run_metadata: 59055

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_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	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
59055	SRR11585433	SRX8152986	SRS6515536	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 design: RNA sequencing of 13 samples. Pancreatic endocrine cell pax6b:GFP + transcriptomic profiles of 27 hpf wild type WT and pax6b / MUT zebrafish embryos were generated in triplicates. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4d wild type WT and pax6b / MUT zebrafish emryos were generated in 4 replicates and 3 replicates respectively.		pubmed:32867764;pubmed:35286299		PEC WT 2	GSM4490213		source name:Pancreatic endocrine cells PECs\|strain:AB\|tissue:Endocrine pancreas\|age:27 hpf\|genotype:Wild type	PEC 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	Pancreatic endocrine cells PECs	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 Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.	Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al. 1995.	strain:AB\|tissue:Endocrine pancreas\|age:27 hpf\|genotype:Wild type	GSM4490213	GSM4490213: PEC WT 2; Danio rerio; RNA Seq	GSM4490213		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 Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.	GEO Accession:GSM4490213	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP257811			NGS14-B808_G_TCCTGAGC_L008_R1_001.fastq.gz NGS14-B808_G_TCCTGAGC_L008_R2_001.fastq.gz	fastq fastq	10503079890.0	51995445.0	GSM4490213 r1	0:101 1:101	A:2976843650;C:2276866070;G:2085770808;T:3145487654;N:18111708	101	101			2976843650	2276866070	2085770808	3145487654	18111708	SRX8152986	SRS6515536	SRA1067841	GEO	GIGA, University of Liège	2	0.86353	0.86275	0.20842	0.20846	0.77684	0.778	0.58056	0.58259	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq		Belgium	2020-04-21	Pharyngula	Embryo	Pancreas	Endocrine System