metadata: run_metadata: 329 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "cDNA" and tissue_curation

329 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "cDNA" and tissue_curation_coarse = "Digestive System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
29041	29041	SRR26990794	SRX22683825	SRS19677539	SRP474986	PRJNA1046526	ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease	GSE248975	Transcriptome Analysis	Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.		pubmed:39526957		WT gut3	GSM7924158	source name:gut\|tissue:gut\|genotype:wildtype\|time:50dpf\|geo loc name:missing\|collection date:missing	WT gut3	The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.	gut	Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.	RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.	For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.	tissue:gut\|genotype:wildtype\|time:50dpf	GSM7924158	GSM7924158: WT gut3; Danio rerio; RNA Seq	GSM7924158 r1	GSM7924158	1	RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP474986	loader:fastq load.py	12_WT_3G_S27_L001_R2_001.fastq.gz 12_WT_3G_S27_L001_R1_001.fastq.gz	fastq fastq	6066709786.0	20088443.0	GSM7924158 r1	0:151 1:151	A:1673762656;C:1360901090;G:1385125931;T:1646863953;N:56156	151	151			1673762656	1360901090	1385125931	1646863953	56156	SRX22683825	SRS19677539	SRA1760061	Muise Lab, Cell Biology, The Hospital for Sick Children	Muise Lab, Cell Biology, The Hospital for Sick Children	2	0.92515	0.9297	0.0691	0.0659	0.75041	0.75022	0.53007	0.53064	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	Canada	2023-11-29	Multi-stage	Multi-stage	Gut	Digestive System
29042	29042	SRR26990795	SRX22683824	SRS19677538	SRP474986	PRJNA1046526	ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease	GSE248975	Transcriptome Analysis	Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.		pubmed:39526957		WT gut2	GSM7924157	source name:gut\|tissue:gut\|genotype:wildtype\|time:50dpf\|geo loc name:missing\|collection date:missing	WT gut2	The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.	gut	Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.	RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.	For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.	tissue:gut\|genotype:wildtype\|time:50dpf	GSM7924157	GSM7924157: WT gut2; Danio rerio; RNA Seq	GSM7924157 r1	GSM7924157	1	RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP474986	loader:fastq load.py	11_WT_2G_S26_L001_R2_001.fastq.gz 11_WT_2G_S26_L001_R1_001.fastq.gz	fastq fastq	5406867570.0	17903535.0	GSM7924157 r1	0:151 1:151	A:1464846243;C:1237183908;G:1259215309;T:1445572498;N:49612	151	151			1464846243	1237183908	1259215309	1445572498	49612	SRX22683824	SRS19677538	SRA1760061	Muise Lab, Cell Biology, The Hospital for Sick Children	Muise Lab, Cell Biology, The Hospital for Sick Children	2	0.93795	0.94322	0.05952	0.05592	0.75933	0.75887	0.54179	0.53451	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	Canada	2023-11-29	Multi-stage	Multi-stage	Gut	Digestive System
29043	29043	SRR26990796	SRX22683823	SRS19677537	SRP474986	PRJNA1046526	ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease	GSE248975	Transcriptome Analysis	Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.		pubmed:39526957		WT gut1	GSM7924156	source name:gut\|tissue:gut\|genotype:wildtype\|time:50dpf\|geo loc name:missing\|collection date:missing	WT gut1	The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.	gut	Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.	RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.	For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.	tissue:gut\|genotype:wildtype\|time:50dpf	GSM7924156	GSM7924156: WT gut1; Danio rerio; RNA Seq	GSM7924156 r1	GSM7924156	1	RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP474986	loader:fastq load.py	10_WT_1G_S25_L001_R1_001.fastq.gz 10_WT_1G_S25_L001_R2_001.fastq.gz	fastq fastq	5162192908.0	17093354.0	GSM7924156 r1	0:151 1:151	A:1404682153;C:1175657030;G:1196829496;T:1384975886;N:48343	151	151			1404682153	1175657030	1196829496	1384975886	48343	SRX22683823	SRS19677537	SRA1760061	Muise Lab, Cell Biology, The Hospital for Sick Children	Muise Lab, Cell Biology, The Hospital for Sick Children	2	0.93119	0.93585	0.06122	0.05809	0.74757	0.74757	0.54124	0.54417	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	Canada	2023-11-29	Multi-stage	Multi-stage	Gut	Digestive System
29044	29044	SRR26990797	SRX22683822	SRS19677536	SRP474986	PRJNA1046526	ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease	GSE248975	Transcriptome Analysis	Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.		pubmed:39526957		itgavKO gut3	GSM7924155	source name:gut\|tissue:gut\|genotype:itgavKO mutant\|time:50dpf\|geo loc name:missing\|collection date:missing	itgavKO gut3	The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.	gut	Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.	RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.	For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.	tissue:gut\|genotype:itgavKO mutant\|time:50dpf	GSM7924155	GSM7924155: itgavKO gut3; Danio rerio; RNA Seq	GSM7924155 r1	GSM7924155	1	RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP474986	loader:fastq load.py	9_itgavKO_3G_S24_L001_R2_001.fastq.gz 9_itgavKO_3G_S24_L001_R1_001.fastq.gz	fastq fastq	4146743578.0	13730939.0	GSM7924155 r1	0:151 1:151	A:1130002132;C:943522869;G:958031732;T:1115146458;N:40387	151	151			1130002132	943522869	958031732	1115146458	40387	SRX22683822	SRS19677536	SRA1760061	Muise Lab, Cell Biology, The Hospital for Sick Children	Muise Lab, Cell Biology, The Hospital for Sick Children	2	0.93764	0.94144	0.05938	0.05594	0.7553	0.75485	0.55535	0.55018	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	Canada	2023-11-29	Multi-stage	Multi-stage	Gut	Digestive System
29045	29045	SRR26990798	SRX22683821	SRS19677535	SRP474986	PRJNA1046526	ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease	GSE248975	Transcriptome Analysis	Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.		pubmed:39526957		itgavKO gut2	GSM7924154	source name:gut\|tissue:gut\|genotype:itgavKO mutant\|time:50dpf\|geo loc name:missing\|collection date:missing	itgavKO gut2	The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.	gut	Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.	RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.	For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.	tissue:gut\|genotype:itgavKO mutant\|time:50dpf	GSM7924154	GSM7924154: itgavKO gut2; Danio rerio; RNA Seq	GSM7924154 r1	GSM7924154	1	RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP474986	loader:fastq load.py	8_itgavKO_2G_S23_L001_R1_001.fastq.gz 8_itgavKO_2G_S23_L001_R2_001.fastq.gz	fastq fastq	4225756140.0	13992570.0	GSM7924154 r1	0:151 1:151	A:1133211420;C:974497998;G:995876972;T:1122129220;N:40530	151	151			1133211420	974497998	995876972	1122129220	40530	SRX22683821	SRS19677535	SRA1760061	Muise Lab, Cell Biology, The Hospital for Sick Children	Muise Lab, Cell Biology, The Hospital for Sick Children	2	0.95341	0.95884	0.05109	0.04883	0.77542	0.77368	0.51301	0.50704	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	Canada	2023-11-29	Multi-stage	Multi-stage	Gut	Digestive System
29046	29046	SRR26990799	SRX22683820	SRS19677534	SRP474986	PRJNA1046526	ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease	GSE248975	Transcriptome Analysis	Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.		pubmed:39526957		itagvKO gut1	GSM7924153	source name:gut\|tissue:gut\|genotype:itgavKO mutant\|time:50dpf\|geo loc name:missing\|collection date:missing	itagvKO gut1	The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.	gut	Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.	RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.	For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.	tissue:gut\|genotype:itgavKO mutant\|time:50dpf	GSM7924153	GSM7924153: itagvKO gut1; Danio rerio; RNA Seq	GSM7924153 r1	GSM7924153	1	RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP474986	loader:fastq load.py	7_itagvKO_1G_S22_L001_R1_001.fastq.gz 7_itagvKO_1G_S22_L001_R2_001.fastq.gz	fastq fastq	5954117844.0	19715622.0	GSM7924153 r1	0:151 1:151	A:1600496071;C:1372939932;G:1393534700;T:1587094282;N:52859	151	151			1600496071	1372939932	1393534700	1587094282	52859	SRX22683820	SRS19677534	SRA1760061	Muise Lab, Cell Biology, The Hospital for Sick Children	Muise Lab, Cell Biology, The Hospital for Sick Children	2	0.94807	0.95298	0.05682	0.05385	0.74004	0.73925	0.54423	0.54484	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	Canada	2023-11-29	Multi-stage	Multi-stage	Gut	Digestive System
30620	30620	SRR27907608	SRX23567386	SRS20412878	SRP488782	PRJNA1074407	Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq]	GSE255304	Transcriptome Analysis	Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		pubmed:40392591		KO12. Ctla 4 knockout	GSM8068839	source name:intestine\|tissue:intestine\|cell type:leukocyte\|genotype:Ctla 4 KO\|geo loc name:missing\|collection date:missing	KO12. Ctla 4 knockout	The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	intestine		Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		tissue:intestine\|cell type:leukocyte\|genotype:Ctla 4 KO	GSM8068839	GSM8068839: KO12. Ctla 4 knockout; Danio rerio; RNA Seq	GSM8068839 r1	GSM8068839	1	Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP488782	loader:fastq load.py	KO12_Clean_Data2.fq.gz KO12_Clean_Data1.fq.gz	fastq fastq	5415971621.0	18199812.0	GSM8068839 r1	0:148.79 1:148.79	A:1482389043;C:1213758088;G:1232295642;T:1487496355;N:32493	148	148			1482389043	1213758088	1232295642	1487496355	32493	SRX23567386	SRS20412878	SRA1799527	zhejiang university	zhejiang university	2	0.86496	0.86584	0.08493	0.08156	0.73553	0.73588	0.50941	0.5104	149	149	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2024-02-07	Undetermined	Undetermined	Gut	Digestive System
30621	30621	SRR27907609	SRX23567385	SRS20412877	SRP488782	PRJNA1074407	Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq]	GSE255304	Transcriptome Analysis	Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		pubmed:40392591		KO11 Ctla 4 knockout	GSM8068838	source name:intestine\|tissue:intestine\|cell type:leukocyte\|genotype:Ctla 4 KO\|geo loc name:missing\|collection date:missing	KO11 Ctla 4 knockout	The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	intestine		Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		tissue:intestine\|cell type:leukocyte\|genotype:Ctla 4 KO	GSM8068838	GSM8068838: KO11 Ctla 4 knockout; Danio rerio; RNA Seq	GSM8068838 r1	GSM8068838	1	Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP488782	loader:fastq load.py	KO11_Clean_Data2.fq.gz KO11_Clean_Data1.fq.gz	fastq fastq	5443694370.0	18290488.0	GSM8068838 r1	0:148.81 1:148.81	A:1480267395;C:1230300897;G:1247791644;T:1485302181;N:32253	148	148			1480267395	1230300897	1247791644	1485302181	32253	SRX23567385	SRS20412877	SRA1799527	zhejiang university	zhejiang university	2	0.86445	0.86409	0.07094	0.06652	0.74738	0.74897	0.51339	0.51762	149	149	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2024-02-07	Undetermined	Undetermined	Gut	Digestive System
30622	30622	SRR27907610	SRX23567384	SRS20412876	SRP488782	PRJNA1074407	Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq]	GSE255304	Transcriptome Analysis	Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		pubmed:40392591		KO9 Ctla 4 knockout	GSM8068837	source name:intestine\|tissue:intestine\|cell type:leukocyte\|genotype:Ctla 4 KO\|geo loc name:missing\|collection date:missing	KO9 Ctla 4 knockout	The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	intestine		Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		tissue:intestine\|cell type:leukocyte\|genotype:Ctla 4 KO	GSM8068837	GSM8068837: KO9 Ctla 4 knockout; Danio rerio; RNA Seq	GSM8068837 r1	GSM8068837	1	Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP488782	loader:fastq load.py	KO9_Clean_Data2.fq.gz KO9_Clean_Data1.fq.gz	fastq fastq	5971590749.0	20072217.0	GSM8068837 r1	0:148.76 1:148.75	A:1640322573;C:1334570646;G:1352953128;T:1643708463;N:35939	148	148			1640322573	1334570646	1352953128	1643708463	35939	SRX23567384	SRS20412876	SRA1799527	zhejiang university	zhejiang university	2	0.86793	0.86937	0.07855	0.07588	0.74393	0.74523	0.50694	0.51104	149	149	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2024-02-07	Undetermined	Undetermined	Gut	Digestive System
30623	30623	SRR27907611	SRX23567383	SRS20412875	SRP488782	PRJNA1074407	Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq]	GSE255304	Transcriptome Analysis	Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		pubmed:40392591		WT8 control	GSM8068836	source name:intestine\|tissue:intestine\|cell type:leukocyte\|genotype:Wildtype\|geo loc name:missing\|collection date:missing	WT8 control	The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	intestine		Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		tissue:intestine\|cell type:leukocyte\|genotype:Wildtype	GSM8068836	GSM8068836: WT8 control; Danio rerio; RNA Seq	GSM8068836 r1	GSM8068836	1	Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP488782	loader:fastq load.py	WT8_Clean_Data1.fq.gz WT8_Clean_Data2.fq.gz	fastq fastq	5740688401.0	19287992.0	GSM8068836 r1	0:148.82 1:148.81	A:1586419463;C:1274440057;G:1291660517;T:1588132746;N:35618	148	148			1586419463	1274440057	1291660517	1588132746	35618	SRX23567383	SRS20412875	SRA1799527	zhejiang university	zhejiang university	2	0.85516	0.85653	0.07987	0.07551	0.74515	0.74497	0.52575	0.52057	149	149	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2024-02-07	Undetermined	Undetermined	Gut	Digestive System
30624	30624	SRR27907612	SRX23567382	SRS20412874	SRP488782	PRJNA1074407	Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq]	GSE255304	Transcriptome Analysis	Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		pubmed:40392591		WT7 control	GSM8068835	source name:intestine\|tissue:intestine\|cell type:leukocyte\|genotype:Wildtype\|geo loc name:missing\|collection date:missing	WT7 control	The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	intestine		Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		tissue:intestine\|cell type:leukocyte\|genotype:Wildtype	GSM8068835	GSM8068835: WT7 control; Danio rerio; RNA Seq	GSM8068835 r1	GSM8068835	1	Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP488782	loader:fastq load.py	WT7_Clean_Data2.fq.gz WT7_Clean_Data1.fq.gz	fastq fastq	5810188177.0	19521216.0	GSM8068835 r1	0:148.82 1:148.81	A:1609284873;C:1285068093;G:1302652710;T:1613147856;N:34645	148	148			1609284873	1285068093	1302652710	1613147856	34645	SRX23567382	SRS20412874	SRA1799527	zhejiang university	zhejiang university	2	0.83558	0.83684	0.08427	0.08011	0.75741	0.75836	0.52403	0.52405	149	149	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2024-02-07	Undetermined	Undetermined	Gut	Digestive System
30625	30625	SRR27907613	SRX23567381	SRS20412873	SRP488782	PRJNA1074407	Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq]	GSE255304	Transcriptome Analysis	Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		pubmed:40392591		WT1 control	GSM8068834	source name:intestine\|tissue:intestine\|cell type:leukocyte\|genotype:Wildtype\|geo loc name:missing\|collection date:missing	WT1 control	The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	intestine		Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		tissue:intestine\|cell type:leukocyte\|genotype:Wildtype	GSM8068834	GSM8068834: WT1 control; Danio rerio; RNA Seq	GSM8068834 r1	GSM8068834	1	Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP488782	loader:fastq load.py	WT1_Clean_Data2.fq.gz WT1_Clean_Data1.fq.gz	fastq fastq	5771161671.0	19396834.0	GSM8068834 r1	0:148.77 1:148.76	A:1593780869;C:1284499295;G:1300298518;T:1592548515;N:34474	148	148			1593780869	1284499295	1300298518	1592548515	34474	SRX23567381	SRS20412873	SRA1799527	zhejiang university	zhejiang university	2	0.85731	0.85944	0.0704	0.06703	0.76601	0.76607	0.53065	0.53445	149	149	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2024-02-07	Undetermined	Undetermined	Gut	Digestive System
30626	30626	SRR27907720	SRX23567476	SRS20412967	SRP488787	PRJNA1074408	Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [scRNA seq]	GSE255303	Transcriptome Analysis	Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: intestine leukocyte WT and KO Ctla 4 deficiency of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.		pubmed:40392591		KO scRNAseq	GSM8068833	source name:intestine\|tissue:intestine\|cell type:leukocyte\|genotype:Ctla 4 KO\|geo loc name:missing\|collection date:missing	KO scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	intestine		Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.		tissue:intestine\|cell type:leukocyte\|genotype:Ctla 4 KO	GSM8068833	GSM8068833: KO scRNAseq; Danio rerio; RNA Seq	GSM8068833 r1	GSM8068833	1	Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP488787	loader:fastq load.py	KO_S1_L001_R2_001.fastq.gz KO_S1_L001_R1_001.fastq.gz	fastq fastq	40958285011.0	344187269.0	GSM8068833 r1	0:28 1:91	A:11614416767;C:9247684357;G:9480911439;T:10614469263;N:803185	28	91			11614416767	9247684357	9480911439	10614469263	803185	SRX23567476	SRS20412967	SRA1799569	zhejiang university	zhejiang university	2	0.00982	0.9431	0.00356	0.10625	0.99277	0.8187	0.41297	0.63838	28	91	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2024-02-07	Undetermined	Undetermined	Gut	Digestive System
30627	30627	SRR27907721	SRX23567475	SRS20412966	SRP488787	PRJNA1074408	Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [scRNA seq]	GSE255303	Transcriptome Analysis	Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: intestine leukocyte WT and KO Ctla 4 deficiency of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.		pubmed:40392591		WT scRNAseq	GSM8068832	source name:intestine\|tissue:intestine\|cell type:leukocyte\|genotype:Wildtype\|geo loc name:missing\|collection date:missing	WT scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	intestine		Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.		tissue:intestine\|cell type:leukocyte\|genotype:Wildtype	GSM8068832	GSM8068832: WT scRNAseq; Danio rerio; RNA Seq	GSM8068832 r1	GSM8068832	1	Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP488787	loader:fastq load.py	WT_S1_L001_R1_001.fastq.gz WT_S1_L001_R2_001.fastq.gz	fastq fastq	36724066995.0	308605605.0	GSM8068832 r1	0:28 1:91	A:10425178276;C:8399183780;G:8411777361;T:9487202777;N:724801	28	91			10425178276	8399183780	8411777361	9487202777	724801	SRX23567475	SRS20412966	SRA1799569	zhejiang university	zhejiang university	2	0.01141	0.94944	0.0039	0.1092	0.99324	0.841	0.43558	0.73314	28	91	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2024-02-07	Undetermined	Undetermined	Gut	Digestive System
30694	30694	SRR28272066	SRX23882001	SRS20705714	SRP494129	PRJNA1085664	Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile	GSE261163	Transcriptome Analysis	Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.		pubmed:39584740		GC122775 HuNoV infected replicate 2 scRNAseq	GSM8136771	source name:Intestines\|tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:HuNoV infected\|geo loc name:missing\|collection date:missing	GC122775 HuNoV infected replicate 2 scRNAseq	Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger	Intestines		Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.		tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:HuNoV infected	GSM8136771	GSM8136771: GC122775 HuNoV infected replicate 2 scRNAseq; Danio rerio; RNA Seq	GSM8136771 r1	GSM8136771	1	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP494129		GC122775_SI-GA-D7_S4_L001_R1_001.fastq.gz GC122775_SI-GA-D7_S4_L001_R2_001.fastq.gz	fastq fastq	6487168261.0	54514019.0	GSM8136771 r1	0:28 1:91	A:1754199332;C:1533792234;G:1687916105;T:1511168304;N:92286	28	91			1754199332	1533792234	1687916105	1511168304	92286	SRX23882001	SRS20705714	SRA1820104	Genomics Core Leuven	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-03-08	Larval	Larval	Gut	Digestive System
30695	30695	SRR28272067	SRX23882001	SRS20705714	SRP494129	PRJNA1085664	Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile	GSE261163	Transcriptome Analysis	Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.		pubmed:39584740		GC122775 HuNoV infected replicate 2 scRNAseq	GSM8136771	source name:Intestines\|tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:HuNoV infected\|geo loc name:missing\|collection date:missing	GC122775 HuNoV infected replicate 2 scRNAseq	Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger	Intestines		Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.		tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:HuNoV infected	GSM8136771	GSM8136771: GC122775 HuNoV infected replicate 2 scRNAseq; Danio rerio; RNA Seq	GSM8136771 r1	GSM8136771	1	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP494129		GC122775_SI-GA-D7_S4_L002_R1_001.fastq.gz GC122775_SI-GA-D7_S4_L002_R2_001.fastq.gz	fastq fastq	6313572727.0	53055233.0	GSM8136771 r2	0:28 1:91	A:1709609257;C:1491468410;G:1640296277;T:1472111501;N:87282	28	91			1709609257	1491468410	1640296277	1472111501	87282	SRX23882001	SRS20705714	SRA1820104	Genomics Core Leuven	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-03-08	Larval	Larval	Gut	Digestive System
30696	30696	SRR28272068	SRX23882000	SRS20705713	SRP494129	PRJNA1085664	Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile	GSE261163	Transcriptome Analysis	Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.		pubmed:39584740		GC122774 HuNoV infected replicate 1 scRNAseq	GSM8136770	source name:Intestines\|tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:HuNoV infected\|geo loc name:missing\|collection date:missing	GC122774 HuNoV infected replicate 1 scRNAseq	Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger	Intestines		Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.		tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:HuNoV infected	GSM8136770	GSM8136770: GC122774 HuNoV infected replicate 1 scRNAseq; Danio rerio; RNA Seq	GSM8136770 r1	GSM8136770	1	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP494129		GC122774_SI-GA-C7_S3_L001_R1_001.fastq.gz GC122774_SI-GA-C7_S3_L001_R2_001.fastq.gz	fastq fastq	15738518978.0	132256462.0	GSM8136770 r1	0:28 1:91	A:4181691582;C:3761213961;G:4083789142;T:3711597081;N:227212	28	91			4181691582	3761213961	4083789142	3711597081	227212	SRX23882000	SRS20705713	SRA1820104	Genomics Core Leuven	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-03-08	Larval	Larval	Gut	Digestive System
30697	30697	SRR28272069	SRX23882000	SRS20705713	SRP494129	PRJNA1085664	Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile	GSE261163	Transcriptome Analysis	Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.		pubmed:39584740		GC122774 HuNoV infected replicate 1 scRNAseq	GSM8136770	source name:Intestines\|tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:HuNoV infected\|geo loc name:missing\|collection date:missing	GC122774 HuNoV infected replicate 1 scRNAseq	Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger	Intestines		Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.		tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:HuNoV infected	GSM8136770	GSM8136770: GC122774 HuNoV infected replicate 1 scRNAseq; Danio rerio; RNA Seq	GSM8136770 r1	GSM8136770	1	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP494129		GC122774_SI-GA-C7_S3_L002_R1_001.fastq.gz GC122774_SI-GA-C7_S3_L002_R2_001.fastq.gz	fastq fastq	15261653253.0	128249187.0	GSM8136770 r2	0:28 1:91	A:4059552936;C:3644406570;G:3954261902;T:3603216152;N:215693	28	91			4059552936	3644406570	3954261902	3603216152	215693	SRX23882000	SRS20705713	SRA1820104	Genomics Core Leuven	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-03-08	Larval	Larval	Gut	Digestive System
30698	30698	SRR28272070	SRX23881999	SRS20705712	SRP494129	PRJNA1085664	Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile	GSE261163	Transcriptome Analysis	Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.		pubmed:39584740		GC122773 uninfected replicate 2 scRNAseq	GSM8136769	source name:Intestines\|tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:uninfected\|geo loc name:missing\|collection date:missing	GC122773 uninfected replicate 2 scRNAseq	Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger	Intestines		Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.		tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:uninfected	GSM8136769	GSM8136769: GC122773 uninfected replicate 2 scRNAseq; Danio rerio; RNA Seq	GSM8136769 r1	GSM8136769	1	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP494129		GC122773_SI-GA-B7_S2_L001_R1_001.fastq.gz GC122773_SI-GA-B7_S2_L001_R2_001.fastq.gz	fastq fastq	15150656598.0	127316442.0	GSM8136769 r1	0:28 1:91	A:4100783574;C:3526779401;G:3845684506;T:3677189004;N:220113	28	91			4100783574	3526779401	3845684506	3677189004	220113	SRX23881999	SRS20705712	SRA1820104	Genomics Core Leuven	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-03-08	Larval	Larval	Gut	Digestive System
30699	30699	SRR28272071	SRX23881999	SRS20705712	SRP494129	PRJNA1085664	Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile	GSE261163	Transcriptome Analysis	Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.		pubmed:39584740		GC122773 uninfected replicate 2 scRNAseq	GSM8136769	source name:Intestines\|tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:uninfected\|geo loc name:missing\|collection date:missing	GC122773 uninfected replicate 2 scRNAseq	Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger	Intestines		Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.		tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:uninfected	GSM8136769	GSM8136769: GC122773 uninfected replicate 2 scRNAseq; Danio rerio; RNA Seq	GSM8136769 r1	GSM8136769	1	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP494129		GC122773_SI-GA-B7_S2_L002_R1_001.fastq.gz GC122773_SI-GA-B7_S2_L002_R2_001.fastq.gz	fastq fastq	14942015326.0	125563154.0	GSM8136769 r2	0:28 1:91	A:4048600218;C:3475105088;G:3787275869;T:3630822343;N:211808	28	91			4048600218	3475105088	3787275869	3630822343	211808	SRX23881999	SRS20705712	SRA1820104	Genomics Core Leuven	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-03-08	Larval	Larval	Gut	Digestive System
30700	30700	SRR28272072	SRX23881998	SRS20705711	SRP494129	PRJNA1085664	Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile	GSE261163	Transcriptome Analysis	Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.		pubmed:39584740		GC122772 uninfected replicate 1 scRNAseq	GSM8136768	source name:Intestines\|tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:uninfected\|geo loc name:missing\|collection date:missing	GC122772 uninfected replicate 1 scRNAseq	Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger	Intestines		Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.		tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:uninfected	GSM8136768	GSM8136768: GC122772 uninfected replicate 1 scRNAseq; Danio rerio; RNA Seq	GSM8136768 r1	GSM8136768	1	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP494129		GC122772_SI-GA-A7_S1_L001_R1_001.fastq.gz GC122772_SI-GA-A7_S1_L001_R2_001.fastq.gz	fastq fastq	7397061301.0	62160179.0	GSM8136768 r1	0:28 1:91	A:2023651844;C:1711760729;G:1860691426;T:1800850496;N:106806	28	91			2023651844	1711760729	1860691426	1800850496	106806	SRX23881998	SRS20705711	SRA1820104	Genomics Core Leuven	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-03-08	Larval	Larval	Gut	Digestive System
30701	30701	SRR28272073	SRX23881998	SRS20705711	SRP494129	PRJNA1085664	Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile	GSE261163	Transcriptome Analysis	Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.		pubmed:39584740		GC122772 uninfected replicate 1 scRNAseq	GSM8136768	source name:Intestines\|tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:uninfected\|geo loc name:missing\|collection date:missing	GC122772 uninfected replicate 1 scRNAseq	Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger	Intestines		Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.		tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:uninfected	GSM8136768	GSM8136768: GC122772 uninfected replicate 1 scRNAseq; Danio rerio; RNA Seq	GSM8136768 r1	GSM8136768	1	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP494129		GC122772_SI-GA-A7_S1_L002_R1_001.fastq.gz GC122772_SI-GA-A7_S1_L002_R2_001.fastq.gz	fastq fastq	7290496444.0	61264676.0	GSM8136768 r2	0:28 1:91	A:1996736343;C:1685693360;G:1830823892;T:1777138653;N:104196	28	91			1996736343	1685693360	1830823892	1777138653	104196	SRX23881998	SRS20705711	SRA1820104	Genomics Core Leuven	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-03-08	Larval	Larval	Gut	Digestive System
33014	33014	SRR29633212	SRX25139207	SRS21831220	SRP516661	PRJNA1129181	A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing	GSE271002	Transcriptome Analysis	To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation and DAPI live cells were sorted by FACS.		pubmed:40252728		Mtz 5dpf	GSM8366963	source name:Dissected larval intestines\|tissue:Dissected larval intestines\|cell type:Mix of intestinal cells\|genotype:AB\|treatment:Metronidazole\|geo loc name:missing\|collection date:missing	Mtz 5dpf	Demultiplexing of raw Illumina sequencing files barcoding processing gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files	Dissected larval intestines		Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.		tissue:Dissected larval intestines\|cell type:Mix of intestinal cells\|genotype:AB\|treatment:Metronidazole	GSM8366963	GSM8366963: Mtz 5dpf; Danio rerio; RNA Seq	GSM8366963 r1	GSM8366963	1	Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP516661	loader:fastq load.py	NTR-Mtz-d5_R1.fastq.gz NTR-Mtz-d5_R2.fastq.gz	fastq fastq	105173263361.0	348971465.0	GSM8366963 r1	0:150.76 1:150.62	A:29260313483;C:18342577741;G:20471735616;T:37097033318;N:1603203	150	150			29260313483	18342577741	20471735616	37097033318	1603203	SRX25139207	SRS21831220	SRA1911905	Karolinska Institutet	Karolinska Institutet	2	0.56019	0.89517	0.13273	0.11945	0.9795	0.82258	0.63676	0.6161	151	150	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Sweden	2024-06-27	Larval	Larval	Gut	Digestive System
33015	33015	SRR29633213	SRX25139206	SRS21831219	SRP516661	PRJNA1129181	A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing	GSE271002	Transcriptome Analysis	To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation and DAPI live cells were sorted by FACS.		pubmed:40252728		Control 5dpf	GSM8366962	source name:Dissected larval intestines\|tissue:Dissected larval intestines\|cell type:Mix of intestinal cells\|genotype:AB\|treatment:Control\|geo loc name:missing\|collection date:missing	Control 5dpf	Demultiplexing of raw Illumina sequencing files barcoding processing gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files	Dissected larval intestines		Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.		tissue:Dissected larval intestines\|cell type:Mix of intestinal cells\|genotype:AB\|treatment:Control	GSM8366962	GSM8366962: Control 5dpf; Danio rerio; RNA Seq	GSM8366962 r1	GSM8366962	1	Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP516661	loader:fastq load.py	NTR-Control-d5_R1.fastq.gz NTR-Control-d5_R2.fastq.gz	fastq fastq	139967773505.0	464402100.0	GSM8366962 r1	0:150.76 1:150.63	A:39202616731;C:24289494719;G:27175225437;T:49298534102;N:1902516	150	150			39202616731	24289494719	27175225437	49298534102	1902516	SRX25139206	SRS21831219	SRA1911905	Karolinska Institutet	Karolinska Institutet	2	0.54902	0.89315	0.13449	0.13341	0.97954	0.80553	0.69256	0.59244	151	151	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Sweden	2024-06-27	Larval	Larval	Gut	Digestive System
33016	33016	SRR29633214	SRX25139205	SRS21831218	SRP516661	PRJNA1129181	A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing	GSE271002	Transcriptome Analysis	To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation and DAPI live cells were sorted by FACS.		pubmed:40252728		Mtz ablation 4dpf	GSM8366961	source name:Dissected larval intestines\|tissue:Dissected larval intestines\|cell type:Mix of intestinal cells\|genotype:AB\|treatment:Metronidazole\|geo loc name:missing\|collection date:missing	Mtz ablation 4dpf	Demultiplexing of raw Illumina sequencing files barcoding processing gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files	Dissected larval intestines		Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.		tissue:Dissected larval intestines\|cell type:Mix of intestinal cells\|genotype:AB\|treatment:Metronidazole	GSM8366961	GSM8366961: Mtz ablation 4dpf; Danio rerio; RNA Seq	GSM8366961 r1	GSM8366961	1	Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP516661	loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 R1 001.fastq.gz read2PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 R2 001.fastq.gz read3PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 I1 001.fastq.gz read4PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 I2 001.fastq.gz	Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_R2_001.fastq.gz Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_R1_001.fastq.gz Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_I2_001.fastq.gz Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_I1_001.fastq.gz	fastq fastq fastq fastq	33049837760.0	103280743.0	GSM8366961 r1	0:150 1:150 2:10 3:10	A:9739096160;C:6338831532;G:6106096444;T:8799858219;N:340545	150	150	10	10	9739096160	6338831532	6106096444	8799858219	340545	SRX25139205	SRS21831218	SRA1911905	Karolinska Institutet	Karolinska Institutet	2	0.0	0.91169	0.0	0.19328	1.0	0.81722		0.64993	150	150	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Sweden	2024-06-27	Larval	Larval	Gut	Digestive System
33017	33017	SRR29633215	SRX25139204	SRS21831217	SRP516661	PRJNA1129181	A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing	GSE271002	Transcriptome Analysis	To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation and DAPI live cells were sorted by FACS.		pubmed:40252728		Control ablation 4dpf	GSM8366960	source name:Dissected larval intestines\|tissue:Dissected larval intestines\|cell type:Mix of intestinal cells\|genotype:AB\|treatment:Control\|geo loc name:missing\|collection date:missing	Control ablation 4dpf	Demultiplexing of raw Illumina sequencing files barcoding processing gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files	Dissected larval intestines		Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.		tissue:Dissected larval intestines\|cell type:Mix of intestinal cells\|genotype:AB\|treatment:Control	GSM8366960	GSM8366960: Control ablation 4dpf; Danio rerio; RNA Seq	GSM8366960 r1	GSM8366960	1	Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP516661	loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 R1 001.fastq.gz read2PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 R2 001.fastq.gz read3PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 I1 001.fastq.gz read4PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 I2 001.fastq.gz	Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_R2_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_R1_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_I2_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_I1_001.fastq.gz	fastq fastq fastq fastq	115286504000.0	360270325.0	GSM8366960 r1	0:150 1:150 2:10 3:10	A:32679027944;C:17748865933;G:17885040590;T:39764959491;N:3203542	150	150	10	10	32679027944	17748865933	17885040590	39764959491	3203542	SRX25139204	SRS21831217	SRA1911905	Karolinska Institutet	Karolinska Institutet	2	0.39015	0.90036	0.10989	0.19421	0.97845	0.79401	0.69547	0.6103	150	150	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Sweden	2024-06-27	Larval	Larval	Gut	Digestive System
33351	33351	SRR30125634	SRX25595192	SRS22245033	SRP524094	PRJNA1144090	Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis	GSE273916	Transcriptome Analysis	The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.				SBM1 3	GSM8439539	source name:intestine\|tissue:intestine\|geo loc name:missing\|collection date:missing	SBM1 3	CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample	intestine		RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.		tissue:intestine	GSM8439539	GSM8439539: SBM1 3; Danio rerio; RNA Seq	GSM8439539 r1	GSM8439539	1	RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP524094		SBM1-3.R1.fq.gz SBM1-3.R2.fq.gz	fastq fastq	6920938402.0	24030624.0	GSM8439539 r1	0:144.00 1:144.00	A:1848518187;C:1602695225;G:1609135376;T:1860572175;N:17439	144	144			1848518187	1602695225	1609135376	1860572175	17439	SRX25595192	SRS22245033	SRA1939628	Beibu Gulf University	Beibu Gulf University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-08-04	Undetermined	Undetermined	Gut	Digestive System
33352	33352	SRR30125635	SRX25595191	SRS22245032	SRP524094	PRJNA1144090	Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis	GSE273916	Transcriptome Analysis	The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.				SBM1 2	GSM8439538	source name:intestine\|tissue:intestine\|geo loc name:missing\|collection date:missing	SBM1 2	CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample	intestine		RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.		tissue:intestine	GSM8439538	GSM8439538: SBM1 2; Danio rerio; RNA Seq	GSM8439538 r1	GSM8439538	1	RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP524094		SBM1-2.R1.fq.gz SBM1-2.R2.fq.gz	fastq fastq	6873386097.0	23812133.0	GSM8439538 r1	0:144.32 1:144.33	A:1794801562;C:1631426136;G:1638460090;T:1808681001;N:17308	144	144			1794801562	1631426136	1638460090	1808681001	17308	SRX25595191	SRS22245032	SRA1939628	Beibu Gulf University	Beibu Gulf University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-08-04	Undetermined	Undetermined	Gut	Digestive System
33353	33353	SRR30125636	SRX25595190	SRS22245031	SRP524094	PRJNA1144090	Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis	GSE273916	Transcriptome Analysis	The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.				SBM1 1	GSM8439537	source name:intestine\|tissue:intestine\|geo loc name:missing\|collection date:missing	SBM1 1	CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample	intestine		RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.		tissue:intestine	GSM8439537	GSM8439537: SBM1 1; Danio rerio; RNA Seq	GSM8439537 r1	GSM8439537	1	RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP524094		SBM1-1.R1.fq.gz SBM1-1.R2.fq.gz	fastq fastq	6893638362.0	23881631.0	GSM8439537 r1	0:144.33 1:144.33	A:1801507713;C:1634518350;G:1642455999;T:1815139080;N:17220	144	144			1801507713	1634518350	1642455999	1815139080	17220	SRX25595190	SRS22245031	SRA1939628	Beibu Gulf University	Beibu Gulf University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-08-04	Undetermined	Undetermined	Gut	Digestive System
33354	33354	SRR30125637	SRX25595189	SRS22245030	SRP524094	PRJNA1144090	Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis	GSE273916	Transcriptome Analysis	The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.				FM1 3	GSM8439536	source name:intestine\|tissue:intestine\|geo loc name:missing\|collection date:missing	FM1 3	CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample	intestine		RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.		tissue:intestine	GSM8439536	GSM8439536: FM1 3; Danio rerio; RNA Seq	GSM8439536 r1	GSM8439536	1	RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP524094		FM1-3.R1.fq.gz FM1-3.R2.fq.gz	fastq fastq	6926890624.0	24044310.0	GSM8439536 r1	0:144.04 1:144.05	A:1814868011;C:1638590076;G:1645410775;T:1828004537;N:17225	144	144			1814868011	1638590076	1645410775	1828004537	17225	SRX25595189	SRS22245030	SRA1939628	Beibu Gulf University	Beibu Gulf University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-08-04	Undetermined	Undetermined	Gut	Digestive System
33355	33355	SRR30125638	SRX25595188	SRS22245029	SRP524094	PRJNA1144090	Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis	GSE273916	Transcriptome Analysis	The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.				FM1 2	GSM8439535	source name:intestine\|tissue:intestine\|geo loc name:missing\|collection date:missing	FM1 2	CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample	intestine		RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.		tissue:intestine	GSM8439535	GSM8439535: FM1 2; Danio rerio; RNA Seq	GSM8439535 r1	GSM8439535	1	RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP524094		FM1-2.R1.fq.gz FM1-2.R2.fq.gz	fastq fastq	6932329149.0	24050700.0	GSM8439535 r1	0:144.12 1:144.12	A:1821635965;C:1634568957;G:1641356498;T:1834750114;N:17615	144	144			1821635965	1634568957	1641356498	1834750114	17615	SRX25595188	SRS22245029	SRA1939628	Beibu Gulf University	Beibu Gulf University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-08-04	Undetermined	Undetermined	Gut	Digestive System
33356	33356	SRR30125639	SRX25595187	SRS22245028	SRP524094	PRJNA1144090	Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis	GSE273916	Transcriptome Analysis	The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.				FM1 1	GSM8439534	source name:intestine\|tissue:intestine\|geo loc name:missing\|collection date:missing	FM1 1	CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample	intestine		RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.		tissue:intestine	GSM8439534	GSM8439534: FM1 1; Danio rerio; RNA Seq	GSM8439534 r1	GSM8439534	1	RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP524094		FM1-1.R1.fq.gz FM1-1.R2.fq.gz	fastq fastq	6915521492.0	24044109.0	GSM8439534 r1	0:143.81 1:143.81	A:1851629842;C:1595942468;G:1602547587;T:1865384194;N:17401	143	143			1851629842	1595942468	1602547587	1865384194	17401	SRX25595187	SRS22245028	SRA1939628	Beibu Gulf University	Beibu Gulf University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-08-04	Undetermined	Undetermined	Gut	Digestive System
33357	33357	SRR30125640	SRX25595186	SRS22245027	SRP524094	PRJNA1144090	Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis	GSE273916	Transcriptome Analysis	The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.				D3 4 3	GSM8439533	source name:intestine\|tissue:intestine\|geo loc name:missing\|collection date:missing	D3 4 3	CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample	intestine		RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.		tissue:intestine	GSM8439533	GSM8439533: D3 4 3; Danio rerio; RNA Seq	GSM8439533 r1	GSM8439533	1	RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP524094		D3-4-3.R1.fq.gz D3-4-3.R2.fq.gz	fastq fastq	6934859246.0	24095045.0	GSM8439533 r1	0:143.91 1:143.91	A:1815846879;C:1641161510;G:1648091770;T:1829741658;N:17429	143	143			1815846879	1641161510	1648091770	1829741658	17429	SRX25595186	SRS22245027	SRA1939628	Beibu Gulf University	Beibu Gulf University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-08-04	Undetermined	Undetermined	Gut	Digestive System
33358	33358	SRR30125641	SRX25595185	SRS22245026	SRP524094	PRJNA1144090	Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis	GSE273916	Transcriptome Analysis	The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.				D3 4 2	GSM8439532	source name:intestine\|tissue:intestine\|geo loc name:missing\|collection date:missing	D3 4 2	CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample	intestine		RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.		tissue:intestine	GSM8439532	GSM8439532: D3 4 2; Danio rerio; RNA Seq	GSM8439532 r1	GSM8439532	1	RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP524094		D3-4-2.R1.fq.gz D3-4-2.R2.fq.gz	fastq fastq	7053487385.0	24519028.0	GSM8439532 r1	0:143.83 1:143.84	A:1888591272;C:1630003556;G:1636509489;T:1898365125;N:17943	143	143			1888591272	1630003556	1636509489	1898365125	17943	SRX25595185	SRS22245026	SRA1939628	Beibu Gulf University	Beibu Gulf University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-08-04	Undetermined	Undetermined	Gut	Digestive System
33359	33359	SRR30125642	SRX25595184	SRS22245025	SRP524094	PRJNA1144090	Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis	GSE273916	Transcriptome Analysis	The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.				D3 4 1	GSM8439531	source name:intestine\|tissue:intestine\|geo loc name:missing\|collection date:missing	D3 4 1	CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample	intestine		RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.		tissue:intestine	GSM8439531	GSM8439531: D3 4 1; Danio rerio; RNA Seq	GSM8439531 r1	GSM8439531	1	RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP524094		D3-4-1.R1.fq.gz D3-4-1.R2.fq.gz	fastq fastq	6996797279.0	24229469.0	GSM8439531 r1	0:144.38 1:144.39	A:1841905352;C:1647600285;G:1654313322;T:1852960597;N:17723	144	144			1841905352	1647600285	1654313322	1852960597	17723	SRX25595184	SRS22245025	SRA1939628	Beibu Gulf University	Beibu Gulf University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-08-04	Undetermined	Undetermined	Gut	Digestive System
33417	33417	SRR30186672	SRX25652379	SRS22295184	SRP525362	PRJNA1146366	Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level	GSE274407	Transcriptome Analysis	Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.		pubmed:39642879		ENS6dpf	GSM8448586	source name:intestine\|tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:6dpf\|geo loc name:missing\|collection date:missing	ENS6dpf	The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files	intestine		To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:6dpf	GSM8448586	GSM8448586: ENS6dpf; Danio rerio; RNA Seq	GSM8448586 r1	GSM8448586	1	To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP525362	loader:fastq load.py	FT-SA26637_S5_L005_I1_001.fastq.gz FT-SA26637_S5_L005_R1_001.fastq.gz FT-SA26637_S5_L005_R2_001.fastq.gz	fastq fastq fastq	40502433410.0	130653011.0	GSM8448586 r1	0:8 1:151 2:151	A:10014178947;C:5704376875;G:6596271508;T:17137143949;N:5238043	8	151	151		10014178947	5704376875	6596271508	17137143949	5238043	SRX25652379	SRS22295184	SRA1943746	Bronner lab, Biology and Biological Engineering, Caltech	Bronner lab, Biology and Biological Engineering, Caltech												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2024-08-09	Larval	Larval	Gut	Digestive System
33418	33418	SRR30186673	SRX25652379	SRS22295184	SRP525362	PRJNA1146366	Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level	GSE274407	Transcriptome Analysis	Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.		pubmed:39642879		ENS6dpf	GSM8448586	source name:intestine\|tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:6dpf\|geo loc name:missing\|collection date:missing	ENS6dpf	The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files	intestine		To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:6dpf	GSM8448586	GSM8448586: ENS6dpf; Danio rerio; RNA Seq	GSM8448586 r1	GSM8448586	1	To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP525362	loader:fastq load.py	FT-SA26637_S5_L006_I1_001.fastq.gz FT-SA26637_S5_L006_R1_001.fastq.gz FT-SA26637_S5_L006_R2_001.fastq.gz	fastq fastq fastq	41972742020.0	135395942.0	GSM8448586 r2	0:8 1:151 2:151	A:10346550415;C:6105559893;G:6757897068;T:17672755179;N:6811929	8	151	151		10346550415	6105559893	6757897068	17672755179	6811929	SRX25652379	SRS22295184	SRA1943746	Bronner lab, Biology and Biological Engineering, Caltech	Bronner lab, Biology and Biological Engineering, Caltech												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2024-08-09	Larval	Larval	Gut	Digestive System
33419	33419	SRR30186674	SRX25652378	SRS22295179	SRP525362	PRJNA1146366	Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level	GSE274407	Transcriptome Analysis	Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.		pubmed:39642879		ENS5dpf	GSM8448585	source name:intestine\|tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:5dpf\|geo loc name:missing\|collection date:missing	ENS5dpf	The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files	intestine		To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:5dpf	GSM8448585	GSM8448585: ENS5dpf; Danio rerio; RNA Seq	GSM8448585 r1	GSM8448585	1	To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP525362	loader:fastq load.py	FT-SA26636_S4_L005_I1_001.fastq.gz FT-SA26636_S4_L005_R1_001.fastq.gz FT-SA26636_S4_L005_R2_001.fastq.gz	fastq fastq fastq	21590505830.0	69646793.0	GSM8448585 r1	0:8 1:151 2:151	A:5324745627;C:3047288539;G:3517496789;T:9140955618;N:2844913	8	151	151		5324745627	3047288539	3517496789	9140955618	2844913	SRX25652378	SRS22295179	SRA1943746	Bronner lab, Biology and Biological Engineering, Caltech	Bronner lab, Biology and Biological Engineering, Caltech												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2024-08-09	Larval	Larval	Gut	Digestive System
33420	33420	SRR30186675	SRX25652378	SRS22295179	SRP525362	PRJNA1146366	Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level	GSE274407	Transcriptome Analysis	Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.		pubmed:39642879		ENS5dpf	GSM8448585	source name:intestine\|tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:5dpf\|geo loc name:missing\|collection date:missing	ENS5dpf	The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files	intestine		To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:5dpf	GSM8448585	GSM8448585: ENS5dpf; Danio rerio; RNA Seq	GSM8448585 r1	GSM8448585	1	To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP525362	loader:fastq load.py	FT-SA26636_S4_L006_I1_001.fastq.gz FT-SA26636_S4_L006_R1_001.fastq.gz FT-SA26636_S4_L006_R2_001.fastq.gz	fastq fastq fastq	22493595040.0	72559984.0	GSM8448585 r2	0:8 1:151 2:151	A:5532271824;C:3275587569;G:3623404196;T:9478183540;N:3668039	8	151	151		5532271824	3275587569	3623404196	9478183540	3668039	SRX25652378	SRS22295179	SRA1943746	Bronner lab, Biology and Biological Engineering, Caltech	Bronner lab, Biology and Biological Engineering, Caltech												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2024-08-09	Larval	Larval	Gut	Digestive System
33421	33421	SRR30186676	SRX25652377	SRS22295180	SRP525362	PRJNA1146366	Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level	GSE274407	Transcriptome Analysis	Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.		pubmed:39642879		ENS4dpf	GSM8448584	source name:intestine\|tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:4dpf\|geo loc name:missing\|collection date:missing	ENS4dpf	The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files	intestine		To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:4dpf	GSM8448584	GSM8448584: ENS4dpf; Danio rerio; RNA Seq	GSM8448584 r1	GSM8448584	1	To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP525362	loader:fastq load.py	FT-SA26635_S3_L005_I1_001.fastq.gz FT-SA26635_S3_L005_R1_001.fastq.gz FT-SA26635_S3_L005_R2_001.fastq.gz	fastq fastq fastq	29011782450.0	93586395.0	GSM8448584 r1	0:8 1:151 2:151	A:7041483148;C:4220842692;G:4903817651;T:12093250712;N:3697087	8	151	151		7041483148	4220842692	4903817651	12093250712	3697087	SRX25652377	SRS22295180	SRA1943746	Bronner lab, Biology and Biological Engineering, Caltech	Bronner lab, Biology and Biological Engineering, Caltech												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2024-08-09	Larval	Larval	Gut	Digestive System
33422	33422	SRR30186677	SRX25652377	SRS22295180	SRP525362	PRJNA1146366	Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level	GSE274407	Transcriptome Analysis	Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.		pubmed:39642879		ENS4dpf	GSM8448584	source name:intestine\|tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:4dpf\|geo loc name:missing\|collection date:missing	ENS4dpf	The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files	intestine		To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:4dpf	GSM8448584	GSM8448584: ENS4dpf; Danio rerio; RNA Seq	GSM8448584 r1	GSM8448584	1	To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP525362	loader:fastq load.py	FT-SA26635_S3_L006_I1_001.fastq.gz FT-SA26635_S3_L006_R1_001.fastq.gz FT-SA26635_S3_L006_R2_001.fastq.gz	fastq fastq fastq	30061975960.0	96974116.0	GSM8448584 r2	0:8 1:151 2:151	A:7272472037;C:4518131790;G:5023942263;T:12466801069;N:4835873	8	151	151		7272472037	4518131790	5023942263	12466801069	4835873	SRX25652377	SRS22295180	SRA1943746	Bronner lab, Biology and Biological Engineering, Caltech	Bronner lab, Biology and Biological Engineering, Caltech												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2024-08-09	Larval	Larval	Gut	Digestive System
33423	33423	SRR30186678	SRX25652376	SRS22295175	SRP525362	PRJNA1146366	Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level	GSE274407	Transcriptome Analysis	Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.		pubmed:39642879		ENS3dpf	GSM8448583	source name:intestine\|tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:3dpf\|geo loc name:missing\|collection date:missing	ENS3dpf	The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files	intestine		To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:3dpf	GSM8448583	GSM8448583: ENS3dpf; Danio rerio; RNA Seq	GSM8448583 r1	GSM8448583	1	To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP525362	loader:fastq load.py	FT-SA26634_S2_L005_I1_001.fastq.gz FT-SA26634_S2_L005_R1_001.fastq.gz FT-SA26634_S2_L005_R2_001.fastq.gz	fastq fastq fastq	28701845380.0	92586598.0	GSM8448583 r1	0:8 1:151 2:151	A:6898569356;C:4281479855;G:4993869601;T:11783488306;N:3745478	8	151	151		6898569356	4281479855	4993869601	11783488306	3745478	SRX25652376	SRS22295175	SRA1943746	Bronner lab, Biology and Biological Engineering, Caltech	Bronner lab, Biology and Biological Engineering, Caltech												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2024-08-09	Larval	Larval	Gut	Digestive System
33424	33424	SRR30186679	SRX25652376	SRS22295175	SRP525362	PRJNA1146366	Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level	GSE274407	Transcriptome Analysis	Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.		pubmed:39642879		ENS3dpf	GSM8448583	source name:intestine\|tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:3dpf\|geo loc name:missing\|collection date:missing	ENS3dpf	The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files	intestine		To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:3dpf	GSM8448583	GSM8448583: ENS3dpf; Danio rerio; RNA Seq	GSM8448583 r1	GSM8448583	1	To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP525362	loader:fastq load.py	FT-SA26634_S2_L006_I1_001.fastq.gz FT-SA26634_S2_L006_R1_001.fastq.gz FT-SA26634_S2_L006_R2_001.fastq.gz	fastq fastq fastq	29814490250.0	96175775.0	GSM8448583 r2	0:8 1:151 2:151	A:7143218463;C:4592538828;G:5130593993;T:12173956857;N:4775909	8	151	151		7143218463	4592538828	5130593993	12173956857	4775909	SRX25652376	SRS22295175	SRA1943746	Bronner lab, Biology and Biological Engineering, Caltech	Bronner lab, Biology and Biological Engineering, Caltech												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2024-08-09	Larval	Larval	Gut	Digestive System
33425	33425	SRR30186680	SRX25652375	SRS22295177	SRP525362	PRJNA1146366	Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level	GSE274407	Transcriptome Analysis	Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.		pubmed:39642879		ENS2dpf	GSM8448582	source name:intestine\|tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:2dpf\|geo loc name:missing\|collection date:missing	ENS2dpf	The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files	intestine		To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:2dpf	GSM8448582	GSM8448582: ENS2dpf; Danio rerio; RNA Seq	GSM8448582 r1	GSM8448582	1	To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP525362	loader:fastq load.py	FT-SA26633_S1_L005_I1_001.fastq.gz FT-SA26633_S1_L005_R1_001.fastq.gz FT-SA26633_S1_L005_R2_001.fastq.gz	fastq fastq fastq	16641390240.0	53681904.0	GSM8448582 r1	0:8 1:151 2:151	A:3957785280;C:2573469243;G:2993166279;T:6685407270;N:2106936	8	151	151		3957785280	2573469243	2993166279	6685407270	2106936	SRX25652375	SRS22295177	SRA1943746	Bronner lab, Biology and Biological Engineering, Caltech	Bronner lab, Biology and Biological Engineering, Caltech												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2024-08-09	Hatching	Embryo	Gut	Digestive System
33426	33426	SRR30186681	SRX25652375	SRS22295177	SRP525362	PRJNA1146366	Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level	GSE274407	Transcriptome Analysis	Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.		pubmed:39642879		ENS2dpf	GSM8448582	source name:intestine\|tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:2dpf\|geo loc name:missing\|collection date:missing	ENS2dpf	The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files	intestine		To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:2dpf	GSM8448582	GSM8448582: ENS2dpf; Danio rerio; RNA Seq	GSM8448582 r1	GSM8448582	1	To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP525362	loader:fastq load.py	FT-SA26633_S1_L006_I1_001.fastq.gz FT-SA26633_S1_L006_R1_001.fastq.gz FT-SA26633_S1_L006_R2_001.fastq.gz	fastq fastq fastq	17304656010.0	55821471.0	GSM8448582 r2	0:8 1:151 2:151	A:4101777717;C:2763806899;G:3078134302;T:6911601509;N:2763815	8	151	151		4101777717	2763806899	3078134302	6911601509	2763815	SRX25652375	SRS22295177	SRA1943746	Bronner lab, Biology and Biological Engineering, Caltech	Bronner lab, Biology and Biological Engineering, Caltech												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2024-08-09	Hatching	Embryo	Gut	Digestive System
34137	34137	SRR31360761	SRX26734629	SRS23224778	SRP545397	PRJNA1186411	Zebrafish intestine sequencing	PRJNA1186411	Other	To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions					WT3	strain:AB\|isolate:WT3\|age:larvae\|collection date:2019 04\|geo loc name:China:Chongqing\|sex:pooled male and female\|tissue:intestine\|BioSampleModel:Model organism or animal									RNA Seq of Danio Rerio: larvae intestine	WT3.fq	WT3.fq	nomal RAN Seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP545397		WT3_R1.fq.gz WT3_R2.fq.gz	fastq fastq	7045875300.0	23486251.0	WT3 R1.fq.gz	0:150 1:150	A:1817741681;C:1708030651;G:1712073267;T:1808003621;N:26080	150	150			1817741681	1708030651	1712073267	1808003621	26080	SRX26734629	SRS23224778	SRA2015506	Fudan University\|School of Life Sciences	Fudan University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-11-15	Larval	Larval	Gut	Digestive System
34138	34138	SRR31360762	SRX26734628	SRS23224777	SRP545397	PRJNA1186411	Zebrafish intestine sequencing	PRJNA1186411	Other	To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions					WT2	strain:AB\|isolate:WT2\|age:larvae\|collection date:2019 04\|geo loc name:China:Chongqing\|sex:pooled male and female\|tissue:intestine\|BioSampleModel:Model organism or animal									RNA Seq of Danio Rerio: larvae intestine	WT2.fq	WT2.fq	nomal RAN Seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP545397		WT2_R1.fq.gz WT2_R2.fq.gz	fastq fastq	6888570900.0	22961903.0	WT2 R1.fq.gz	0:150 1:150	A:1774584110;C:1673773734;G:1678866397;T:1761321702;N:24957	150	150			1774584110	1673773734	1678866397	1761321702	24957	SRX26734628	SRS23224777	SRA2015506	Fudan University\|School of Life Sciences	Fudan University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-11-15	Larval	Larval	Gut	Digestive System
34139	34139	SRR31360763	SRX26734627	SRS23224776	SRP545397	PRJNA1186411	Zebrafish intestine sequencing	PRJNA1186411	Other	To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions					WT1	strain:AB\|isolate:WT1\|age:larvae\|collection date:2019 04\|geo loc name:China:Chongqing\|sex:pooled male and female\|tissue:intestine\|BioSampleModel:Model organism or animal									RNA Seq of Danio Rerio: larvae intestine	WT1.fq	WT1.fq	nomal RAN Seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP545397		WT1_R1.fq.gz WT1_R2.fq.gz	fastq fastq	6815123400.0	22717078.0	WT1 R1.fq.gz	0:150 1:150	A:1758536338;C:1650339290;G:1657619698;T:1748603714;N:24360	150	150			1758536338	1650339290	1657619698	1748603714	24360	SRX26734627	SRS23224776	SRA2015506	Fudan University\|School of Life Sciences	Fudan University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-11-15	Larval	Larval	Gut	Digestive System
34140	34140	SRR31360764	SRX26734626	SRS23224775	SRP545397	PRJNA1186411	Zebrafish intestine sequencing	PRJNA1186411	Other	To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions					mu3	strain:AB\|isolate:mu3\|age:larvae\|collection date:2019 04\|geo loc name:China:Chongqing\|sex:pooled male and female\|tissue:intestine\|BioSampleModel:Model organism or animal									RNA Seq of Danio Rerio: larvae intestine	mu3.fq	mu3.fq	nomal RAN Seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP545397		mu3_R1.fq.gz mu3_R2.fq.gz	fastq fastq	7304650200.0	24348834.0	mu3 R1.fq.gz	0:150 1:150	A:1934717193;C:1720864609;G:1730177787;T:1918863192;N:27419	150	150			1934717193	1720864609	1730177787	1918863192	27419	SRX26734626	SRS23224775	SRA2015506	Fudan University\|School of Life Sciences	Fudan University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-11-15	Larval	Larval	Gut	Digestive System
34141	34141	SRR31360765	SRX26734625	SRS23224774	SRP545397	PRJNA1186411	Zebrafish intestine sequencing	PRJNA1186411	Other	To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions					mu2	strain:AB\|isolate:mu2\|age:larvae\|collection date:2019 04\|geo loc name:China:Chongqing\|sex:pooled male and female\|tissue:intestine\|BioSampleModel:Model organism or animal									RNA Seq of Danio Rerio: larvae intestine	mu2.fq	mu2.fq	nomal RAN Seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP545397		mu2_R1.fq.gz mu2_R2.fq.gz	fastq fastq	7168114200.0	23893714.0	mu2 R1.fq.gz	0:150 1:150	A:1896004564;C:1692025000;G:1701080897;T:1878977280;N:26459	150	150			1896004564	1692025000	1701080897	1878977280	26459	SRX26734625	SRS23224774	SRA2015506	Fudan University\|School of Life Sciences	Fudan University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-11-15	Larval	Larval	Gut	Digestive System
34142	34142	SRR31360766	SRX26734624	SRS23224773	SRP545397	PRJNA1186411	Zebrafish intestine sequencing	PRJNA1186411	Other	To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions					mu1	strain:AB\|isolate:mu1\|age:larvae\|collection date:2019 04\|geo loc name:China:Chongqing\|sex:pooled male and female\|tissue:intestine\|BioSampleModel:Model organism or animal									RNA Seq of Danio Rerio: larvae intestine	mu1.fq	mu1.fq	nomal RAN Seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP545397		mu1_R1.fq.gz mu1_R2.fq.gz	fastq fastq	7262664600.0	24208882.0	mu1 R1.fq.gz	0:150 1:150	A:1922666653;C:1711620445;G:1720530432;T:1907824480;N:22590	150	150			1922666653	1711620445	1720530432	1907824480	22590	SRX26734624	SRS23224773	SRA2015506	Fudan University\|School of Life Sciences	Fudan University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-11-15	Larval	Larval	Gut	Digestive System
34491	34491	SRR31852177	SRX27211969	SRS23661292	SRP554424	PRJNA1204310	Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish	GSE285528	Transcriptome Analysis	Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection				Zebrafish BG rep3	GSM8703891	source name:Intestine\|tissue:Intestine\|strain:AB\|genotype:WT\|treatment:Beta Glucan training and E. piscicida infection\|time:Day 7\|geo loc name:missing\|collection date:missing	Zebrafish BG rep3	Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample	Intestine	10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection	The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.	Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.	tissue:Intestine\|strain:AB\|genotype:WT\|treatment:Beta Glucan training and E. piscicida infection\|time:Day 7	GSM8703891	GSM8703891: Zebrafish BG rep3; Danio rerio; RNA Seq	GSM8703891 r1	GSM8703891	1	The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500		SRP554424		BG_3_R1.fastq.gz BG_3_R2.fastq.gz	fastq fastq	6899655382.0	22846541.0	GSM8703891 r1	0:151 1:151	A:1811966008;C:1615713130;G:1645022233;T:1826840592;N:113419	151	151			1811966008	1615713130	1645022233	1826840592	113419	SRX27211969	SRS23661292	SRA2042566	Ahua lab, East China University of Science and Technology	Ahua lab, East China University of Science and Technology												B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	China	2024-12-30	Adult	Adult	Gut	Digestive System
34492	34492	SRR31852178	SRX27211968	SRS23661291	SRP554424	PRJNA1204310	Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish	GSE285528	Transcriptome Analysis	Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection				Zebrafish BG rep2	GSM8703890	source name:Intestine\|tissue:Intestine\|strain:AB\|genotype:WT\|treatment:Beta Glucan training and E. piscicida infection\|time:Day 7\|geo loc name:missing\|collection date:missing	Zebrafish BG rep2	Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample	Intestine	10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection	The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.	Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.	tissue:Intestine\|strain:AB\|genotype:WT\|treatment:Beta Glucan training and E. piscicida infection\|time:Day 7	GSM8703890	GSM8703890: Zebrafish BG rep2; Danio rerio; RNA Seq	GSM8703890 r1	GSM8703890	1	The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500		SRP554424		BG_2_R1.fastq.gz BG_2_R2.fastq.gz	fastq fastq	6320533538.0	20928919.0	GSM8703890 r1	0:151 1:151	A:1636247942;C:1501072316;G:1530315619;T:1652793962;N:103699	151	151			1636247942	1501072316	1530315619	1652793962	103699	SRX27211968	SRS23661291	SRA2042566	Ahua lab, East China University of Science and Technology	Ahua lab, East China University of Science and Technology												B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	China	2024-12-30	Adult	Adult	Gut	Digestive System
34493	34493	SRR31852179	SRX27211967	SRS23661290	SRP554424	PRJNA1204310	Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish	GSE285528	Transcriptome Analysis	Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection				Zebrafish BG rep1	GSM8703889	source name:Intestine\|tissue:Intestine\|strain:AB\|genotype:WT\|treatment:Beta Glucan training and E. piscicida infection\|time:Day 7\|geo loc name:missing\|collection date:missing	Zebrafish BG rep1	Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample	Intestine	10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection	The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.	Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.	tissue:Intestine\|strain:AB\|genotype:WT\|treatment:Beta Glucan training and E. piscicida infection\|time:Day 7	GSM8703889	GSM8703889: Zebrafish BG rep1; Danio rerio; RNA Seq	GSM8703889 r1	GSM8703889	1	The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500		SRP554424		BG_1_R1.fastq.gz BG_1_R2.fastq.gz	fastq fastq	6720003132.0	22251666.0	GSM8703889 r1	0:151 1:151	A:1771169227;C:1572565291;G:1597071360;T:1779087569;N:109685	151	151			1771169227	1572565291	1597071360	1779087569	109685	SRX27211967	SRS23661290	SRA2042566	Ahua lab, East China University of Science and Technology	Ahua lab, East China University of Science and Technology												B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	China	2024-12-30	Adult	Adult	Gut	Digestive System
34494	34494	SRR31852180	SRX27211966	SRS23661289	SRP554424	PRJNA1204310	Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish	GSE285528	Transcriptome Analysis	Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection				Zebrafish EIB202 rep3	GSM8703888	source name:Intestine\|tissue:Intestine\|strain:AB\|genotype:WT\|treatment:E. piscicida infection\|time:Day 7\|geo loc name:missing\|collection date:missing	Zebrafish EIB202 rep3	Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample	Intestine	10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection	The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.	Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.	tissue:Intestine\|strain:AB\|genotype:WT\|treatment:E. piscicida infection\|time:Day 7	GSM8703888	GSM8703888: Zebrafish EIB202 rep3; Danio rerio; RNA Seq	GSM8703888 r1	GSM8703888	1	The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500		SRP554424		EIB202_3_R1.fastq.gz EIB202_3_R2.fastq.gz	fastq fastq	6653244824.0	22030612.0	GSM8703888 r1	0:151 1:151	A:1715767195;C:1587994105;G:1617241387;T:1732132934;N:109203	151	151			1715767195	1587994105	1617241387	1732132934	109203	SRX27211966	SRS23661289	SRA2042566	Ahua lab, East China University of Science and Technology	Ahua lab, East China University of Science and Technology												B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	China	2024-12-30	Adult	Adult	Gut	Digestive System
34495	34495	SRR31852181	SRX27211965	SRS23661288	SRP554424	PRJNA1204310	Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish	GSE285528	Transcriptome Analysis	Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection				Zebrafish EIB202 rep2	GSM8703887	source name:Intestine\|tissue:Intestine\|strain:AB\|genotype:WT\|treatment:E. piscicida infection\|time:Day 7\|geo loc name:missing\|collection date:missing	Zebrafish EIB202 rep2	Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample	Intestine	10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection	The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.	Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.	tissue:Intestine\|strain:AB\|genotype:WT\|treatment:E. piscicida infection\|time:Day 7	GSM8703887	GSM8703887: Zebrafish EIB202 rep2; Danio rerio; RNA Seq	GSM8703887 r1	GSM8703887	1	The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500		SRP554424		EIB202_2_R1.fastq.gz EIB202_2_R2.fastq.gz	fastq fastq	7203983198.0	23854249.0	GSM8703887 r1	0:151 1:151	A:1847641462;C:1731806146;G:1763208826;T:1861209998;N:116766	151	151			1847641462	1731806146	1763208826	1861209998	116766	SRX27211965	SRS23661288	SRA2042566	Ahua lab, East China University of Science and Technology	Ahua lab, East China University of Science and Technology												B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	China	2024-12-30	Adult	Adult	Gut	Digestive System
34496	34496	SRR31852182	SRX27211964	SRS23661287	SRP554424	PRJNA1204310	Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish	GSE285528	Transcriptome Analysis	Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection				Zebrafish EIB202 rep1	GSM8703886	source name:Intestine\|tissue:Intestine\|strain:AB\|genotype:WT\|treatment:E. piscicida infection\|time:Day 7\|geo loc name:missing\|collection date:missing	Zebrafish EIB202 rep1	Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample	Intestine	10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection	The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.	Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.	tissue:Intestine\|strain:AB\|genotype:WT\|treatment:E. piscicida infection\|time:Day 7	GSM8703886	GSM8703886: Zebrafish EIB202 rep1; Danio rerio; RNA Seq	GSM8703886 r1	GSM8703886	1	The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500		SRP554424		EIB202_1_R1.fastq.gz EIB202_1_R2.fastq.gz	fastq fastq	6634863292.0	21969746.0	GSM8703886 r1	0:151 1:151	A:1708949626;C:1589664250;G:1615939413;T:1720201415;N:108588	151	151			1708949626	1589664250	1615939413	1720201415	108588	SRX27211964	SRS23661287	SRA2042566	Ahua lab, East China University of Science and Technology	Ahua lab, East China University of Science and Technology												B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	China	2024-12-30	Adult	Adult	Gut	Digestive System
34497	34497	SRR31852183	SRX27211963	SRS23661286	SRP554424	PRJNA1204310	Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish	GSE285528	Transcriptome Analysis	Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection				Zebrafish mock rep3	GSM8703885	source name:Intestine\|tissue:Intestine\|strain:AB\|genotype:WT\|treatment:no\|time:Day 7\|geo loc name:missing\|collection date:missing	Zebrafish mock rep3	Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample	Intestine	10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection	The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.	Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.	tissue:Intestine\|strain:AB\|genotype:WT\|treatment:no\|time:Day 7	GSM8703885	GSM8703885: Zebrafish mock rep3; Danio rerio; RNA Seq	GSM8703885 r1	GSM8703885	1	The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500		SRP554424		Mock_3_R1.fastq.gz Mock_3_R2.fastq.gz	fastq fastq	6938479596.0	22975098.0	GSM8703885 r1	0:151 1:151	A:1771058080;C:1670207033;G:1705035413;T:1792066207;N:112863	151	151			1771058080	1670207033	1705035413	1792066207	112863	SRX27211963	SRS23661286	SRA2042566	Ahua lab, East China University of Science and Technology	Ahua lab, East China University of Science and Technology												B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	China	2024-12-30	Adult	Adult	Gut	Digestive System
34498	34498	SRR31852184	SRX27211962	SRS23661285	SRP554424	PRJNA1204310	Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish	GSE285528	Transcriptome Analysis	Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection				Zebrafish mock rep2	GSM8703884	source name:Intestine\|tissue:Intestine\|strain:AB\|genotype:WT\|treatment:no\|time:Day 7\|geo loc name:missing\|collection date:missing	Zebrafish mock rep2	Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample	Intestine	10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection	The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.	Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.	tissue:Intestine\|strain:AB\|genotype:WT\|treatment:no\|time:Day 7	GSM8703884	GSM8703884: Zebrafish mock rep2; Danio rerio; RNA Seq	GSM8703884 r1	GSM8703884	1	The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500		SRP554424		Mock_2_R1.fastq.gz Mock_2_R2.fastq.gz	fastq fastq	7374531658.0	24418979.0	GSM8703884 r1	0:151 1:151	A:1885070518;C:1779385428;G:1810157081;T:1899798486;N:120145	151	151			1885070518	1779385428	1810157081	1899798486	120145	SRX27211962	SRS23661285	SRA2042566	Ahua lab, East China University of Science and Technology	Ahua lab, East China University of Science and Technology												B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	China	2024-12-30	Adult	Adult	Gut	Digestive System
34499	34499	SRR31852185	SRX27211961	SRS23661284	SRP554424	PRJNA1204310	Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish	GSE285528	Transcriptome Analysis	Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection				Zebrafish mock rep1	GSM8703883	source name:Intestine\|tissue:Intestine\|strain:AB\|genotype:WT\|treatment:no\|time:Day 7\|geo loc name:missing\|collection date:missing	Zebrafish mock rep1	Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample	Intestine	10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection	The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.	Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.	tissue:Intestine\|strain:AB\|genotype:WT\|treatment:no\|time:Day 7	GSM8703883	GSM8703883: Zebrafish mock rep1; Danio rerio; RNA Seq	GSM8703883 r1	GSM8703883	1	The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500		SRP554424		Mock_1_R1.fastq.gz Mock_1_R2.fastq.gz	fastq fastq	6563252448.0	21732624.0	GSM8703883 r1	0:151 1:151	A:1759569033;C:1514211809;G:1536003223;T:1753362072;N:106311	151	151			1759569033	1514211809	1536003223	1753362072	106311	SRX27211961	SRS23661284	SRA2042566	Ahua lab, East China University of Science and Technology	Ahua lab, East China University of Science and Technology												B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	China	2024-12-30	Adult	Adult	Gut	Digestive System
34517	34517	SRR32044795	SRX27393953	SRS23824014	SRP558295	PRJNA1212482	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212482	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.				Cr+VC 3	I	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 14\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:gut\|death date:2023 8 14\|health state:health\|sample type:tissue\|replication:Cr+VC 3\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	Cr+VC 3	Cr+VC 3	normal			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7		SRP558295		Cr+VC-3.R1.raw.fastq.gz Cr+VC-3.R2.raw.fastq.gz	fastq fastq	6773536558.0	22428929.0	Cr+VC 3.R1.raw.fastq.gz	0:151 1:151	A:1792253952;C:1581454013;G:1629330621;T:1770470694;N:27278	151	151			1792253952	1581454013	1629330621	1770470694	27278	SRX27393953	SRS23824014	SRA2054568	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-19	Adult	Adult	Gut	Digestive System
34518	34518	SRR32044796	SRX27393952	SRS23824013	SRP558295	PRJNA1212482	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212482	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.				Cr+VC 2	H	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 14\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:gut\|death date:2023 8 14\|health state:health\|sample type:tissue\|replication:Cr+VC 2\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	Cr+VC 2	Cr+VC 2	normal			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7		SRP558295		Cr+VC-2.R1.raw.fastq.gz Cr+VC-2.R2.raw.fastq.gz	fastq fastq	7449518862.0	24667281.0	Cr+VC 2.R1.raw.fastq.gz	0:151 1:151	A:1969693675;C:1748150730;G:1771267240;T:1960378098;N:29119	151	151			1969693675	1748150730	1771267240	1960378098	29119	SRX27393952	SRS23824013	SRA2054568	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-19	Adult	Adult	Gut	Digestive System
34519	34519	SRR32044797	SRX27393951	SRS23824012	SRP558295	PRJNA1212482	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212482	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.				Cr+VC 1	G	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 14\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:gut\|death date:2023 8 14\|health state:health\|sample type:tissue\|replication:Cr+VC 1\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	Cr+VC 1	Cr+VC 1	normal			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7		SRP558295	loader:fastq load.py\|options: doNotUseSharq	Cr+VC-1.R1.raw.fastq Cr+VC-1.R2.raw.fastq	fastq fastq	6865491179.0	45466829.0	Cr+VC 1.R1.raw.fastq.gz	0:151	A:1830069736;C:1600281531;G:1626303427;T:1808809011;N:27474	151				1830069736	1600281531	1626303427	1808809011	27474	SRX27393951	SRS23824012	SRA2054568	Hainan University\|School of Life and Health Sciences	Hainan University												B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-19	Adult	Adult	Gut	Digestive System
34520	34520	SRR32044798	SRX27393950	SRS23824011	SRP558295	PRJNA1212482	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212482	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.				Cr 3	F	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 13\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:gut\|death date:2023 8 13\|health state:health\|sample type:tissue\|replication:Cr 3\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	Cr 3	Cr 3	normal			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7		SRP558295		Cr-3.R1.raw.fastq.gz Cr-3.R2.raw.fastq.gz	fastq fastq	6069804078.0	20098689.0	Cr 3.R1.raw.fastq.gz	0:151 1:151	A:1603886661;C:1431213970;G:1440806224;T:1593873144;N:24079	151	151			1603886661	1431213970	1440806224	1593873144	24079	SRX27393950	SRS23824011	SRA2054568	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-19	Adult	Adult	Gut	Digestive System
34521	34521	SRR32044799	SRX27393949	SRS23824010	SRP558295	PRJNA1212482	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212482	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.				Cr 2	E	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 13\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:gut\|death date:2023 8 13\|health state:health\|sample type:tissue\|replication:Cr 2\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	Cr 2	Cr 2	normal			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7		SRP558295	loader:fastq load.py\|options: doNotUseSharq	Cr-2.R1.raw.fastq Cr-2.R2.raw.fastq	fastq fastq	8327156985.0	55146735.0	Cr 2.R1.raw.fastq.gz	0:151	A:2181317777;C:1974793526;G:2003240106;T:2167771431;N:34145	151				2181317777	1974793526	2003240106	2167771431	34145	SRX27393949	SRS23824010	SRA2054568	Hainan University\|School of Life and Health Sciences	Hainan University												B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-19	Adult	Adult	Gut	Digestive System
34522	34522	SRR32044800	SRX27393948	SRS23824009	SRP558295	PRJNA1212482	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212482	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.				Cr 1	D	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 13\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:gut\|death date:2023 8 13\|health state:health\|sample type:tissue\|replication:Cr 1\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	Cr 1	Cr 1	normal			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7		SRP558295		Cr-1.R1.raw.fastq.gz Cr-1.R2.raw.fastq.gz	fastq fastq	7322067614.0	24245257.0	Cr 1.R1.raw.fastq.gz	0:151 1:151	A:1927213281;C:1727973559;G:1748866497;T:1917985720;N:28557	151	151			1927213281	1727973559	1748866497	1917985720	28557	SRX27393948	SRS23824009	SRA2054568	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-19	Adult	Adult	Gut	Digestive System
34523	34523	SRR32044801	SRX27393947	SRS23824008	SRP558295	PRJNA1212482	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212482	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.				Con 3	C	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 12\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:gut\|death date:2023 8 12\|health state:health\|sample type:tissue\|replication:Con 3\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	Con 3	Con 3	normal			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7		SRP558295		Con-3.R1.raw.fastq.gz Con-3.R2.raw.fastq.gz	fastq fastq	10329187314.0	34202607.0	Con 3.R1.raw.fastq.gz	0:151 1:151	A:2805764955;C:2343400161;G:2421657823;T:2758323021;N:41354	151	151			2805764955	2343400161	2421657823	2758323021	41354	SRX27393947	SRS23824008	SRA2054568	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-19	Adult	Adult	Gut	Digestive System
34524	34524	SRR32044802	SRX27393946	SRS23824007	SRP558295	PRJNA1212482	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212482	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.				Con 2	B	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 12\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:gut\|death date:2023 8 12\|health state:health\|sample type:tissue\|replication:Con 2\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	Con 2	Con 2	normal			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7		SRP558295		Con-2.R1.raw.fastq.gz Con-2.R2.raw.fastq.gz	fastq fastq	10789961398.0	35728349.0	Con 2.R1.raw.fastq.gz	0:151 1:151	A:2983305704;C:2396592872;G:2488165589;T:2921853880;N:43353	151	151			2983305704	2396592872	2488165589	2921853880	43353	SRX27393946	SRS23824007	SRA2054568	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-19	Adult	Adult	Gut	Digestive System
34525	34525	SRR32044803	SRX27393945	SRS23824006	SRP558295	PRJNA1212482	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212482	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.				Con 1	A	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 12\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:gut\|death date:2023 8 12\|health state:health\|sample type:tissue\|replication:Con 1\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	Con 1	Con 1	normal			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7		SRP558295		Con-1.R1.raw.fastq.gz Con-1.R2.raw.fastq.gz	fastq fastq	7118179260.0	23570130.0	Con 1.R1.raw.fastq.gz	0:151 1:151	A:1874284939;C:1673861890;G:1718740497;T:1851263659;N:28275	151	151			1874284939	1673861890	1718740497	1851263659	28275	SRX27393945	SRS23824006	SRA2054568	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-19	Adult	Adult	Gut	Digestive System
38059	38059	SRR1524245	SRX661010	SRS665985	SRP044781	PRJNA255848	Danio rerio Transcriptome	PRJNA255848	Transcriptome Analysis	Transcriptome analysis of 12 zebrafish tissues	parent bioproject:PRJNA255979	pubmed:27189481	Zebrafish intestine	Zebrafish intestine	F Dr 9	strain:AB\|age:5 month\|biomaterial provider:INRA\|sex:female\|tissue:Intestine\|BioSampleModel:Model organism or animal									Zebrafish intestine	F Dr 9	F Dr 9	Total RNA was qualified using an Agilent BioAnalyzer and 1 µg was used for polyA selection and library construction with Illumina's TruSeq stranded total RNA sample preparation kit according to the manufacturer's instructions TruSeq stranded total RNA SamplePrep Guide RevC			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP044781		F_Dr_9_GCCAAT_L005_R2.fastq.gz F_Dr_9_GCCAAT_L005_R1.fastq.gz	fastq fastq	8637468200.0	43187341.0	F Dr 9 files	0:100 1:100	A:2270309093;C:2039596980;G:2056249938;T:2263331787;N:7980402	100	100			2270309093	2039596980	2056249938	2263331787	7980402	SRX661010	SRS665985	SRA176464	INRA\|Fish Physiology and Genomics	INRA PhyloFish	2	0.94661	0.94511	0.06033	0.06049	0.75743	0.75747	0.43604	0.43901	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	France	2015-07-24	Adult	Adult	Gut	Digestive System
38269	38269	SRR1609746	SRX730399	SRS719620	SRP048807	PRJNA263496	Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish	GSE62221	Transcriptome Analysis	The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures		pubmed:26227973		intestine10	GSM1523041	source name:intestine\|tissue:intestine\|temperature:10°C\|strain:Tubingen\|age:6 mpf	intestine10	Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	intestine	fish were maintained 12h to adapt low temperatures and then killed by pithing	Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:intestine\|temperature:10°C\|strain:Tubingen\|age:6 mpf	GSM1523041	GSM1523041: intestine10; Danio rerio; RNA Seq	GSM1523041		1	Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM1523041	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP048807		intestine10_2.fq.gz intestine10_1.fq.gz	fastq fastq	3638953000.0	18194765.0	GSM1523041 r1	0:100 1:100	A:944286084;C:877180113;G:870958371;T:946463708;N:64724	100	100			944286084	877180113	870958371	946463708	64724	SRX730399	SRS719620	SRA189240	GEO	Shanghai Ocean University	2	0.95871	0.95555	0.03654	0.03737	0.77546	0.77597	0.49972	0.50867	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	China	2014-10-09	Adult	Adult	Gut	Digestive System
38270	38270	SRR1609745	SRX730398	SRS719619	SRP048807	PRJNA263496	Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish	GSE62221	Transcriptome Analysis	The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures		pubmed:26227973		intestine18	GSM1523040	source name:intestine\|tissue:intestine\|temperature:18°C\|strain:Tubingen\|age:6 mpf	intestine18	Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	intestine	fish were maintained 12h to adapt low temperatures and then killed by pithing	Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:intestine\|temperature:18°C\|strain:Tubingen\|age:6 mpf	GSM1523040	GSM1523040: intestine18; Danio rerio; RNA Seq	GSM1523040		1	Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM1523040	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP048807		intestine18_1.fq.gz intestine18_2.fq.gz	fastq fastq	3870426800.0	19352134.0	GSM1523040 r1	0:100 1:100	A:1034436410;C:900862332;G:899347839;T:1035707094;N:73125	100	100			1034436410	900862332	899347839	1035707094	73125	SRX730398	SRS719619	SRA189240	GEO	Shanghai Ocean University	2	0.93279	0.92997	0.0455	0.04571	0.76152	0.76228	0.44545	0.44882	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	China	2014-10-09	Adult	Adult	Gut	Digestive System
38271	38271	SRR1609744	SRX730397	SRS719618	SRP048807	PRJNA263496	Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish	GSE62221	Transcriptome Analysis	The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures		pubmed:26227973		intestine28	GSM1523039	source name:intestine\|tissue:intestine\|temperature:28°C\|strain:Tubingen\|age:6 mpf	intestine28	Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	intestine	fish were maintained 12h to adapt low temperatures and then killed by pithing	Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:intestine\|temperature:28°C\|strain:Tubingen\|age:6 mpf	GSM1523039	GSM1523039: intestine28; Danio rerio; RNA Seq	GSM1523039		1	Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM1523039	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP048807		intestine28_1.fq.gz intestine28_2.fq.gz	fastq fastq	3710350200.0	18551751.0	GSM1523039 r1	0:100 1:100	A:987499090;C:870092319;G:865419689;T:987267641;N:71461	100	100			987499090	870092319	865419689	987267641	71461	SRX730397	SRS719618	SRA189240	GEO	Shanghai Ocean University	2	0.94613	0.94058	0.04736	0.04784	0.7599	0.76288	0.51653	0.51797	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	China	2014-10-09	Adult	Adult	Gut	Digestive System
41844	41844	SRR5259817	SRX2564548	SRS1981207	SRP099850	PRJNA374872	Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells [zebrafish]	GSE94933	Other	We profiled genome wide accesssible chromatin data and RNA seq from four species zebrafish stickleback mouse and human to identify commonly regulated genes and regulatory metods in intestinal epithelial cells IECs. We identify a group genes that are commonly expressed in IECs and genes that are commonly expressed along the length of the intestine in fish and mammals. Using accessible chromatin data we identified enriched transcription factor binding site motifs In IECs and sites that are commonly accessible in IECs in all species. Finally we confirm the ability for these regions from multiple species to drive conserved expression in IECs using a zebrafish reporter assay. Overall design: Examination of expression levels and chromatin accessibility in intestinal epithelaial cells in zebrafish	parent bioproject:PRJNA374867	pubmed:28850571		zIEC3 mRNA	GSM2492108	tissue:Intestinal Epithelial Cells RNA seq\|strain:TL\|cell type:Zebrafish Adult Intestinal Epithelial Cells	zIEC3 mRNA	Paired End Adapter trimmed reads from Duke Sequencing and Genomic Technologies Shared Resource were mapped to the danRer7 genome using Tophat2v2.0.9 with default conditions using Galaxy0.5 Cufflinks v2.0.2 was used to generate FPKM values using default peramaters and Zv9/danRer7 Ensembl annotationsEnsemble genes 71 using Galaxy0.0.5 bigWig files were generated using bamCoverage Galaxy verion 2.2.3.0 and read normalized Genome build: danRer7 Supplementary files format and content: Bigwig represents single base pair genomewide sequencing coverage; Bed files are tabular files containing peak coordinates; Tabular Files Contain Gene Expression Information	Intestinal Epithelial Cells RNA seq		To isolate zebrafish IECs intestines were dissected splayed and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia adipocytes and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA 1.5 mM DTT 0.5x Complete protease inhibitors Roche in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA 0.5x Complete protease inhibitors Roche in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4°C washed once with 13 ml of cold 1X PBS and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at 80°C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0 2% vol/vol Triton X 100 1% SDS 100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst 0.5 second pause for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.	TL strain zebrafish at Aquaculture Core Facility at UNC Chapel Hill were grown using standard zebrafish diets	strain:TL\|cell type:Zebrafish Adult Intestinal Epithelial Cells	GSM2492108	GSM2492108: zIEC3 mRNA; Danio rerio; RNA Seq	GSM2492108		1	To isolate zebrafish IECs intestines were dissected splayed and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia adipocytes and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA 1.5 mM DTT 0.5x Complete protease inhibitors Roche in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA 0.5x Complete protease inhibitors Roche in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4°C washed once with 13 ml of cold 1X PBS and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at 80°C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0 2% vol/vol Triton X 100 1% SDS 100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst 0.5 second pause for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.	GEO Accession:GSM2492108	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP099850		ZIEC3_GCCAAT_L001_R2_001.fastq.gz ZIEC3_GCCAAT_L001_R1_001.fastq.gz	fastq fastq	2644689216.0	27548846.0	GSM2492108 r1	0:48 1:48	A:687890725;C:632255900;G:620389531;T:703494916;N:658144	48	48			687890725	632255900	620389531	703494916	658144	SRX2564548	SRS1981207	SRA538156	GEO	John Rawls, Duke University	2	0.87587	0.87862	0.06582	0.06632	0.73931	0.73878	0.53496	0.53653	48	48	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2017-02-15	Adult	Adult	Gut	Digestive System
41845	41845	SRR5259816	SRX2564547	SRS1981208	SRP099850	PRJNA374872	Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells [zebrafish]	GSE94933	Other	We profiled genome wide accesssible chromatin data and RNA seq from four species zebrafish stickleback mouse and human to identify commonly regulated genes and regulatory metods in intestinal epithelial cells IECs. We identify a group genes that are commonly expressed in IECs and genes that are commonly expressed along the length of the intestine in fish and mammals. Using accessible chromatin data we identified enriched transcription factor binding site motifs In IECs and sites that are commonly accessible in IECs in all species. Finally we confirm the ability for these regions from multiple species to drive conserved expression in IECs using a zebrafish reporter assay. Overall design: Examination of expression levels and chromatin accessibility in intestinal epithelaial cells in zebrafish	parent bioproject:PRJNA374867	pubmed:28850571		zIEC2 mRNA	GSM2492107	tissue:Intestinal Epithelial Cells RNA seq\|strain:TL\|cell type:Zebrafish Adult Intestinal Epithelial Cells	zIEC2 mRNA	Paired End Adapter trimmed reads from Duke Sequencing and Genomic Technologies Shared Resource were mapped to the danRer7 genome using Tophat2v2.0.9 with default conditions using Galaxy0.5 Cufflinks v2.0.2 was used to generate FPKM values using default peramaters and Zv9/danRer7 Ensembl annotationsEnsemble genes 71 using Galaxy0.0.5 bigWig files were generated using bamCoverage Galaxy verion 2.2.3.0 and read normalized Genome build: danRer7 Supplementary files format and content: Bigwig represents single base pair genomewide sequencing coverage; Bed files are tabular files containing peak coordinates; Tabular Files Contain Gene Expression Information	Intestinal Epithelial Cells RNA seq		To isolate zebrafish IECs intestines were dissected splayed and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia adipocytes and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA 1.5 mM DTT 0.5x Complete protease inhibitors Roche in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA 0.5x Complete protease inhibitors Roche in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4°C washed once with 13 ml of cold 1X PBS and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at 80°C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0 2% vol/vol Triton X 100 1% SDS 100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst 0.5 second pause for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.	TL strain zebrafish at Aquaculture Core Facility at UNC Chapel Hill were grown using standard zebrafish diets	strain:TL\|cell type:Zebrafish Adult Intestinal Epithelial Cells	GSM2492107	GSM2492107: zIEC2 mRNA; Danio rerio; RNA Seq	GSM2492107		1	To isolate zebrafish IECs intestines were dissected splayed and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia adipocytes and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA 1.5 mM DTT 0.5x Complete protease inhibitors Roche in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA 0.5x Complete protease inhibitors Roche in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4°C washed once with 13 ml of cold 1X PBS and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at 80°C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0 2% vol/vol Triton X 100 1% SDS 100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst 0.5 second pause for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.	GEO Accession:GSM2492107	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP099850		ZIEC2_GCCAAT_L005_R1_001.fastq.gz ZIEC2_GCCAAT_L005_R2_001.fastq.gz	fastq fastq	1785594816.0	18599946.0	GSM2492107 r1	0:48 1:48	A:466092820;C:422828003;G:420238032;T:476324795;N:111166	48	48			466092820	422828003	420238032	476324795	111166	SRX2564547	SRS1981208	SRA538156	GEO	John Rawls, Duke University	2	0.85545	0.86359	0.08337	0.08488	0.74635	0.74677	0.52663	0.53064	48	48	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2017-02-15	Adult	Adult	Gut	Digestive System
41846	41846	SRR5259815	SRX2564546	SRS1981206	SRP099850	PRJNA374872	Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells [zebrafish]	GSE94933	Other	We profiled genome wide accesssible chromatin data and RNA seq from four species zebrafish stickleback mouse and human to identify commonly regulated genes and regulatory metods in intestinal epithelial cells IECs. We identify a group genes that are commonly expressed in IECs and genes that are commonly expressed along the length of the intestine in fish and mammals. Using accessible chromatin data we identified enriched transcription factor binding site motifs In IECs and sites that are commonly accessible in IECs in all species. Finally we confirm the ability for these regions from multiple species to drive conserved expression in IECs using a zebrafish reporter assay. Overall design: Examination of expression levels and chromatin accessibility in intestinal epithelaial cells in zebrafish	parent bioproject:PRJNA374867	pubmed:28850571		zIEC1 mRNA	GSM2492106	tissue:Intestinal Epithelial Cells RNA seq\|strain:TL\|cell type:Zebrafish Adult Intestinal Epithelial Cells	zIEC1 mRNA	Paired End Adapter trimmed reads from Duke Sequencing and Genomic Technologies Shared Resource were mapped to the danRer7 genome using Tophat2v2.0.9 with default conditions using Galaxy0.5 Cufflinks v2.0.2 was used to generate FPKM values using default peramaters and Zv9/danRer7 Ensembl annotationsEnsemble genes 71 using Galaxy0.0.5 bigWig files were generated using bamCoverage Galaxy verion 2.2.3.0 and read normalized Genome build: danRer7 Supplementary files format and content: Bigwig represents single base pair genomewide sequencing coverage; Bed files are tabular files containing peak coordinates; Tabular Files Contain Gene Expression Information	Intestinal Epithelial Cells RNA seq		To isolate zebrafish IECs intestines were dissected splayed and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia adipocytes and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA 1.5 mM DTT 0.5x Complete protease inhibitors Roche in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA 0.5x Complete protease inhibitors Roche in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4°C washed once with 13 ml of cold 1X PBS and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at 80°C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0 2% vol/vol Triton X 100 1% SDS 100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst 0.5 second pause for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.	TL strain zebrafish at Aquaculture Core Facility at UNC Chapel Hill were grown using standard zebrafish diets	strain:TL\|cell type:Zebrafish Adult Intestinal Epithelial Cells	GSM2492106	GSM2492106: zIEC1 mRNA; Danio rerio; RNA Seq	GSM2492106		1	To isolate zebrafish IECs intestines were dissected splayed and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia adipocytes and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA 1.5 mM DTT 0.5x Complete protease inhibitors Roche in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA 0.5x Complete protease inhibitors Roche in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4°C washed once with 13 ml of cold 1X PBS and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at 80°C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0 2% vol/vol Triton X 100 1% SDS 100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst 0.5 second pause for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.	GEO Accession:GSM2492106	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP099850		ZIEC1_CGATGT_L004_R1_001.fastq.gz ZIEC1_CGATGT_L004_R2_001.fastq.gz	fastq fastq	1953396576.0	20347881.0	GSM2492106 r1	0:48 1:48	A:510243495;C:461085497;G:464477553;T:517509152;N:80879	48	48			510243495	461085497	464477553	517509152	80879	SRX2564546	SRS1981206	SRA538156	GEO	John Rawls, Duke University	2	0.87991	0.88564	0.09576	0.0974	0.74789	0.74909	0.54326	0.54368	48	48	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2017-02-15	Adult	Adult	Gut	Digestive System
44033	44033	SRR6231893	SRX3340325	SRS2641976	SRP122541	PRJNA415856	Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment	PRJNA415856	Transcriptome Analysis	Transcriptomic analysis of genetic expression in enteric neurons as compared to other intestinal cells.		pubmed:28403821		GFP positive cells	en GFP positive JK	strain:phox2b Tgphox2b:EGFP w37\|dev stage:7 dpf male and female\|tissue:Intestine\|biomaterial provider:Kuhlman lab\|cell type:Intestinal neurons\|BioSampleModel:Model organism or animal									en GFP positive JK r1	en GFP positive JK r1 fwd	en GFP positive JK r1 fwd	The library was prepapred by the Iowa State DNA facility.			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP122541		d7phoGFPA_GCCAAT_R1_001.fastq.gz d7phoGFPA_GCCAAT_R2_001.fastq.gz	fastq fastq	22618935400.0	113094677.0	d7phoGFPA GCCAAT R1 001.fastq.gz	0:100 1:100	A:6233619158;C:5097706589;G:5045972110;T:6222785585;N:18851958	100	100			6233619158	5097706589	5045972110	6222785585	18851958	SRX3340325	SRS2641976	SRA625723	Iowa State University\|Genetics Development and Cell Biology	Iowa State University	2	0.91266	0.9056	0.16638	0.16643	0.68008	0.68367	0.48483	0.48254	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-10-27	Larval	Larval	Gut	Digestive System
44034	44034	SRR6231894	SRX3340324	SRS2641976	SRP122541	PRJNA415856	Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment	PRJNA415856	Transcriptome Analysis	Transcriptomic analysis of genetic expression in enteric neurons as compared to other intestinal cells.		pubmed:28403821		GFP positive cells	en GFP positive JK	strain:phox2b Tgphox2b:EGFP w37\|dev stage:7 dpf male and female\|tissue:Intestine\|biomaterial provider:Kuhlman lab\|cell type:Intestinal neurons\|BioSampleModel:Model organism or animal									en GFP positive JK r2	en GFP positive JK r2 fwd	en GFP positive JK r2 fwd	The library was prepapred by the Iowa State DNA facility.			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP122541		d7phoGFPB_GTGAAA_R2_001.fastq.gz d7phoGFPB_GTGAAA_R1_001.fastq.gz	fastq fastq	13753541400.0	68767707.0	d7phoGFPB GTGAAA R1 001.fastq.gz	0:100 1:100	A:3807602619;C:3077358417;G:3063510819;T:3793560543;N:11509002	100	100			3807602619	3077358417	3063510819	3793560543	11509002	SRX3340324	SRS2641976	SRA625723	Iowa State University\|Genetics Development and Cell Biology	Iowa State University	2	0.90465	0.89478	0.20689	0.2048	0.68402	0.68738	0.4887	0.48279	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-10-27	Larval	Larval	Gut	Digestive System
44035	44035	SRR6231895	SRX3340323	SRS2641979	SRP122541	PRJNA415856	Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment	PRJNA415856	Transcriptome Analysis	Transcriptomic analysis of genetic expression in enteric neurons as compared to other intestinal cells.		pubmed:28403821		GFP negative cells	en GFP negative JK	strain:phox2b Tgphox2b:EGFP w37\|dev stage:7 dpf male and female\|tissue:Intestine\|biomaterial provider:Kuhlman lab\|cell type:Intestinal non neurons\|BioSampleModel:Model organism or animal									en GFP negative JK r1	en GFP negative JK r1 fwd	en GFP negative JK r1 fwd	The library was prepapred by the Iowa State DNA facility.			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP122541		d7phoGFP-A_ACAGTG_R1_001.fastq.gz d7phoGFP-A_ACAGTG_R2_001.fastq.gz	fastq fastq	17591029600.0	87955148.0	d7phoGFP A ACAGTG R2 001.fastq.gz	0:100 1:100	A:4757105599;C:4046056704;G:4012427038;T:4760767597;N:14672662	100	100			4757105599	4046056704	4012427038	4760767597	14672662	SRX3340323	SRS2641979	SRA625723	Iowa State University\|Genetics Development and Cell Biology	Iowa State University	2	0.91795	0.92394	0.12634	0.12565	0.69479	0.68976	0.50879	0.5095	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-10-27	Larval	Larval	Gut	Digestive System
44036	44036	SRR6231897	SRX3340321	SRS2641979	SRP122541	PRJNA415856	Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment	PRJNA415856	Transcriptome Analysis	Transcriptomic analysis of genetic expression in enteric neurons as compared to other intestinal cells.		pubmed:28403821		GFP negative cells	en GFP negative JK	strain:phox2b Tgphox2b:EGFP w37\|dev stage:7 dpf male and female\|tissue:Intestine\|biomaterial provider:Kuhlman lab\|cell type:Intestinal non neurons\|BioSampleModel:Model organism or animal									en GFP negative JK r2	en GFP negative JK r2 rev	en GFP negative JK r2 rev	The library was prepapred by the Iowa State DNA facility.			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP122541		d7phoGFP-B_CTTGTA_R1_001.fastq.gz d7phoGFP-B_CTTGTA_R2_001.fastq.gz	fastq fastq	21627852000.0	108139260.0	d7phoGFP B CTTGTA R2 001.fastq.gz	0:100 1:100	A:5802401896;C:5026391965;G:4975450919;T:5805553498;N:18053722	100	100			5802401896	5026391965	4975450919	5805553498	18053722	SRX3340321	SRS2641979	SRA625723	Iowa State University\|Genetics Development and Cell Biology	Iowa State University	2	0.93032	0.9242	0.11858	0.1194	0.69209	0.69544	0.50104	0.50121	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-11-02	Larval	Larval	Gut	Digestive System
49070	49070	SRR7641841	SRX4505270	SRS3625663	SRP156282	PRJNA484346	Epigenetic regulation of zebrafish intestinal development	GSE118076	Other	The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5 7 9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5 7 9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines pools of 10 intestines in triplicates at 5 7 and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines pools of 25 intesines +5 set aside for input DNA in duplicates at 5 7 and 9 dpf for H3K4me3 and H3K27me3.				Danio rerio RNAseq intestine 9dpf wt3	GSM3318287	source name:intestine\|strain:AB\|tissue:intestine\|age:9 dpf\|genotype:wild type tgcldn15la:GFP\|chip antibody:n/a	Danio rerio RNAseq intestine 9dpf wt3	RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	intestine		Dissected intestines were lyzed in Trizol and total RNA was extracted followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis standard Illumina KAPA HYPERprep library preparations were made.	Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch reared in E3 medium at 28.5°C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.	strain:AB\|tissue:intestine\|age:9 dpf\|genotype:wild type tgcldn15la:GFP\|chip antibody:n/a	GSM3318287	GSM3318287: Danio rerio RNAseq intestine 9dpf wt3; Danio rerio; RNA Seq	GSM3318287		1	Dissected intestines were lyzed in Trizol and total RNA was extracted followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis standard Illumina KAPA HYPERprep library preparations were made.	GEO Accession:GSM3318287	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP156282		lane1_BSwt9dpf3_AGTCAA_R2.fastq.gz lane1_BSwt9dpf3_AGTCAA_R1.fastq.gz	fastq fastq	2761029656.0	32104996.0	GSM3318287 r1	0:43 1:43	A:708766648;C:643915678;G:711330854;T:696326829;N:689647	43	43			708766648	643915678	711330854	696326829	689647	SRX4505270	SRS3625663	SRA751578	GEO	Molecular Biology, Radboud University	2	0.89599	0.88107	0.38979	0.37161	0.72523	0.72705	0.60581	0.60845	43	43	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2018-08-03	Larval	Larval	Gut	Digestive System
49071	49071	SRR7641840	SRX4505269	SRS3625661	SRP156282	PRJNA484346	Epigenetic regulation of zebrafish intestinal development	GSE118076	Other	The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5 7 9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5 7 9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines pools of 10 intestines in triplicates at 5 7 and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines pools of 25 intesines +5 set aside for input DNA in duplicates at 5 7 and 9 dpf for H3K4me3 and H3K27me3.				Danio rerio RNAseq intestine 9dpf wt2	GSM3318286	source name:intestine\|strain:AB\|tissue:intestine\|age:9 dpf\|genotype:wild type tgcldn15la:GFP\|chip antibody:n/a	Danio rerio RNAseq intestine 9dpf wt2	RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	intestine		Dissected intestines were lyzed in Trizol and total RNA was extracted followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis standard Illumina KAPA HYPERprep library preparations were made.	Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch reared in E3 medium at 28.5°C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.	strain:AB\|tissue:intestine\|age:9 dpf\|genotype:wild type tgcldn15la:GFP\|chip antibody:n/a	GSM3318286	GSM3318286: Danio rerio RNAseq intestine 9dpf wt2; Danio rerio; RNA Seq	GSM3318286		1	Dissected intestines were lyzed in Trizol and total RNA was extracted followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis standard Illumina KAPA HYPERprep library preparations were made.	GEO Accession:GSM3318286	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP156282		lane1_BSwt9dpf2_GGCTAC_R2.fastq.gz lane1_BSwt9dpf2_GGCTAC_R1.fastq.gz	fastq fastq	3774884086.0	43894001.0	GSM3318286 r1	0:43 1:43	A:912580559;C:950011527;G:1000247169;T:911105213;N:939618	43	43			912580559	950011527	1000247169	911105213	939618	SRX4505269	SRS3625661	SRA751578	GEO	Molecular Biology, Radboud University	2	0.91348	0.89692	0.32028	0.31	0.75479	0.76398	0.64335	0.62378	43	43	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2018-08-03	Larval	Larval	Gut	Digestive System
49072	49072	SRR7641838	SRX4505267	SRS3625659	SRP156282	PRJNA484346	Epigenetic regulation of zebrafish intestinal development	GSE118076	Other	The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5 7 9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5 7 9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines pools of 10 intestines in triplicates at 5 7 and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines pools of 25 intesines +5 set aside for input DNA in duplicates at 5 7 and 9 dpf for H3K4me3 and H3K27me3.				Danio rerio RNAseq intestine 9dpf wt1	GSM3318285	source name:intestine\|strain:AB\|tissue:intestine\|age:9 dpf\|genotype:wild type tgcldn15la:GFP\|chip antibody:n/a	Danio rerio RNAseq intestine 9dpf wt1	RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	intestine		Dissected intestines were lyzed in Trizol and total RNA was extracted followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis standard Illumina KAPA HYPERprep library preparations were made.	Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch reared in E3 medium at 28.5°C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.	strain:AB\|tissue:intestine\|age:9 dpf\|genotype:wild type tgcldn15la:GFP\|chip antibody:n/a	GSM3318285	GSM3318285: Danio rerio RNAseq intestine 9dpf wt1; Danio rerio; RNA Seq	GSM3318285		1	Dissected intestines were lyzed in Trizol and total RNA was extracted followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis standard Illumina KAPA HYPERprep library preparations were made.	GEO Accession:GSM3318285	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP156282		lane1_BSwt9dpf1_TAGCTT_R2.fastq.gz lane1_BSwt9dpf1_TAGCTT_R1.fastq.gz	fastq fastq	2839107938.0	33012883.0	GSM3318285 r1	0:43 1:43	A:706052485;C:678593541;G:744406061;T:709347067;N:708784	43	43			706052485	678593541	744406061	709347067	708784	SRX4505267	SRS3625659	SRA751578	GEO	Molecular Biology, Radboud University	2	0.90142	0.89053	0.40928	0.39461	0.72622	0.72768	0.51721	0.5385	43	43	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2018-08-03	Larval	Larval	Gut	Digestive System
49073	49073	SRR7641837	SRX4505266	SRS3625658	SRP156282	PRJNA484346	Epigenetic regulation of zebrafish intestinal development	GSE118076	Other	The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5 7 9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5 7 9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines pools of 10 intestines in triplicates at 5 7 and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines pools of 25 intesines +5 set aside for input DNA in duplicates at 5 7 and 9 dpf for H3K4me3 and H3K27me3.				Danio rerio RNAseq intestine 7dpf wt3	GSM3318284	source name:intestine\|strain:AB\|tissue:intestine\|age:7 dpf\|genotype:wild type tgcldn15la:GFP\|chip antibody:n/a	Danio rerio RNAseq intestine 7dpf wt3	RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	intestine		Dissected intestines were lyzed in Trizol and total RNA was extracted followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis standard Illumina KAPA HYPERprep library preparations were made.	Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch reared in E3 medium at 28.5°C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.	strain:AB\|tissue:intestine\|age:7 dpf\|genotype:wild type tgcldn15la:GFP\|chip antibody:n/a	GSM3318284	GSM3318284: Danio rerio RNAseq intestine 7dpf wt3; Danio rerio; RNA Seq	GSM3318284		1	Dissected intestines were lyzed in Trizol and total RNA was extracted followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis standard Illumina KAPA HYPERprep library preparations were made.	GEO Accession:GSM3318284	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP156282		lane1_BSwt7dpf3_GATCAG_R1.fastq.gz lane1_BSwt7dpf3_GATCAG_R2.fastq.gz	fastq fastq	3032189462.0	35258017.0	GSM3318284 r1	0:43 1:43	A:728621779;C:727851984;G:867302660;T:707649251;N:763788	43	43			728621779	727851984	867302660	707649251	763788	SRX4505266	SRS3625658	SRA751578	GEO	Molecular Biology, Radboud University	2	0.87964	0.8732	0.36258	0.35306	0.7259	0.72934	0.56793	0.56457	43	43	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2018-08-03	Larval	Larval	Gut	Digestive System
49074	49074	SRR7641836	SRX4505265	SRS3625657	SRP156282	PRJNA484346	Epigenetic regulation of zebrafish intestinal development	GSE118076	Other	The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5 7 9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5 7 9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines pools of 10 intestines in triplicates at 5 7 and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines pools of 25 intesines +5 set aside for input DNA in duplicates at 5 7 and 9 dpf for H3K4me3 and H3K27me3.				Danio rerio RNAseq intestine 7dpf wt2	GSM3318283	source name:intestine\|strain:AB\|tissue:intestine\|age:7 dpf\|genotype:wild type tgcldn15la:GFP\|chip antibody:n/a	Danio rerio RNAseq intestine 7dpf wt2	RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	intestine		Dissected intestines were lyzed in Trizol and total RNA was extracted followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis standard Illumina KAPA HYPERprep library preparations were made.	Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch reared in E3 medium at 28.5°C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.	strain:AB\|tissue:intestine\|age:7 dpf\|genotype:wild type tgcldn15la:GFP\|chip antibody:n/a	GSM3318283	GSM3318283: Danio rerio RNAseq intestine 7dpf wt2; Danio rerio; RNA Seq	GSM3318283		1	Dissected intestines were lyzed in Trizol and total RNA was extracted followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis standard Illumina KAPA HYPERprep library preparations were made.	GEO Accession:GSM3318283	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP156282		lane1_BSwt7dpf2_ACTTGA_R2.fastq.gz lane1_BSwt7dpf2_ACTTGA_R1.fastq.gz	fastq fastq	2796267812.0	32514742.0	GSM3318283 r1	0:43 1:43	A:678627733;C:682194336;G:763077086;T:671672090;N:696567	43	43			678627733	682194336	763077086	671672090	696567	SRX4505265	SRS3625657	SRA751578	GEO	Molecular Biology, Radboud University	2	0.88818	0.88174	0.43784	0.42578	0.72531	0.72417	0.51845	0.53225	43	43	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2018-08-03	Larval	Larval	Gut	Digestive System
49075	49075	SRR7641834	SRX4505264	SRS3625656	SRP156282	PRJNA484346	Epigenetic regulation of zebrafish intestinal development	GSE118076	Other	The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5 7 9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5 7 9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines pools of 10 intestines in triplicates at 5 7 and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines pools of 25 intesines +5 set aside for input DNA in duplicates at 5 7 and 9 dpf for H3K4me3 and H3K27me3.				Danio rerio RNAseq intestine 7dpf wt1	GSM3318282	source name:intestine\|strain:AB\|tissue:intestine\|age:7 dpf\|genotype:wild type tgcldn15la:GFP\|chip antibody:n/a	Danio rerio RNAseq intestine 7dpf wt1	RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	intestine		Dissected intestines were lyzed in Trizol and total RNA was extracted followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis standard Illumina KAPA HYPERprep library preparations were made.	Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch reared in E3 medium at 28.5°C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.	strain:AB\|tissue:intestine\|age:7 dpf\|genotype:wild type tgcldn15la:GFP\|chip antibody:n/a	GSM3318282	GSM3318282: Danio rerio RNAseq intestine 7dpf wt1; Danio rerio; RNA Seq	GSM3318282		1	Dissected intestines were lyzed in Trizol and total RNA was extracted followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis standard Illumina KAPA HYPERprep library preparations were made.	GEO Accession:GSM3318282	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP156282		lane1_BSwt7dpf1_TTAGGC_R2.fastq.gz lane1_BSwt7dpf1_TTAGGC_R1.fastq.gz	fastq fastq	2657998302.0	30906957.0	GSM3318282 r1	0:43 1:43	A:670335271;C:630669243;G:685436534;T:670905092;N:652162	43	43			670335271	630669243	685436534	670905092	652162	SRX4505264	SRS3625656	SRA751578	GEO	Molecular Biology, Radboud University	2	0.87993	0.87022	0.42578	0.40713	0.69828	0.70244	0.54254	0.55209	43	43	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2018-08-03	Larval	Larval	Gut	Digestive System
49076	49076	SRR7641833	SRX4505263	SRS3625655	SRP156282	PRJNA484346	Epigenetic regulation of zebrafish intestinal development	GSE118076	Other	The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5 7 9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5 7 9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines pools of 10 intestines in triplicates at 5 7 and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines pools of 25 intesines +5 set aside for input DNA in duplicates at 5 7 and 9 dpf for H3K4me3 and H3K27me3.				Danio rerio RNAseq intestine 5dpf wt3	GSM3318281	source name:intestine\|strain:AB\|tissue:intestine\|age:5 dpf\|genotype:wild type tgcldn15la:GFP\|chip antibody:n/a	Danio rerio RNAseq intestine 5dpf wt3	RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	intestine		Dissected intestines were lyzed in Trizol and total RNA was extracted followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis standard Illumina KAPA HYPERprep library preparations were made.	Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch reared in E3 medium at 28.5°C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.	strain:AB\|tissue:intestine\|age:5 dpf\|genotype:wild type tgcldn15la:GFP\|chip antibody:n/a	GSM3318281	GSM3318281: Danio rerio RNAseq intestine 5dpf wt3; Danio rerio; RNA Seq	GSM3318281		1	Dissected intestines were lyzed in Trizol and total RNA was extracted followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis standard Illumina KAPA HYPERprep library preparations were made.	GEO Accession:GSM3318281	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP156282		lane1_BSwt5dpf3_CAGATC_R1.fastq.gz lane1_BSwt5dpf3_CAGATC_R2.fastq.gz	fastq fastq	3471426378.0	40365423.0	GSM3318281 r1	0:43 1:43	A:816007186;C:888388842;G:957708559;T:808447064;N:874727	43	43			816007186	888388842	957708559	808447064	874727	SRX4505263	SRS3625655	SRA751578	GEO	Molecular Biology, Radboud University	2	0.86569	0.86483	0.38669	0.37568	0.7277	0.73148	0.51986	0.52105	43	43	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2018-08-03	Larval	Larval	Gut	Digestive System
49077	49077	SRR7641832	SRX4505262	SRS3625654	SRP156282	PRJNA484346	Epigenetic regulation of zebrafish intestinal development	GSE118076	Other	The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5 7 9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5 7 9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines pools of 10 intestines in triplicates at 5 7 and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines pools of 25 intesines +5 set aside for input DNA in duplicates at 5 7 and 9 dpf for H3K4me3 and H3K27me3.				Danio rerio RNAseq intestine 5dpf wt2	GSM3318280	source name:intestine\|strain:AB\|tissue:intestine\|age:5 dpf\|genotype:wild type tgcldn15la:GFP\|chip antibody:n/a	Danio rerio RNAseq intestine 5dpf wt2	RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	intestine		Dissected intestines were lyzed in Trizol and total RNA was extracted followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis standard Illumina KAPA HYPERprep library preparations were made.	Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch reared in E3 medium at 28.5°C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.	strain:AB\|tissue:intestine\|age:5 dpf\|genotype:wild type tgcldn15la:GFP\|chip antibody:n/a	GSM3318280	GSM3318280: Danio rerio RNAseq intestine 5dpf wt2; Danio rerio; RNA Seq	GSM3318280		1	Dissected intestines were lyzed in Trizol and total RNA was extracted followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis standard Illumina KAPA HYPERprep library preparations were made.	GEO Accession:GSM3318280	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP156282		lane1_BSwt5dpf2_GCCAAT_R2.fastq.gz lane1_BSwt5dpf2_GCCAAT_R1.fastq.gz	fastq fastq	2424100404.0	28187214.0	GSM3318280 r1	0:43 1:43	A:657799034;C:534330605;G:575770800;T:655604713;N:595252	43	43			657799034	534330605	575770800	655604713	595252	SRX4505262	SRS3625654	SRA751578	GEO	Molecular Biology, Radboud University	2	0.85487	0.83514	0.56287	0.53286	0.69583	0.69658	0.54518	0.55246	43	43	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2018-08-03	Larval	Larval	Gut	Digestive System
49078	49078	SRR7641830	SRX4505261	SRS3625653	SRP156282	PRJNA484346	Epigenetic regulation of zebrafish intestinal development	GSE118076	Other	The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5 7 9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5 7 9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines pools of 10 intestines in triplicates at 5 7 and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines pools of 25 intesines +5 set aside for input DNA in duplicates at 5 7 and 9 dpf for H3K4me3 and H3K27me3.				Danio rerio RNAseq intestine 5dpf wt1	GSM3318279	source name:intestine\|strain:AB\|tissue:intestine\|age:5 dpf\|genotype:wild type tgcldn15la:GFP\|chip antibody:n/a	Danio rerio RNAseq intestine 5dpf wt1	RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	intestine		Dissected intestines were lyzed in Trizol and total RNA was extracted followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis standard Illumina KAPA HYPERprep library preparations were made.	Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch reared in E3 medium at 28.5°C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.	strain:AB\|tissue:intestine\|age:5 dpf\|genotype:wild type tgcldn15la:GFP\|chip antibody:n/a	GSM3318279	GSM3318279: Danio rerio RNAseq intestine 5dpf wt1; Danio rerio; RNA Seq	GSM3318279		1	Dissected intestines were lyzed in Trizol and total RNA was extracted followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis standard Illumina KAPA HYPERprep library preparations were made.	GEO Accession:GSM3318279	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP156282		lane1_BSwt5dpf1_ACAGTG_R1.fastq.gz lane1_BSwt5dpf1_ACAGTG_R2.fastq.gz	fastq fastq	2258154890.0	26257615.0	GSM3318279 r1	0:43 1:43	A:568380294;C:542047927;G:584939179;T:562222871;N:564619	43	43			568380294	542047927	584939179	562222871	564619	SRX4505261	SRS3625653	SRA751578	GEO	Molecular Biology, Radboud University	2	0.89313	0.87302	0.42444	0.40784	0.72096	0.72393	0.58673	0.60423	43	43	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2018-08-03	Larval	Larval	Gut	Digestive System
53020	53020	SRR9662019	SRX6422895	SRS5079685	SRP213938	PRJNA553572	A map of cis regulatory elements and 3D genome structures in zebrafish	GSE134055	Other	The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.		pubmed:33239788;pubmed:35649578		YueLab RNA Seq Intestine rep1	GSM3934887	source name:Tissue\|strain:Tuebingen\|tissue:Intestine	YueLab RNA Seq Intestine rep1	RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged	Tissue		For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.	Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions	strain:Tuebingen\|tissue:Intestine	GSM3934887	GSM3934887: YueLab RNA Seq Intestine rep1; Danio rerio; RNA Seq	GSM3934887		1	For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.	GEO Accession:GSM3934887	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina Genome Analyzer		SRP213938		YueLab-RNA-Seq-Intestine-rep1_1.fastq.gz YueLab-RNA-Seq-Intestine-rep1_2.fastq.gz	fastq fastq	3793725541.0	31407590.0	GSM3934887 r1	0:60.48 1:60.31	A:996160866;C:872713802;G:866478996;T:1058315641;N:56236	60	60			996160866	872713802	866478996	1058315641	56236	SRX6422895	SRS5079685	SRA919194	GEO	Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine	2	0.96494	0.96816	0.10241	0.09966	0.73705	0.73992	0.53336	0.5394	61	61	B	B	biological fallback assumption	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2019-07-09	Pharyngula	Embryo	Gut	Digestive System
53594	53594	SRR9960231	SRX6707776	SRS5261677	SRP218210	PRJNA560029	Single Cell RNA Sequencing Analysis of Polystyrene Microplastic Exposed and control Zebrafish Intestine	GSE135767	Transcriptome Analysis	Microplastics MPs as widespread contamination pose high risk for aquatic organisms. However current understanding of MP toxicities are based on cell population averaged measurements. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 12000 intestinal cells obtained from zebrafishes exposed to 100nm 5µm and 200µm polystyrene MPs PS MPs for xxx days. Eight intestinal cell populations were identified. We found that all the three sizes of PS MPs induced dysfunction of intestinal immune cells including phagosome and regulation of immune system process. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure MPs with different size 100 nm 5 µm and 200 µm.	parent bioproject:PRJNA561326	pubmed:32092251		MPs200vm	GSM4029395	source name:intestinal cells\|tissue:Intestinal single cell suspension\|age:16 wpf\|exposed pollutants:200μm PS MPs	MPs200vm	We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip…	intestinal cells	Exposure solutions were prepared by adding 100 nm 5 μm or 200 μm PS MPs to culture water with a final concentration of 500μg/L. The exposure solution were was replaced every 2 days. Exposure solution in all tanks were was continuously aerated to maintain the dispersion of particles no filtering systems were used in the tanks. post 21 d exposure zebrafish were collected and intestine were rapidly extracted on ice.	The isolated intestinal tissue was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.		tissue:Intestinal single cell suspension\|age:16 wpf\|exposed pollutants:200μm PS MPs	GSM4029395	GSM4029395: MPs200vm; Danio rerio; RNA Seq	GSM4029395		1	The isolated intestinal tissue was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.	GEO Accession:GSM4029395	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP218210		MPs200vm_1.fq.gz MPs200vm_2.fq.gz	fastq fastq	105309618900.0	351032063.0	GSM4029395 r1	0:150 1:150	A:27241602982;C:19773063887;G:28015499540;T:30277575281;N:1877210	150	150			27241602982	19773063887	28015499540	30277575281	1877210	SRX6707776	SRS5261677	SRA938912	GEO	Nanjing University	2	0.0	0.87735	0.0	0.07963	1.0	0.83049		0.55138	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2019-08-13	Adult	Adult	Gut	Digestive System
53595	53595	SRR9960230	SRX6707775	SRS5261676	SRP218210	PRJNA560029	Single Cell RNA Sequencing Analysis of Polystyrene Microplastic Exposed and control Zebrafish Intestine	GSE135767	Transcriptome Analysis	Microplastics MPs as widespread contamination pose high risk for aquatic organisms. However current understanding of MP toxicities are based on cell population averaged measurements. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 12000 intestinal cells obtained from zebrafishes exposed to 100nm 5µm and 200µm polystyrene MPs PS MPs for xxx days. Eight intestinal cell populations were identified. We found that all the three sizes of PS MPs induced dysfunction of intestinal immune cells including phagosome and regulation of immune system process. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure MPs with different size 100 nm 5 µm and 200 µm.	parent bioproject:PRJNA561326	pubmed:32092251		MPs5vm	GSM4029394	source name:intestinal cells\|tissue:Intestinal single cell suspension\|age:16 wpf\|exposed pollutants:5μm PS MPs	MPs5vm	We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip…	intestinal cells	Exposure solutions were prepared by adding 100 nm 5 μm or 200 μm PS MPs to culture water with a final concentration of 500μg/L. The exposure solution were was replaced every 2 days. Exposure solution in all tanks were was continuously aerated to maintain the dispersion of particles no filtering systems were used in the tanks. post 21 d exposure zebrafish were collected and intestine were rapidly extracted on ice.	The isolated intestinal tissue was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.		tissue:Intestinal single cell suspension\|age:16 wpf\|exposed pollutants:5μm PS MPs	GSM4029394	GSM4029394: MPs5vm; Danio rerio; RNA Seq	GSM4029394		1	The isolated intestinal tissue was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.	GEO Accession:GSM4029394	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP218210		MPs5vm_1.fq.gz MPs5vm_2.fq.gz	fastq fastq	98563904100.0	328546347.0	GSM4029394 r1	0:150 1:150	A:26023907285;C:17974044830;G:25736568268;T:28827634883;N:1748834	150	150			26023907285	17974044830	25736568268	28827634883	1748834	SRX6707775	SRS5261676	SRA938912	GEO	Nanjing University	2	0.0	0.86592	0.0	0.09908	1.0	0.81552		0.55476	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2019-08-13	Adult	Adult	Gut	Digestive System
53596	53596	SRR9960229	SRX6707774	SRS5261675	SRP218210	PRJNA560029	Single Cell RNA Sequencing Analysis of Polystyrene Microplastic Exposed and control Zebrafish Intestine	GSE135767	Transcriptome Analysis	Microplastics MPs as widespread contamination pose high risk for aquatic organisms. However current understanding of MP toxicities are based on cell population averaged measurements. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 12000 intestinal cells obtained from zebrafishes exposed to 100nm 5µm and 200µm polystyrene MPs PS MPs for xxx days. Eight intestinal cell populations were identified. We found that all the three sizes of PS MPs induced dysfunction of intestinal immune cells including phagosome and regulation of immune system process. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure MPs with different size 100 nm 5 µm and 200 µm.	parent bioproject:PRJNA561326	pubmed:32092251		MPs100nm	GSM4029393	source name:intestinal cells\|tissue:Intestinal single cell suspension\|age:16 wpf\|exposed pollutants:100nm PS MPs	MPs100nm	We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip…	intestinal cells	Exposure solutions were prepared by adding 100 nm 5 μm or 200 μm PS MPs to culture water with a final concentration of 500μg/L. The exposure solution were was replaced every 2 days. Exposure solution in all tanks were was continuously aerated to maintain the dispersion of particles no filtering systems were used in the tanks. post 21 d exposure zebrafish were collected and intestine were rapidly extracted on ice.	The isolated intestinal tissue was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.		tissue:Intestinal single cell suspension\|age:16 wpf\|exposed pollutants:100nm PS MPs	GSM4029393	GSM4029393: MPs100nm; Danio rerio; RNA Seq	GSM4029393		1	The isolated intestinal tissue was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.	GEO Accession:GSM4029393	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP218210		MPs100nm_1.fq.gz MPs100nm_2.fq.gz	fastq fastq	122539718400.0	408465728.0	GSM4029393 r1	0:150 1:150	A:32283417066;C:22576112318;G:30470461014;T:37207888685;N:1839317	150	150			32283417066	22576112318	30470461014	37207888685	1839317	SRX6707774	SRS5261675	SRA938912	GEO	Nanjing University	2	0.0	0.88187	0.0	0.09087	1.0	0.82428		0.53597	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2019-08-13	Adult	Adult	Gut	Digestive System
53597	53597	SRR9960228	SRX6707773	SRS5261674	SRP218210	PRJNA560029	Single Cell RNA Sequencing Analysis of Polystyrene Microplastic Exposed and control Zebrafish Intestine	GSE135767	Transcriptome Analysis	Microplastics MPs as widespread contamination pose high risk for aquatic organisms. However current understanding of MP toxicities are based on cell population averaged measurements. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 12000 intestinal cells obtained from zebrafishes exposed to 100nm 5µm and 200µm polystyrene MPs PS MPs for xxx days. Eight intestinal cell populations were identified. We found that all the three sizes of PS MPs induced dysfunction of intestinal immune cells including phagosome and regulation of immune system process. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure MPs with different size 100 nm 5 µm and 200 µm.	parent bioproject:PRJNA561326	pubmed:32092251		CK	GSM4029392	source name:intestinal cells\|tissue:Intestinal single cell suspension\|age:16 wpf\|exposed pollutants:n1	CK	We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip…	intestinal cells	Exposure solutions were prepared by adding 100 nm 5 μm or 200 μm PS MPs to culture water with a final concentration of 500μg/L. The exposure solution were was replaced every 2 days. Exposure solution in all tanks were was continuously aerated to maintain the dispersion of particles no filtering systems were used in the tanks. post 21 d exposure zebrafish were collected and intestine were rapidly extracted on ice.	The isolated intestinal tissue was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.		tissue:Intestinal single cell suspension\|age:16 wpf\|exposed pollutants:n1	GSM4029392	GSM4029392: CK; Danio rerio; RNA Seq	GSM4029392		1	The isolated intestinal tissue was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.	GEO Accession:GSM4029392	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP218210		CK_1.fq.gz CK_2.fq.gz	fastq fastq	111761141100.0	372537137.0	GSM4029392 r1	0:150 1:150	A:29264568248;C:21295511514;G:29897320083;T:31301732224;N:2009031	150	150			29264568248	21295511514	29897320083	31301732224	2009031	SRX6707773	SRS5261674	SRA938912	GEO	Nanjing University	2	0.0	0.88395	0.0	0.08593	1.0	0.80466		0.46326	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2019-08-13	Adult	Adult	Gut	Digestive System
56883	56883	SRR11178131	SRX7798810	SRS6213687	SRP250666	PRJNA608660	Expression analysis of adult zebrafish enteric nervous system	GSE145885	Transcriptome Analysis	The enteric nervous system ENS encompasses the intrinsic neuroglia networks of the gastrointestinal GI tract that are essential for digestive function and gut homeostasis. To investigate the ENS of zebrafish we carried out bulk RNA sequencing on nuclei purified by FACS fluorescent activated cell sorting representing both the Cherry+ ENS and Cherry non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut. Overall design: The smooth muscle layers and associated myenteric plexus were separated from the epithelial layers of the adult gut and subjected to Dounce homogenization. post filtering the homogenate to remove large debris samples were centrifuged at 1000 x G for 10 min at 4°C to obtain a pellet containing muscularis externa nuclei. For flow cytometric analysis doublet discrimination gating was applied to exclude aggregated nuclei and intact nuclei were determined by subsequent gating on the area and height of DAPI intensity. Both Cherry+ ENS and Cherry non ENS nuclear populations were collected directly into 1.5mL tubes containing Trizol LS reagent. For each replicate sorted cells from an average of 30 adult guts were pooled containing approximately 30 000 Cherry+ or Cherry nuclear populations.		pubmed:32851974		Adult gut sox10:cre;Cherry negative 5	GSM4338415	source name:Adult gut sox10:cre;Cherry negative\|tissue:adult gut\|cell type:non ENS\|rna fraction:Nuclear mRNA	Adult gut sox10:cre;Cherry negative 5	The RSEM package version 1.3.0 in conjunction with the STAR alignment algorithm version 2.5.2 was used for the mapping and subsequent gene level counting of the sequenced reads with respect to Ensembl GRCm38 release 89 transcriptome Differential expression analysis was performed with the DESeq2 package version 1.10.1 within the R programming environment version 3.3.2 Genome build: GRCm38 Supplementary files format and content: Tab delimited text file containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.	Adult gut sox10:cre;Cherry negative	Nuclei were purified by FACS fluorescent activated cell sorting representing both the Cherry+ entire ENS and Cherry non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut	Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer’s instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific Inc. and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris Inc. at standard settings. The fragmented cDNA was then normalized to 100ng which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies Inc.. The libraries were then normalized to 4 nM pooled and loaded onto a HiSeq4000 Illumina Inc. to generate 100 bp paired end reads.	N/A	tissue:adult gut\|cell type:non ENS\|rna fraction:Nuclear mRNA	GSM4338415	GSM4338415: Adult gut sox10:cre;Cherry negative 5; Danio rerio; RNA Seq	GSM4338415		1	Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer's instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific Inc. and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris Inc. at standard settings. The fragmented cDNA was then normalized to 100ng which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies Inc.. The libraries were then normalized to 4 nM pooled and loaded onto a HiSeq4000 Illumina Inc. to generate 100 bp paired end reads.	GEO Accession:GSM4338415	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP250666		PE_neg_5_R1.fastq.gz PE_neg_5_R2.fastq.gz	fastq fastq	7402006796.0	36643598.0	GSM4338415 r1	0:101 1:101	A:2141100609;C:1495392069;G:1539459100;T:2225819644;N:235374	101	101			2141100609	1495392069	1539459100	2225819644	235374	SRX7798810	SRS6213687	SRA1047946	GEO	Pachnis, Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute	2	0.79957	0.80443	0.53128	0.53529	0.74728	0.75968	0.53126	0.55373	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	unknown	bulk	bulk	bulk	United Kingdom	2020-02-25	Adult	Adult	Gut	Digestive System
56884	56884	SRR11178130	SRX7798809	SRS6213686	SRP250666	PRJNA608660	Expression analysis of adult zebrafish enteric nervous system	GSE145885	Transcriptome Analysis	The enteric nervous system ENS encompasses the intrinsic neuroglia networks of the gastrointestinal GI tract that are essential for digestive function and gut homeostasis. To investigate the ENS of zebrafish we carried out bulk RNA sequencing on nuclei purified by FACS fluorescent activated cell sorting representing both the Cherry+ ENS and Cherry non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut. Overall design: The smooth muscle layers and associated myenteric plexus were separated from the epithelial layers of the adult gut and subjected to Dounce homogenization. post filtering the homogenate to remove large debris samples were centrifuged at 1000 x G for 10 min at 4°C to obtain a pellet containing muscularis externa nuclei. For flow cytometric analysis doublet discrimination gating was applied to exclude aggregated nuclei and intact nuclei were determined by subsequent gating on the area and height of DAPI intensity. Both Cherry+ ENS and Cherry non ENS nuclear populations were collected directly into 1.5mL tubes containing Trizol LS reagent. For each replicate sorted cells from an average of 30 adult guts were pooled containing approximately 30 000 Cherry+ or Cherry nuclear populations.		pubmed:32851974		Adult gut sox10:cre;Cherry negative 4	GSM4338414	source name:Adult gut sox10:cre;Cherry negative\|tissue:adult gut\|cell type:non ENS\|rna fraction:Nuclear mRNA	Adult gut sox10:cre;Cherry negative 4	The RSEM package version 1.3.0 in conjunction with the STAR alignment algorithm version 2.5.2 was used for the mapping and subsequent gene level counting of the sequenced reads with respect to Ensembl GRCm38 release 89 transcriptome Differential expression analysis was performed with the DESeq2 package version 1.10.1 within the R programming environment version 3.3.2 Genome build: GRCm38 Supplementary files format and content: Tab delimited text file containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.	Adult gut sox10:cre;Cherry negative	Nuclei were purified by FACS fluorescent activated cell sorting representing both the Cherry+ entire ENS and Cherry non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut	Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer’s instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific Inc. and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris Inc. at standard settings. The fragmented cDNA was then normalized to 100ng which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies Inc.. The libraries were then normalized to 4 nM pooled and loaded onto a HiSeq4000 Illumina Inc. to generate 100 bp paired end reads.	N/A	tissue:adult gut\|cell type:non ENS\|rna fraction:Nuclear mRNA	GSM4338414	GSM4338414: Adult gut sox10:cre;Cherry negative 4; Danio rerio; RNA Seq	GSM4338414		1	Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer's instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific Inc. and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris Inc. at standard settings. The fragmented cDNA was then normalized to 100ng which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies Inc.. The libraries were then normalized to 4 nM pooled and loaded onto a HiSeq4000 Illumina Inc. to generate 100 bp paired end reads.	GEO Accession:GSM4338414	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP250666		PE_neg_4_R1.fastq.gz PE_neg_4_R2.fastq.gz	fastq fastq	6742235406.0	33377403.0	GSM4338414 r1	0:101 1:101	A:1943591079;C:1353703348;G:1421710867;T:2023006494;N:223618	101	101			1943591079	1353703348	1421710867	2023006494	223618	SRX7798809	SRS6213686	SRA1047946	GEO	Pachnis, Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute	2	0.77924	0.7849	0.57144	0.57418	0.74612	0.76177	0.55304	0.49173	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	unknown	bulk	bulk	bulk	United Kingdom	2020-02-25	Adult	Adult	Gut	Digestive System
56885	56885	SRR11178129	SRX7798808	SRS6213685	SRP250666	PRJNA608660	Expression analysis of adult zebrafish enteric nervous system	GSE145885	Transcriptome Analysis	The enteric nervous system ENS encompasses the intrinsic neuroglia networks of the gastrointestinal GI tract that are essential for digestive function and gut homeostasis. To investigate the ENS of zebrafish we carried out bulk RNA sequencing on nuclei purified by FACS fluorescent activated cell sorting representing both the Cherry+ ENS and Cherry non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut. Overall design: The smooth muscle layers and associated myenteric plexus were separated from the epithelial layers of the adult gut and subjected to Dounce homogenization. post filtering the homogenate to remove large debris samples were centrifuged at 1000 x G for 10 min at 4°C to obtain a pellet containing muscularis externa nuclei. For flow cytometric analysis doublet discrimination gating was applied to exclude aggregated nuclei and intact nuclei were determined by subsequent gating on the area and height of DAPI intensity. Both Cherry+ ENS and Cherry non ENS nuclear populations were collected directly into 1.5mL tubes containing Trizol LS reagent. For each replicate sorted cells from an average of 30 adult guts were pooled containing approximately 30 000 Cherry+ or Cherry nuclear populations.		pubmed:32851974		Adult gut sox10:cre;Cherry negative 3	GSM4338413	source name:Adult gut sox10:cre;Cherry negative\|tissue:adult gut\|cell type:non ENS\|rna fraction:Nuclear mRNA	Adult gut sox10:cre;Cherry negative 3	The RSEM package version 1.3.0 in conjunction with the STAR alignment algorithm version 2.5.2 was used for the mapping and subsequent gene level counting of the sequenced reads with respect to Ensembl GRCm38 release 89 transcriptome Differential expression analysis was performed with the DESeq2 package version 1.10.1 within the R programming environment version 3.3.2 Genome build: GRCm38 Supplementary files format and content: Tab delimited text file containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.	Adult gut sox10:cre;Cherry negative	Nuclei were purified by FACS fluorescent activated cell sorting representing both the Cherry+ entire ENS and Cherry non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut	Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer’s instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific Inc. and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris Inc. at standard settings. The fragmented cDNA was then normalized to 100ng which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies Inc.. The libraries were then normalized to 4 nM pooled and loaded onto a HiSeq4000 Illumina Inc. to generate 100 bp paired end reads.	N/A	tissue:adult gut\|cell type:non ENS\|rna fraction:Nuclear mRNA	GSM4338413	GSM4338413: Adult gut sox10:cre;Cherry negative 3; Danio rerio; RNA Seq	GSM4338413		1	Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer's instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific Inc. and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris Inc. at standard settings. The fragmented cDNA was then normalized to 100ng which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies Inc.. The libraries were then normalized to 4 nM pooled and loaded onto a HiSeq4000 Illumina Inc. to generate 100 bp paired end reads.	GEO Accession:GSM4338413	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP250666		PE_neg_3_R2.fastq.gz PE_neg_3_R1.fastq.gz	fastq fastq	6277972140.0	31079070.0	GSM4338413 r1	0:101 1:101	A:1793266465;C:1274475049;G:1339662110;T:1870363568;N:204948	101	101			1793266465	1274475049	1339662110	1870363568	204948	SRX7798808	SRS6213685	SRA1047946	GEO	Pachnis, Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute	2	0.77642	0.78334	0.54202	0.54381	0.75564	0.76467	0.55282	0.55504	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	unknown	bulk	bulk	bulk	United Kingdom	2020-02-25	Adult	Adult	Gut	Digestive System
56886	56886	SRR11178128	SRX7798807	SRS6213684	SRP250666	PRJNA608660	Expression analysis of adult zebrafish enteric nervous system	GSE145885	Transcriptome Analysis	The enteric nervous system ENS encompasses the intrinsic neuroglia networks of the gastrointestinal GI tract that are essential for digestive function and gut homeostasis. To investigate the ENS of zebrafish we carried out bulk RNA sequencing on nuclei purified by FACS fluorescent activated cell sorting representing both the Cherry+ ENS and Cherry non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut. Overall design: The smooth muscle layers and associated myenteric plexus were separated from the epithelial layers of the adult gut and subjected to Dounce homogenization. post filtering the homogenate to remove large debris samples were centrifuged at 1000 x G for 10 min at 4°C to obtain a pellet containing muscularis externa nuclei. For flow cytometric analysis doublet discrimination gating was applied to exclude aggregated nuclei and intact nuclei were determined by subsequent gating on the area and height of DAPI intensity. Both Cherry+ ENS and Cherry non ENS nuclear populations were collected directly into 1.5mL tubes containing Trizol LS reagent. For each replicate sorted cells from an average of 30 adult guts were pooled containing approximately 30 000 Cherry+ or Cherry nuclear populations.		pubmed:32851974		Adult gut sox10:cre;Cherry negative 2	GSM4338412	source name:Adult gut sox10:cre;Cherry negative\|tissue:adult gut\|cell type:non ENS\|rna fraction:Nuclear mRNA	Adult gut sox10:cre;Cherry negative 2	The RSEM package version 1.3.0 in conjunction with the STAR alignment algorithm version 2.5.2 was used for the mapping and subsequent gene level counting of the sequenced reads with respect to Ensembl GRCm38 release 89 transcriptome Differential expression analysis was performed with the DESeq2 package version 1.10.1 within the R programming environment version 3.3.2 Genome build: GRCm38 Supplementary files format and content: Tab delimited text file containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.	Adult gut sox10:cre;Cherry negative	Nuclei were purified by FACS fluorescent activated cell sorting representing both the Cherry+ entire ENS and Cherry non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut	Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer’s instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific Inc. and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris Inc. at standard settings. The fragmented cDNA was then normalized to 100ng which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies Inc.. The libraries were then normalized to 4 nM pooled and loaded onto a HiSeq4000 Illumina Inc. to generate 100 bp paired end reads.	N/A	tissue:adult gut\|cell type:non ENS\|rna fraction:Nuclear mRNA	GSM4338412	GSM4338412: Adult gut sox10:cre;Cherry negative 2; Danio rerio; RNA Seq	GSM4338412		1	Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer's instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific Inc. and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris Inc. at standard settings. The fragmented cDNA was then normalized to 100ng which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies Inc.. The libraries were then normalized to 4 nM pooled and loaded onto a HiSeq4000 Illumina Inc. to generate 100 bp paired end reads.	GEO Accession:GSM4338412	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP250666		PE_neg_2_R1.fastq.gz PE_neg_2_R2.fastq.gz	fastq fastq	6124177824.0	30317712.0	GSM4338412 r1	0:101 1:101	A:1748043042;C:1241789616;G:1297992638;T:1836153062;N:199466	101	101			1748043042	1241789616	1297992638	1836153062	199466	SRX7798807	SRS6213684	SRA1047946	GEO	Pachnis, Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute	2	0.80191	0.80757	0.51449	0.51588	0.76504	0.77477	0.54934	0.55455	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	unknown	bulk	bulk	bulk	United Kingdom	2020-02-25	Adult	Adult	Gut	Digestive System
56887	56887	SRR11178127	SRX7798806	SRS6213683	SRP250666	PRJNA608660	Expression analysis of adult zebrafish enteric nervous system	GSE145885	Transcriptome Analysis	The enteric nervous system ENS encompasses the intrinsic neuroglia networks of the gastrointestinal GI tract that are essential for digestive function and gut homeostasis. To investigate the ENS of zebrafish we carried out bulk RNA sequencing on nuclei purified by FACS fluorescent activated cell sorting representing both the Cherry+ ENS and Cherry non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut. Overall design: The smooth muscle layers and associated myenteric plexus were separated from the epithelial layers of the adult gut and subjected to Dounce homogenization. post filtering the homogenate to remove large debris samples were centrifuged at 1000 x G for 10 min at 4°C to obtain a pellet containing muscularis externa nuclei. For flow cytometric analysis doublet discrimination gating was applied to exclude aggregated nuclei and intact nuclei were determined by subsequent gating on the area and height of DAPI intensity. Both Cherry+ ENS and Cherry non ENS nuclear populations were collected directly into 1.5mL tubes containing Trizol LS reagent. For each replicate sorted cells from an average of 30 adult guts were pooled containing approximately 30 000 Cherry+ or Cherry nuclear populations.		pubmed:32851974		Adult gut sox10:cre;Cherry negative 1	GSM4338411	source name:Adult gut sox10:cre;Cherry negative\|tissue:adult gut\|cell type:non ENS\|rna fraction:Nuclear mRNA	Adult gut sox10:cre;Cherry negative 1	The RSEM package version 1.3.0 in conjunction with the STAR alignment algorithm version 2.5.2 was used for the mapping and subsequent gene level counting of the sequenced reads with respect to Ensembl GRCm38 release 89 transcriptome Differential expression analysis was performed with the DESeq2 package version 1.10.1 within the R programming environment version 3.3.2 Genome build: GRCm38 Supplementary files format and content: Tab delimited text file containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.	Adult gut sox10:cre;Cherry negative	Nuclei were purified by FACS fluorescent activated cell sorting representing both the Cherry+ entire ENS and Cherry non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut	Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer’s instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific Inc. and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris Inc. at standard settings. The fragmented cDNA was then normalized to 100ng which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies Inc.. The libraries were then normalized to 4 nM pooled and loaded onto a HiSeq4000 Illumina Inc. to generate 100 bp paired end reads.	N/A	tissue:adult gut\|cell type:non ENS\|rna fraction:Nuclear mRNA	GSM4338411	GSM4338411: Adult gut sox10:cre;Cherry negative 1; Danio rerio; RNA Seq	GSM4338411		1	Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer's instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific Inc. and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris Inc. at standard settings. The fragmented cDNA was then normalized to 100ng which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies Inc.. The libraries were then normalized to 4 nM pooled and loaded onto a HiSeq4000 Illumina Inc. to generate 100 bp paired end reads.	GEO Accession:GSM4338411	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP250666		PE_neg_1_R1.fastq.gz PE_neg_1_R2.fastq.gz	fastq fastq	6589632890.0	32621945.0	GSM4338411 r1	0:101 1:101	A:1823414720;C:1397729205;G:1451531094;T:1916757475;N:200396	101	101			1823414720	1397729205	1451531094	1916757475	200396	SRX7798806	SRS6213683	SRA1047946	GEO	Pachnis, Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute	2	0.76935	0.77393	0.42629	0.4289	0.75215	0.7623	0.60804	0.60753	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	unknown	bulk	bulk	bulk	United Kingdom	2020-02-25	Adult	Adult	Gut	Digestive System
56888	56888	SRR11178126	SRX7798805	SRS6213682	SRP250666	PRJNA608660	Expression analysis of adult zebrafish enteric nervous system	GSE145885	Transcriptome Analysis	The enteric nervous system ENS encompasses the intrinsic neuroglia networks of the gastrointestinal GI tract that are essential for digestive function and gut homeostasis. To investigate the ENS of zebrafish we carried out bulk RNA sequencing on nuclei purified by FACS fluorescent activated cell sorting representing both the Cherry+ ENS and Cherry non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut. Overall design: The smooth muscle layers and associated myenteric plexus were separated from the epithelial layers of the adult gut and subjected to Dounce homogenization. post filtering the homogenate to remove large debris samples were centrifuged at 1000 x G for 10 min at 4°C to obtain a pellet containing muscularis externa nuclei. For flow cytometric analysis doublet discrimination gating was applied to exclude aggregated nuclei and intact nuclei were determined by subsequent gating on the area and height of DAPI intensity. Both Cherry+ ENS and Cherry non ENS nuclear populations were collected directly into 1.5mL tubes containing Trizol LS reagent. For each replicate sorted cells from an average of 30 adult guts were pooled containing approximately 30 000 Cherry+ or Cherry nuclear populations.		pubmed:32851974		Adult gut sox10:cre;Cherry positive 5	GSM4338410	source name:Adult gut sox10:cre;Cherry positive\|tissue:adult gut\|cell type:ENS\|rna fraction:Nuclear mRNA	Adult gut sox10:cre;Cherry positive 5	The RSEM package version 1.3.0 in conjunction with the STAR alignment algorithm version 2.5.2 was used for the mapping and subsequent gene level counting of the sequenced reads with respect to Ensembl GRCm38 release 89 transcriptome Differential expression analysis was performed with the DESeq2 package version 1.10.1 within the R programming environment version 3.3.2 Genome build: GRCm38 Supplementary files format and content: Tab delimited text file containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.	Adult gut sox10:cre;Cherry positive	Nuclei were purified by FACS fluorescent activated cell sorting representing both the Cherry+ entire ENS and Cherry non ENS muscularis externa cell populations of Tgsox10:Cre;Cherry zebrafish gut	Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer’s instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific Inc. and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris Inc. at standard settings. The fragmented cDNA was then normalized to 100ng which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies Inc.. The libraries were then normalized to 4 nM pooled and loaded onto a HiSeq4000 Illumina Inc. to generate 100 bp paired end reads.	N/A	tissue:adult gut\|cell type:ENS\|rna fraction:Nuclear mRNA	GSM4338410	GSM4338410: Adult gut sox10:cre;Cherry positive 5; Danio rerio; RNA Seq	GSM4338410		1	Nuclear RNA was isolated using PureLink RNA Micro Kit Invitrogen #12183016 according to the manufacturer's instructions. Double stranded full length cDNA was generated using the Ovation RNA Seq System V2 NuGen Technologies Inc.. cDNA was quantified on a Qubit 3.0 fluorometer Thermo Fisher Scientific Inc. and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument Covaris Inc. at standard settings. The fragmented cDNA was then normalized to 100ng which was used for sequencing library preparation using the Ovation Ultralow System V2 1 96 protocol NuGen Technologies Inc.. A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay Agilent Technologies Inc.. The libraries were then normalized to 4 nM pooled and loaded onto a HiSeq4000 Illumina Inc. to generate 100 bp paired end reads.	GEO Accession:GSM4338410	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP250666		PE_SOX10_5_R2.fastq.gz PE_SOX10_5_R1.fastq.gz	fastq fastq	6227107530.0	30827265.0	GSM4338410 r1	0:101 1:101	A:1778260787;C:1263522409;G:1325803201;T:1859318656;N:202477	101	101			1778260787	1263522409	1325803201	1859318656	202477	SRX7798805	SRS6213682	SRA1047946	GEO	Pachnis, Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute	2	0.75911	0.76709	0.54861	0.55238	0.76055	0.77112	0.50252	0.50202	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	unknown	bulk	bulk	bulk	United Kingdom	2020-02-25	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");;