Enteroendocrine cells EECs	The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al. 2008b TgBACpdx1:EGFPbns13 Helker et al. 2019 TG 8.5nkx2.2a:GFPia2 Pauls et al. 2007 pax6bsa0086 and pax6bsunrise Verbruggen et al. 2010.	Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications the first in the “yield mode” and the second in “the purity mode” using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al. 2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos the pax6sa0086 line Verbruggen et al. 2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086 transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C according the the Smart seq2 protocol Picelli et al. 2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivi…	Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al. 1995.	strain:AB\|tissue:Enteroendocrine cells\|age:4 dpf\|genotype:Wild type	GSM4490221	GSM4490221: EEC WT 4; Danio rerio; RNA Seq	GSM4490221	1	Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications the first in the “yield mode” and the second in “the purity mode” using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al. 2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos the pax6sa0086 line Verbruggen et al. 2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086 transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C according the the Smart seq2 protocol Picelli et al. 2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivi…	GEO Accession:GSM4490221	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP257811	NGS14-B103_GutcDNA_GTGAAA_L001_R2_001.fastq.gz NGS14-B103_GutcDNA_GTGAAA_L001_R1_001.fastq.gz	fastq fastq	8611929024.0	42633312.0	GSM4490221 r1	0:101 1:101	A:2475490797;C:1609639919;G:1667747515;T:2814782248;N:44268545	101	101	2475490797	1609639919	1667747515	2814782248	44268545	SRX8152994	SRS6515544	SRA1067841	GEO	GIGA, University of Liège	2	0.88123	0.80064	0.22747	0.21643	0.77195	0.80781	0.49886	0.49179	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	Belgium	2020-04-21	Larval	Larval	Gut	Digestive System
59048	59048	SRR11585440	SRX8152993	SRS6515543	SRP257811	PRJNA627266	Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks	GSE149081	Transcriptome Analysis	Background: Endocrine cells of the digestive system including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium play an important role in metabolism. Although EECs and PECs are located in distinct organs they share many features and several common genes control their differentiation. In this study we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap. pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes leading to an increase of ghrelin and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion: This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall desi…	pubmed:32867764;pubmed:35286299	EEC WT 3	GSM4490220	source name:Enteroendocrine cells EECs\|strain:AB\|tissue:Enteroendocrine cells\|age:4 dpf\|genotype:Wild type	EEC WT 3	Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al. 2013 and gene expression was measured from the mapped reads by using built in STAR module quantMode GeneCounts. Genome build: GRCz11 release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample	Enteroendocrine cells EECs	The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al. 2008b TgBACpdx1:EGFPbns13 Helker et al. 2019 TG 8.5nkx2.2a:GFPia2 Pauls et al. 2007 pax6bsa0086 and pax6bsunrise Verbruggen et al. 2010.	Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications the first in the “yield mode” and the second in “the purity mode” using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al. 2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos the pax6sa0086 line Verbruggen et al. 2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086 transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C according the the Smart seq2 protocol Picelli et al. 2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivi…	Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al. 1995.	strain:AB\|tissue:Enteroendocrine cells\|age:4 dpf\|genotype:Wild type	GSM4490220	GSM4490220: EEC WT 3; Danio rerio; RNA Seq	GSM4490220	1	Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications the first in the “yield mode” and the second in “the purity mode” using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al. 2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos the pax6sa0086 line Verbruggen et al. 2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086 transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C according the the Smart seq2 protocol Picelli et al. 2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivi…	GEO Accession:GSM4490220	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP257811	NGS14-B709_K_GGACTCCT_L005_R1_001.fastq.gz NGS14-B709_K_GGACTCCT_L005_R2_001.fastq.gz	fastq fastq	10354295578.0	51258889.0	GSM4490220 r1	0:101 1:101	A:2967030863;C:2195339515;G:2034968623;T:3128829625;N:28126952	101	101	2967030863	2195339515	2034968623	3128829625	28126952	SRX8152993	SRS6515543	SRA1067841	GEO	GIGA, University of Liège	2	0.87011	0.86185	0.17853	0.17636	0.76435	0.76609	0.52736	0.51806	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	Belgium	2020-04-21	Larval	Larval	Gut	Digestive System
59049	59049	SRR11585439	SRX8152992	SRS6515542	SRP257811	PRJNA627266	Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks	GSE149081	Transcriptome Analysis	Background: Endocrine cells of the digestive system including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium play an important role in metabolism. Although EECs and PECs are located in distinct organs they share many features and several common genes control their differentiation. In this study we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap. pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes leading to an increase of ghrelin and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion: This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall desi…	pubmed:32867764;pubmed:35286299	EEC WT 2	GSM4490219	source name:Enteroendocrine cells EECs\|strain:AB\|tissue:Enteroendocrine cells\|age:4 dpf\|genotype:Wild type	EEC WT 2	Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al. 2013 and gene expression was measured from the mapped reads by using built in STAR module quantMode GeneCounts. Genome build: GRCz11 release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample	Enteroendocrine cells EECs	The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al. 2008b TgBACpdx1:EGFPbns13 Helker et al. 2019 TG 8.5nkx2.2a:GFPia2 Pauls et al. 2007 pax6bsa0086 and pax6bsunrise Verbruggen et al. 2010.	Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications the first in the “yield mode” and the second in “the purity mode” using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al. 2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos the pax6sa0086 line Verbruggen et al. 2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086 transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C according the the Smart seq2 protocol Picelli et al. 2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivi…	Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al. 1995.	strain:AB\|tissue:Enteroendocrine cells\|age:4 dpf\|genotype:Wild type	GSM4490219	GSM4490219: EEC WT 2; Danio rerio; RNA Seq	GSM4490219	1	Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications the first in the “yield mode” and the second in “the purity mode” using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al. 2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos the pax6sa0086 line Verbruggen et al. 2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086 transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C according the the Smart seq2 protocol Picelli et al. 2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivi…	GEO Accession:GSM4490219	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP257811	NGS14-B708_D_AGGCAGAA_L005_R1_001.fastq.gz NGS14-B708_D_AGGCAGAA_L005_R2_001.fastq.gz	fastq fastq	12045022246.0	59628823.0	GSM4490219 r1	0:101 1:101	A:3416690974;C:2604045484;G:2417147877;T:3574238685;N:32899226	101	101	3416690974	2604045484	2417147877	3574238685	32899226	SRX8152992	SRS6515542	SRA1067841	GEO	GIGA, University of Liège	2	0.86842	0.86282	0.21951	0.2191	0.75532	0.75879	0.53544	0.53713	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	Belgium	2020-04-21	Larval	Larval	Gut	Digestive System
59050	59050	SRR11585438	SRX8152991	SRS6515541	SRP257811	PRJNA627266	Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks	GSE149081	Transcriptome Analysis	Background: Endocrine cells of the digestive system including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium play an important role in metabolism. Although EECs and PECs are located in distinct organs they share many features and several common genes control their differentiation. In this study we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap. pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes leading to an increase of ghrelin and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion: This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall desi…	pubmed:32867764;pubmed:35286299	EEC WT 1	GSM4490218	source name:Enteroendocrine cells EECs\|strain:AB\|tissue:Enteroendocrine cells\|age:4 dpf\|genotype:Wild type	EEC WT 1	Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al. 2013 and gene expression was measured from the mapped reads by using built in STAR module quantMode GeneCounts. Genome build: GRCz11 release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample	Enteroendocrine cells EECs	The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al. 2008b TgBACpdx1:EGFPbns13 Helker et al. 2019 TG 8.5nkx2.2a:GFPia2 Pauls et al. 2007 pax6bsa0086 and pax6bsunrise Verbruggen et al. 2010.	Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications the first in the “yield mode” and the second in “the purity mode” using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al. 2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos the pax6sa0086 line Verbruggen et al. 2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086 transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C according the the Smart seq2 protocol Picelli et al. 2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivi…	Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al. 1995.	strain:AB\|tissue:Enteroendocrine cells\|age:4 dpf\|genotype:Wild type	GSM4490218	GSM4490218: EEC WT 1; Danio rerio; RNA Seq	GSM4490218	1	Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications the first in the “yield mode” and the second in “the purity mode” using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al. 2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos the pax6sa0086 line Verbruggen et al. 2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086 transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C according the the Smart seq2 protocol Picelli et al. 2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivi…	GEO Accession:GSM4490218	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP257811	NGS15-D205_WT-4dpf_TAAGGCGA_L008_R2_001.fastq.gz NGS15-D205_WT-4dpf_TAAGGCGA_L008_R1_001.fastq.gz	fastq fastq	20091433484.0	99462542.0	GSM4490218 r1	0:101 1:101	A:5656340585;C:4375126690;G:4104085278;T:5941433597;N:14447334	101	101	5656340585	4375126690	4104085278	5941433597	14447334	SRX8152991	SRS6515541	SRA1067841	GEO	GIGA, University of Liège	2	0.86594	0.86466	0.15632	0.15772	0.76081	0.76453	0.53085	0.53533	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	Belgium	2020-04-21	Larval	Larval	Gut	Digestive System
59456	59456	SRR11917488	SRX8463993	SRS6765214	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	CV3 IEC	GSM4588952	tissue:intestine\|group:Conventionalized\|cell type:Other intestinal epithelium cells	CV3 IEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Conventionalized\|cell type:Other intestinal epithelium cells	GSM4588952	GSM4588952: CV3 IEC; Danio rerio; RNA Seq	GSM4588952	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588952	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S12_S12_L006_R1_001.fastq.gz	fastq	989770770.0	19407270.0	GSM4588952 r1	0:51 1:0	A:281534917;C:214882196;G:215847745;T:277443986;N:61926	51	0	281534917	214882196	215847745	277443986	61926	SRX8463993	SRS6765214	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.85529		0.16671		0.87886		0.67632		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59457	59457	SRR11917489	SRX8463993	SRS6765214	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	CV3 IEC	GSM4588952	tissue:intestine\|group:Conventionalized\|cell type:Other intestinal epithelium cells	CV3 IEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Conventionalized\|cell type:Other intestinal epithelium cells	GSM4588952	GSM4588952: CV3 IEC; Danio rerio; RNA Seq	GSM4588952	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588952	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S12_S12_L007_R1_001.fastq.gz	fastq	970629807.0	19031957.0	GSM4588952 r2	0:51 1:0	A:276238559;C:210614378;G:211564800;T:272166193;N:45877	51	0	276238559	210614378	211564800	272166193	45877	SRX8463993	SRS6765214	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.85557		0.16793		0.87819		0.68247		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59458	59458	SRR11917486	SRX8463992	SRS6765213	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	CV3 EEC	GSM4588951	tissue:intestine\|group:Conventionalized\|cell type:Enteroendocrine cells	CV3 EEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Conventionalized\|cell type:Enteroendocrine cells	GSM4588951	GSM4588951: CV3 EEC; Danio rerio; RNA Seq	GSM4588951	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588951	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S11_S11_L006_R1_001.fastq.gz	fastq	1116941667.0	21900817.0	GSM4588951 r1	0:51 1:0	A:320236417;C:240301779;G:240594328;T:315739633;N:69510	51	0	320236417	240301779	240594328	315739633	69510	SRX8463992	SRS6765213	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.60354		0.13851		0.86699		0.49869		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59459	59459	SRR11917487	SRX8463992	SRS6765213	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	CV3 EEC	GSM4588951	tissue:intestine\|group:Conventionalized\|cell type:Enteroendocrine cells	CV3 EEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Conventionalized\|cell type:Enteroendocrine cells	GSM4588951	GSM4588951: CV3 EEC; Danio rerio; RNA Seq	GSM4588951	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588951	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S11_S11_L007_R1_001.fastq.gz	fastq	1100752584.0	21583384.0	GSM4588951 r2	0:51 1:0	A:315761089;C:236724849;G:236992907;T:311222165;N:51574	51	0	315761089	236724849	236992907	311222165	51574	SRX8463992	SRS6765213	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.60449		0.13991		0.86519		0.49824		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59460	59460	SRR11917484	SRX8463991	SRS6765212	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	GF3 IEC	GSM4588950	tissue:intestine\|group:Germ free\|cell type:Other intestinal epithelium cells	GF3 IEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Germ free\|cell type:Other intestinal epithelium cells	GSM4588950	GSM4588950: GF3 IEC; Danio rerio; RNA Seq	GSM4588950	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588950	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S10_S10_L006_R1_001.fastq.gz	fastq	1158251565.0	22710815.0	GSM4588950 r1	0:51 1:0	A:329413690;C:252108273;G:252469757;T:324185740;N:74105	51	0	329413690	252108273	252469757	324185740	74105	SRX8463991	SRS6765212	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.8667		0.17916		0.81631		0.60631		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59461	59461	SRR11917485	SRX8463991	SRS6765212	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	GF3 IEC	GSM4588950	tissue:intestine\|group:Germ free\|cell type:Other intestinal epithelium cells	GF3 IEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Germ free\|cell type:Other intestinal epithelium cells	GSM4588950	GSM4588950: GF3 IEC; Danio rerio; RNA Seq	GSM4588950	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588950	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S10_S10_L007_R1_001.fastq.gz	fastq	1140502902.0	22362802.0	GSM4588950 r2	0:51 1:0	A:324550812;C:248145888;G:248413979;T:319338762;N:53461	51	0	324550812	248145888	248413979	319338762	53461	SRX8463991	SRS6765212	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.86472		0.17957		0.81604		0.60323		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59462	59462	SRR11917482	SRX8463990	SRS6765211	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	GF3 EEC	GSM4588949	tissue:intestine\|group:Germ free\|cell type:Enteroendocrine cells	GF3 EEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Germ free\|cell type:Enteroendocrine cells	GSM4588949	GSM4588949: GF3 EEC; Danio rerio; RNA Seq	GSM4588949	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588949	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S9_S9_L006_R1_001.fastq.gz	fastq	1124335902.0	22045802.0	GSM4588949 r1	0:51 1:0	A:323779238;C:243076994;G:243426022;T:313982480;N:71168	51	0	323779238	243076994	243426022	313982480	71168	SRX8463990	SRS6765211	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.82417		0.22133		0.82262		0.53921		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59463	59463	SRR11917483	SRX8463990	SRS6765211	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	GF3 EEC	GSM4588949	tissue:intestine\|group:Germ free\|cell type:Enteroendocrine cells	GF3 EEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Germ free\|cell type:Enteroendocrine cells	GSM4588949	GSM4588949: GF3 EEC; Danio rerio; RNA Seq	GSM4588949	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588949	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S9_S9_L007_R1_001.fastq.gz	fastq	1102409217.0	21615867.0	GSM4588949 r2	0:51 1:0	A:317592665;C:238208950;G:238561212;T:307994643;N:51747	51	0	317592665	238208950	238561212	307994643	51747	SRX8463990	SRS6765211	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.82287		0.22204		0.82037		0.54199		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59464	59464	SRR11917480	SRX8463989	SRS6765210	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	CV2 IED	GSM4588948	tissue:intestine\|group:Conventionalized\|cell type:Other intestinal epithelium cells	CV2 IED	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Conventionalized\|cell type:Other intestinal epithelium cells	GSM4588948	GSM4588948: CV2 IED; Danio rerio; RNA Seq	GSM4588948	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588948	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S8_S8_L006_R1_001.fastq.gz	fastq	1153200474.0	22611774.0	GSM4588948 r1	0:51 1:0	A:325960158;C:253028514;G:253402635;T:320734834;N:74333	51	0	325960158	253028514	253402635	320734834	74333	SRX8463989	SRS6765210	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.87013		0.18232		0.74217		0.52659		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59465	59465	SRR11917481	SRX8463989	SRS6765210	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	CV2 IED	GSM4588948	tissue:intestine\|group:Conventionalized\|cell type:Other intestinal epithelium cells	CV2 IED	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Conventionalized\|cell type:Other intestinal epithelium cells	GSM4588948	GSM4588948: CV2 IED; Danio rerio; RNA Seq	GSM4588948	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588948	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S8_S8_L007_R1_001.fastq.gz	fastq	1129915098.0	22155198.0	GSM4588948 r2	0:51 1:0	A:319498713;C:247882461;G:248181774;T:314298474;N:53676	51	0	319498713	247882461	248181774	314298474	53676	SRX8463989	SRS6765210	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.8695		0.18113		0.74156		0.52983		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59466	59466	SRR11917478	SRX8463988	SRS6765209	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	CV2 EEC	GSM4588947	tissue:intestine\|group:Conventionalized\|cell type:Enteroendocrine cells	CV2 EEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Conventionalized\|cell type:Enteroendocrine cells	GSM4588947	GSM4588947: CV2 EEC; Danio rerio; RNA Seq	GSM4588947	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588947	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S7_S7_L006_R1_001.fastq.gz	fastq	1378636692.0	27032092.0	GSM4588947 r1	0:51 1:0	A:391264014;C:300388051;G:302055880;T:384841320;N:87427	51	0	391264014	300388051	302055880	384841320	87427	SRX8463988	SRS6765209	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.86069		0.20189		0.74643		0.48529		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59467	59467	SRR11917479	SRX8463988	SRS6765209	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	CV2 EEC	GSM4588947	tissue:intestine\|group:Conventionalized\|cell type:Enteroendocrine cells	CV2 EEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Conventionalized\|cell type:Enteroendocrine cells	GSM4588947	GSM4588947: CV2 EEC; Danio rerio; RNA Seq	GSM4588947	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588947	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S7_S7_L007_R1_001.fastq.gz	fastq	1355490597.0	26578247.0	GSM4588947 r2	0:51 1:0	A:384933467;C:295204222;G:296869394;T:378419448;N:64066	51	0	384933467	295204222	296869394	378419448	64066	SRX8463988	SRS6765209	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.86045		0.20313		0.74667		0.48228		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59468	59468	SRR11917476	SRX8463987	SRS6765208	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	GF2 IEC	GSM4588946	tissue:intestine\|group:Germ free\|cell type:Other intestinal epithelium cells	GF2 IEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Germ free\|cell type:Other intestinal epithelium cells	GSM4588946	GSM4588946: GF2 IEC; Danio rerio; RNA Seq	GSM4588946	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588946	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S6_S6_L006_R1_001.fastq.gz	fastq	1096567014.0	21501314.0	GSM4588946 r1	0:51 1:0	A:310133103;C:241356167;G:241726971;T:303281850;N:68923	51	0	310133103	241356167	241726971	303281850	68923	SRX8463987	SRS6765208	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.87328		0.17387		0.86657		0.64049		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59469	59469	SRR11917477	SRX8463987	SRS6765208	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	GF2 IEC	GSM4588946	tissue:intestine\|group:Germ free\|cell type:Other intestinal epithelium cells	GF2 IEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Germ free\|cell type:Other intestinal epithelium cells	GSM4588946	GSM4588946: GF2 IEC; Danio rerio; RNA Seq	GSM4588946	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588946	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S6_S6_L007_R1_001.fastq.gz	fastq	1077795036.0	21133236.0	GSM4588946 r2	0:51 1:0	A:305006168;C:237104899;G:237493375;T:298139724;N:50870	51	0	305006168	237104899	237493375	298139724	50870	SRX8463987	SRS6765208	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.87121		0.17225		0.86776		0.65328		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59470	59470	SRR11917474	SRX8463986	SRS6765207	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	GF2 EEC	GSM4588945	tissue:intestine\|group:Germ free\|cell type:Enteroendocrine cells	GF2 EEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Germ free\|cell type:Enteroendocrine cells	GSM4588945	GSM4588945: GF2 EEC; Danio rerio; RNA Seq	GSM4588945	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588945	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S5_S5_L006_R1_001.fastq.gz	fastq	993591180.0	19482180.0	GSM4588945 r1	0:51 1:0	A:282890765;C:216703865;G:217669683;T:276263863;N:63004	51	0	282890765	216703865	217669683	276263863	63004	SRX8463986	SRS6765207	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.84026		0.15974		0.84542		0.62819		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59471	59471	SRR11917475	SRX8463986	SRS6765207	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	GF2 EEC	GSM4588945	tissue:intestine\|group:Germ free\|cell type:Enteroendocrine cells	GF2 EEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Germ free\|cell type:Enteroendocrine cells	GSM4588945	GSM4588945: GF2 EEC; Danio rerio; RNA Seq	GSM4588945	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588945	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S5_S5_L007_R1_001.fastq.gz	fastq	974360049.0	19105099.0	GSM4588945 r2	0:51 1:0	A:277539322;C:212402095;G:213358281;T:271014144;N:46207	51	0	277539322	212402095	213358281	271014144	46207	SRX8463986	SRS6765207	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.84253		0.16032		0.84723		0.62874		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59472	59472	SRR11917472	SRX8463985	SRS6765206	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	CV1 IEC	GSM4588944	tissue:intestine\|group:Conventionalized\|cell type:Other intestinal epithelium cells	CV1 IEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Conventionalized\|cell type:Other intestinal epithelium cells	GSM4588944	GSM4588944: CV1 IEC; Danio rerio; RNA Seq	GSM4588944	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588944	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S4_S4_L006_R1_001.fastq.gz	fastq	1125747633.0	22073483.0	GSM4588944 r1	0:51 1:0	A:318281873;C:249238273;G:249957107;T:308199627;N:70753	51	0	318281873	249238273	249957107	308199627	70753	SRX8463985	SRS6765206	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.89074		0.12353		0.82816		0.68204		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59473	59473	SRR11917473	SRX8463985	SRS6765206	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	CV1 IEC	GSM4588944	tissue:intestine\|group:Conventionalized\|cell type:Other intestinal epithelium cells	CV1 IEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Conventionalized\|cell type:Other intestinal epithelium cells	GSM4588944	GSM4588944: CV1 IEC; Danio rerio; RNA Seq	GSM4588944	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588944	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S4_S4_L007_R1_001.fastq.gz	fastq	1105934796.0	21684996.0	GSM4588944 r2	0:51 1:0	A:312851469;C:244757781;G:245446410;T:302827147;N:51989	51	0	312851469	244757781	245446410	302827147	51989	SRX8463985	SRS6765206	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.88843		0.12342		0.82873		0.67656		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59474	59474	SRR11917470	SRX8463984	SRS6765204	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	CV1 EEC	GSM4588943	tissue:intestine\|group:Conventionalized\|cell type:Enteroendocrine cells	CV1 EEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Conventionalized\|cell type:Enteroendocrine cells	GSM4588943	GSM4588943: CV1 EEC; Danio rerio; RNA Seq	GSM4588943	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588943	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S3_S3_L006_R1_001.fastq.gz	fastq	942559764.0	18481564.0	GSM4588943 r1	0:51 1:0	A:263978139;C:208960440;G:211142234;T:258419586;N:59365	51	0	263978139	208960440	211142234	258419586	59365	SRX8463984	SRS6765204	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.84651		0.13502		0.87334		0.60719		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59475	59475	SRR11917471	SRX8463984	SRS6765204	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	CV1 EEC	GSM4588943	tissue:intestine\|group:Conventionalized\|cell type:Enteroendocrine cells	CV1 EEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Conventionalized\|cell type:Enteroendocrine cells	GSM4588943	GSM4588943: CV1 EEC; Danio rerio; RNA Seq	GSM4588943	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588943	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S3_S3_L007_R1_001.fastq.gz	fastq	923680839.0	18111389.0	GSM4588943 r2	0:51 1:0	A:258844956;C:204695214;G:206849563;T:253247421;N:43685	51	0	258844956	204695214	206849563	253247421	43685	SRX8463984	SRS6765204	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.84566		0.13508		0.8746		0.60113		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59476	59476	SRR11917468	SRX8463983	SRS6765205	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	GF1 IEC	GSM4588942	tissue:intestine\|group:Germ free\|cell type:Other intestinal epithelium cells	GF1 IEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Germ free\|cell type:Other intestinal epithelium cells	GSM4588942	GSM4588942: GF1 IEC; Danio rerio; RNA Seq	GSM4588942	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588942	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S2_S2_L006_R1_001.fastq.gz	fastq	1238473698.0	24283798.0	GSM4588942 r1	0:51 1:0	A:341609725;C:281085121;G:281016378;T:334683690;N:78784	51	0	341609725	281085121	281016378	334683690	78784	SRX8463983	SRS6765205	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.88819		0.1308		0.81357		0.57234		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59477	59477	SRR11917469	SRX8463983	SRS6765205	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	GF1 IEC	GSM4588942	tissue:intestine\|group:Germ free\|cell type:Other intestinal epithelium cells	GF1 IEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Germ free\|cell type:Other intestinal epithelium cells	GSM4588942	GSM4588942: GF1 IEC; Danio rerio; RNA Seq	GSM4588942	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588942	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S2_S2_L007_R1_001.fastq.gz	fastq	1215535785.0	23834035.0	GSM4588942 r2	0:51 1:0	A:335462084;C:275714789;G:275686585;T:328614149;N:58178	51	0	335462084	275714789	275686585	328614149	58178	SRX8463983	SRS6765205	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.88988		0.13024		0.81262		0.57631		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59478	59478	SRR11917466	SRX8463982	SRS6765203	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	GF1 EEC	GSM4588941	tissue:intestine\|group:Germ free\|cell type:Enteroendocrine cells	GF1 EEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Germ free\|cell type:Enteroendocrine cells	GSM4588941	GSM4588941: GF1 EEC; Danio rerio; RNA Seq	GSM4588941	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588941	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S1_S1_L006_R1_001.fastq.gz	fastq	1106448264.0	21695064.0	GSM4588941 r1	0:51 1:0	A:312177906;C:243246164;G:244584142;T:306370900;N:69152	51	0	312177906	243246164	244584142	306370900	69152	SRX8463982	SRS6765203	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.7883		0.14389		0.88158		0.55008		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
59479	59479	SRR11917467	SRX8463982	SRS6765203	SRP265808	PRJNA637035	Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	GSE151711	Transcriptome Analysis	RNA seq of isolated zebrafish enteroendocrine cells and other intestinal epithelium cells from germ free GF and conventionalized CV zebrafish Overall design: CV and GF TgBACcldn15la:EGFP; Tgneurod1:TagRFP 8 dpf zebrafish larvae were used for Flow Activated Cell Sorting FACS to isolate zebrafish EECs and other IECs. Samples from three independent experimental replicates were performed. 250 580 EECs n=3 for each CV and GF group and 100 IECs n=3 for each CV and GF group from each experiment were used for library generation and RNA sequencing.	pubmed:38577841	GF1 EEC	GSM4588941	tissue:intestine\|group:Germ free\|cell type:Enteroendocrine cells	GF1 EEC	Adapters were trimmed using Trim Galore!Galaxy Version 0.4.2 by automatic detection Trimmed reads were mapped to the danRer10 genome using HISAT2Galaxy Version 2.0.5.1 using default settings Gene counts were generated using ht seq count Galaxy Version 0.6.1galaxy3 and Ensembl gene annotations GRCz10.82 using default settings and a minimum quality of 10. Gene count tables were used as input for Deseq2 Galaxy Version 2.11.39 using default settings Genome build: danRer10 Supplementary files format and content: Matrix table with gene counts for everygene and every sample	intestine	no treatment	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	Gnotobiotic zebrafish	group:Germ free\|cell type:Enteroendocrine cells	GSM4588941	GSM4588941: GF1 EEC; Danio rerio; RNA Seq	GSM4588941	1	Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit Beckman following the manufacturer's instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART Seq v4 Ultra Low Input RNA Kit Takara was used to generate full length cDNA. mRNA transcripts were converted into cDNA through Clontech's oligodT priming method. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4588941	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP265808	LY-S1_S1_L007_R1_001.fastq.gz	fastq	1082299917.0	21221567.0	GSM4588941 r2	0:51 1:0	A:305489640;C:237873171;G:239135258;T:299751004;N:50844	51	0	305489640	237873171	239135258	299751004	50844	SRX8463982	SRS6765203	SRA1082774	GEO	Rawls lab, MGM Department, Duke University	1	0.78533		0.14463		0.88229		0.56056		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq	United States	2020-06-03	Undetermined	Larval	Gut	Digestive System
60508	60508	SRR12340127	SRX8839914	SRS7103148	SRP273975	PRJNA649247	Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine	GSE155287	Transcriptome Analysis	In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP sox17 gill DsRedx and intestine sox17 intestine GFP sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine including GFP labelled metaphocytes and DsRedx labelled macrophages were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.	pubmed:33027664	sox17 intestine DsRedx 3	GSM4698511	source name:specific cells types in zebrafish intestine\|tissue:intestine\|age:adult\|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP	sox17 intestine DsRedx 3	Raw reads were first aligned to zebrafish reference genome danRer11 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample	specific cells types in zebrafish intestine		30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.		tissue:intestine\|age:adult\|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP	GSM4698511	GSM4698511: sox17 intestine DsRedx 3; Danio rerio; RNA Seq	GSM4698511	1	30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.	GEO Accession:GSM4698511	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP273975	sox17_intestine_DsRedx_3_R1.fq.gz sox17_intestine_DsRedx_3_R2.fq.gz	fastq fastq	6135943356.0	20831675.0	GSM4698511 r1	0:147.55 1:147.00	A:1698794122;C:1364496535;G:1307692475;T:1764931459;N:28765	147	147	1698794122	1364496535	1307692475	1764931459	28765	SRX8839914	SRS7103148	SRA1104756	GEO	Room 6319, Division of Life Science, Hong Kong University of Science and Technology	2	0.868	0.8679	0.19631	0.19595	0.88002	0.88036	0.55312	0.54436	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2020-07-28	Adult	Adult	Gut	Digestive System
60509	60509	SRR12340126	SRX8839913	SRS7103147	SRP273975	PRJNA649247	Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine	GSE155287	Transcriptome Analysis	In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP sox17 gill DsRedx and intestine sox17 intestine GFP sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine including GFP labelled metaphocytes and DsRedx labelled macrophages were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.	pubmed:33027664	sox17 intestine DsRedx 2	GSM4698510	source name:specific cells types in zebrafish intestine\|tissue:intestine\|age:adult\|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP	sox17 intestine DsRedx 2	Raw reads were first aligned to zebrafish reference genome danRer11 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample	specific cells types in zebrafish intestine		30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.		tissue:intestine\|age:adult\|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP	GSM4698510	GSM4698510: sox17 intestine DsRedx 2; Danio rerio; RNA Seq	GSM4698510	1	30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.	GEO Accession:GSM4698510	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP273975	sox17_intestine_DsRedx_2_R1.fq.gz sox17_intestine_DsRedx_2_R2.fq.gz	fastq fastq	5763127951.0	19786561.0	GSM4698510 r1	0:145.82 1:145.44	A:1642307410;C:1243357808;G:1159617669;T:1717817199;N:27865	145	145	1642307410	1243357808	1159617669	1717817199	27865	SRX8839913	SRS7103147	SRA1104756	GEO	Room 6319, Division of Life Science, Hong Kong University of Science and Technology	2	0.83861	0.8393	0.20669	0.20652	0.8647	0.8645	0.58971	0.59768	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2020-07-28	Adult	Adult	Gut	Digestive System
60510	60510	SRR12340125	SRX8839912	SRS7103146	SRP273975	PRJNA649247	Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine	GSE155287	Transcriptome Analysis	In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP sox17 gill DsRedx and intestine sox17 intestine GFP sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine including GFP labelled metaphocytes and DsRedx labelled macrophages were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.	pubmed:33027664	sox17 intestine DsRedx 1	GSM4698509	source name:specific cells types in zebrafish intestine\|tissue:intestine\|age:adult\|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP	sox17 intestine DsRedx 1	Raw reads were first aligned to zebrafish reference genome danRer11 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample	specific cells types in zebrafish intestine		30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.		tissue:intestine\|age:adult\|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP	GSM4698509	GSM4698509: sox17 intestine DsRedx 1; Danio rerio; RNA Seq	GSM4698509	1	30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.	GEO Accession:GSM4698509	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP273975	sox17_intestine_DsRedx_1_R1.fq.gz sox17_intestine_DsRedx_1_R2.fq.gz	fastq fastq	6484425817.0	22330508.0	GSM4698509 r1	0:145.39 1:144.99	A:1857262303;C:1388771553;G:1287877569;T:1950483481;N:30911	145	144	1857262303	1388771553	1287877569	1950483481	30911	SRX8839912	SRS7103146	SRA1104756	GEO	Room 6319, Division of Life Science, Hong Kong University of Science and Technology	2	0.82066	0.82155	0.22814	0.22824	0.87377	0.8743	0.61056	0.60858	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2020-07-28	Adult	Adult	Gut	Digestive System
60511	60511	SRR12340124	SRX8839911	SRS7103145	SRP273975	PRJNA649247	Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine	GSE155287	Transcriptome Analysis	In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP sox17 gill DsRedx and intestine sox17 intestine GFP sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine including GFP labelled metaphocytes and DsRedx labelled macrophages were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.	pubmed:33027664	sox17 intestine GFP 3	GSM4698508	source name:specific cells types in zebrafish intestine\|tissue:intestine\|age:adult\|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP	sox17 intestine GFP 3	Raw reads were first aligned to zebrafish reference genome danRer11 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample	specific cells types in zebrafish intestine		30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.		tissue:intestine\|age:adult\|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP	GSM4698508	GSM4698508: sox17 intestine GFP 3; Danio rerio; RNA Seq	GSM4698508	1	30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.	GEO Accession:GSM4698508	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP273975	sox17_intestine_GFP_3_R1.fq.gz sox17_intestine_GFP_3_R2.fq.gz	fastq fastq	8230115918.0	28247287.0	GSM4698508 r1	0:145.73 1:145.63	A:2279605865;C:1874527297;G:1755943559;T:2320000025;N:39172	145	145	2279605865	1874527297	1755943559	2320000025	39172	SRX8839911	SRS7103145	SRA1104756	GEO	Room 6319, Division of Life Science, Hong Kong University of Science and Technology	2	0.89319	0.89503	0.11227	0.11159	0.83682	0.8367	0.54907	0.54907	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2020-07-28	Adult	Adult	Gut	Digestive System
60512	60512	SRR12340123	SRX8839910	SRS7103144	SRP273975	PRJNA649247	Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine	GSE155287	Transcriptome Analysis	In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP sox17 gill DsRedx and intestine sox17 intestine GFP sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine including GFP labelled metaphocytes and DsRedx labelled macrophages were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.	pubmed:33027664	sox17 intestine GFP 2	GSM4698507	source name:specific cells types in zebrafish intestine\|tissue:intestine\|age:adult\|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP	sox17 intestine GFP 2	Raw reads were first aligned to zebrafish reference genome danRer11 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample	specific cells types in zebrafish intestine		30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.		tissue:intestine\|age:adult\|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP	GSM4698507	GSM4698507: sox17 intestine GFP 2; Danio rerio; RNA Seq	GSM4698507	1	30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.	GEO Accession:GSM4698507	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP273975	sox17_intestine_GFP_2_R1.fq.gz sox17_intestine_GFP_2_R2.fq.gz	fastq fastq	6479576756.0	22453932.0	GSM4698507 r1	0:144.22 1:144.35	A:1778809797;C:1490061179;G:1363677096;T:1846998091;N:30593	144	144	1778809797	1490061179	1363677096	1846998091	30593	SRX8839910	SRS7103144	SRA1104756	GEO	Room 6319, Division of Life Science, Hong Kong University of Science and Technology	2	0.88938	0.89273	0.12556	0.12598	0.81878	0.81931	0.46564	0.46026	134	138	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2020-07-28	Adult	Adult	Gut	Digestive System
60513	60513	SRR12340122	SRX8839909	SRS7103143	SRP273975	PRJNA649247	Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine	GSE155287	Transcriptome Analysis	In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP sox17 gill DsRedx and intestine sox17 intestine GFP sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine including GFP labelled metaphocytes and DsRedx labelled macrophages were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.	pubmed:33027664	sox17 intestine GFP 1	GSM4698506	source name:specific cells types in zebrafish intestine\|tissue:intestine\|age:adult\|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP	sox17 intestine GFP 1	Raw reads were first aligned to zebrafish reference genome danRer11 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample	specific cells types in zebrafish intestine		30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.		tissue:intestine\|age:adult\|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP	GSM4698506	GSM4698506: sox17 intestine GFP 1; Danio rerio; RNA Seq	GSM4698506	1	30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.	GEO Accession:GSM4698506	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP273975	sox17_intestine_GFP_1_R1.fq.gz sox17_intestine_GFP_1_R2.fq.gz	fastq fastq	6530870323.0	22300046.0	GSM4698506 r1	0:146.53 1:146.33	A:1835537904;C:1446222021;G:1365264456;T:1883815076;N:30866	146	146	1835537904	1446222021	1365264456	1883815076	30866	SRX8839909	SRS7103143	SRA1104756	GEO	Room 6319, Division of Life Science, Hong Kong University of Science and Technology	2	0.88552	0.88581	0.16898	0.16914	0.83437	0.83532	0.53121	0.54349	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2020-07-28	Adult	Adult	Gut	Digestive 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");;