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
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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