metadata: run_metadata: 6 rows where experiment.library_strategy = "RNA-Seq", technology = "generic-scrnaseq-only" and tissue_curation

6 rows where experiment.library_strategy = "RNA-Seq", technology = "generic-scrnaseq-only" 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.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	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.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
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

Advanced export

JSON shape: default, array, newline-delimited

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");;