metadata: run_metadata: 64 rows where devstage_curation_coarse = "Larval" and tissue

64 rows where devstage_curation_coarse = "Larval" and tissue_curation = "Kidney"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.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.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
32800	32800	SRR29453136	SRX24965357	SRS21668889	SRP514613	PRJNA1125316	RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection	GSE270136	Transcriptome Analysis	Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish line. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu4 mutation revealed differentially expressed genes compared to WT controls. Differentially expressed genes were associated with neutrophil degranulation haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. Six samples were analyzed three biological replicates in two groups fish homozygous for pycardtpu4 mutation and wild type WT control.	pubmed:39916610	kidney derived neutrophils homozygous Mm infected rep3	GSM8335407	source name:kidney\|tissue:kidney\|cell type:neutrophils\|genotype:homozygous for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB\|infection:M. marinum\|geo loc name:missing\|collection date:missing	kidney derived neutrophils homozygous Mm infected rep3	Reads were aligned to the reference genome GRz11 grcz11 gca 000002035 4 with HISAT2. Raw expression estimates raw read counts for genes grcz11 gca 000002035 4 were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.	kidney	Adult zebrafish were infected with 69 118 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.	Fish homozygous for pycardtpu4 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.	tissue:kidney\|cell type:neutrophils\|genotype:homozygous for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB\|infection:M. marinum	GSM8335407	GSM8335407: kidney derived neutrophils homozygous Mm infected rep3; Danio rerio; RNA Seq	GSM8335407 r1	GSM8335407	1	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP514613		R18_H_MM_1.fq.gz R18_H_MM_2.fq.gz	fastq fastq	6901009500.0	23003365.0	GSM8335407 r1	0:150 1:150	A:1920522839;C:1515700169;G:1537191557;T:1927497878;N:97057	150	150	1920522839	1515700169	1537191557	1927497878	97057	SRX24965357	SRS21668889	SRA1902200	University of Tampere	University of Tampere												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Finland	2024-06-18	Larval	Larval	Kidney	Renal System
32801	32801	SRR29453137	SRX24965356	SRS21668888	SRP514613	PRJNA1125316	RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection	GSE270136	Transcriptome Analysis	Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish line. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu4 mutation revealed differentially expressed genes compared to WT controls. Differentially expressed genes were associated with neutrophil degranulation haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. Six samples were analyzed three biological replicates in two groups fish homozygous for pycardtpu4 mutation and wild type WT control.	pubmed:39916610	kidney derived neutrophils homozygous Mm infected rep2	GSM8335406	source name:kidney\|tissue:kidney\|cell type:neutrophils\|genotype:homozygous for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB\|infection:M. marinum\|geo loc name:missing\|collection date:missing	kidney derived neutrophils homozygous Mm infected rep2	Reads were aligned to the reference genome GRz11 grcz11 gca 000002035 4 with HISAT2. Raw expression estimates raw read counts for genes grcz11 gca 000002035 4 were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.	kidney	Adult zebrafish were infected with 69 118 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.	Fish homozygous for pycardtpu4 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.	tissue:kidney\|cell type:neutrophils\|genotype:homozygous for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB\|infection:M. marinum	GSM8335406	GSM8335406: kidney derived neutrophils homozygous Mm infected rep2; Danio rerio; RNA Seq	GSM8335406 r1	GSM8335406	1	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP514613		R10_H_MM_1.fq.gz R10_H_MM_2.fq.gz	fastq fastq	6877413600.0	22924712.0	GSM8335406 r1	0:150 1:150	A:1901340557;C:1516911325;G:1537883236;T:1921186807;N:91675	150	150	1901340557	1516911325	1537883236	1921186807	91675	SRX24965356	SRS21668888	SRA1902200	University of Tampere	University of Tampere												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Finland	2024-06-18	Larval	Larval	Kidney	Renal System
32802	32802	SRR29453138	SRX24965355	SRS21668887	SRP514613	PRJNA1125316	RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection	GSE270136	Transcriptome Analysis	Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish line. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu4 mutation revealed differentially expressed genes compared to WT controls. Differentially expressed genes were associated with neutrophil degranulation haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. Six samples were analyzed three biological replicates in two groups fish homozygous for pycardtpu4 mutation and wild type WT control.	pubmed:39916610	kidney derived neutrophils homozygous Mm infected rep1	GSM8335405	source name:kidney\|tissue:kidney\|cell type:neutrophils\|genotype:homozygous for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB\|infection:M. marinum\|geo loc name:missing\|collection date:missing	kidney derived neutrophils homozygous Mm infected rep1	Reads were aligned to the reference genome GRz11 grcz11 gca 000002035 4 with HISAT2. Raw expression estimates raw read counts for genes grcz11 gca 000002035 4 were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.	kidney	Adult zebrafish were infected with 69 118 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.	Fish homozygous for pycardtpu4 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.	tissue:kidney\|cell type:neutrophils\|genotype:homozygous for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB\|infection:M. marinum	GSM8335405	GSM8335405: kidney derived neutrophils homozygous Mm infected rep1; Danio rerio; RNA Seq	GSM8335405 r1	GSM8335405	1	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP514613		R8_2_H_MM_1.fq.gz R8_2_H_MM_2.fq.gz	fastq fastq	6921242700.0	23070809.0	GSM8335405 r1	0:150 1:150	A:1923648919;C:1520702661;G:1540739284;T:1936060582;N:91254	150	150	1923648919	1520702661	1540739284	1936060582	91254	SRX24965355	SRS21668887	SRA1902200	University of Tampere	University of Tampere												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Finland	2024-06-18	Larval	Larval	Kidney	Renal System
32803	32803	SRR29453139	SRX24965354	SRS21668886	SRP514613	PRJNA1125316	RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection	GSE270136	Transcriptome Analysis	Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish line. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu4 mutation revealed differentially expressed genes compared to WT controls. Differentially expressed genes were associated with neutrophil degranulation haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. Six samples were analyzed three biological replicates in two groups fish homozygous for pycardtpu4 mutation and wild type WT control.	pubmed:39916610	kidney derived neutrophils wt Mm infected rep3	GSM8335404	source name:kidney\|tissue:kidney\|cell type:neutrophils\|genotype:wild type for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB\|infection:M. marinum\|geo loc name:missing\|collection date:missing	kidney derived neutrophils wt Mm infected rep3	Reads were aligned to the reference genome GRz11 grcz11 gca 000002035 4 with HISAT2. Raw expression estimates raw read counts for genes grcz11 gca 000002035 4 were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.	kidney	Adult zebrafish were infected with 69 118 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.	Fish homozygous for pycardtpu4 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.	tissue:kidney\|cell type:neutrophils\|genotype:wild type for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB\|infection:M. marinum	GSM8335404	GSM8335404: kidney derived neutrophils wt Mm infected rep3; Danio rerio; RNA Seq	GSM8335404 r1	GSM8335404	1	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP514613		R16_WT_MM_1.fq.gz R16_WT_MM_2.fq.gz	fastq fastq	6755682900.0	22518943.0	GSM8335404 r1	0:150 1:150	A:1866248606;C:1494647864;G:1513464764;T:1881229301;N:92365	150	150	1866248606	1494647864	1513464764	1881229301	92365	SRX24965354	SRS21668886	SRA1902200	University of Tampere	University of Tampere												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Finland	2024-06-18	Larval	Larval	Kidney	Renal System
32804	32804	SRR29453140	SRX24965353	SRS21668885	SRP514613	PRJNA1125316	RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection	GSE270136	Transcriptome Analysis	Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish line. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu4 mutation revealed differentially expressed genes compared to WT controls. Differentially expressed genes were associated with neutrophil degranulation haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. Six samples were analyzed three biological replicates in two groups fish homozygous for pycardtpu4 mutation and wild type WT control.	pubmed:39916610	kidney derived neutrophils wt Mm infected rep2	GSM8335403	source name:kidney\|tissue:kidney\|cell type:neutrophils\|genotype:wild type for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB\|infection:M. marinum\|geo loc name:missing\|collection date:missing	kidney derived neutrophils wt Mm infected rep2	Reads were aligned to the reference genome GRz11 grcz11 gca 000002035 4 with HISAT2. Raw expression estimates raw read counts for genes grcz11 gca 000002035 4 were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.	kidney	Adult zebrafish were infected with 69 118 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.	Fish homozygous for pycardtpu4 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.	tissue:kidney\|cell type:neutrophils\|genotype:wild type for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB\|infection:M. marinum	GSM8335403	GSM8335403: kidney derived neutrophils wt Mm infected rep2; Danio rerio; RNA Seq	GSM8335403 r1	GSM8335403	1	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP514613		R7_WT_MM_1.fq.gz R7_WT_MM_2.fq.gz	fastq fastq	6801886200.0	22672954.0	GSM8335403 r1	0:150 1:150	A:1897407228;C:1488944523;G:1508394915;T:1907051254;N:88280	150	150	1897407228	1488944523	1508394915	1907051254	88280	SRX24965353	SRS21668885	SRA1902200	University of Tampere	University of Tampere												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Finland	2024-06-18	Larval	Larval	Kidney	Renal System
32805	32805	SRR29453141	SRX24965352	SRS21668884	SRP514613	PRJNA1125316	RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection	GSE270136	Transcriptome Analysis	Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish line. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu4 mutation revealed differentially expressed genes compared to WT controls. Differentially expressed genes were associated with neutrophil degranulation haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. Six samples were analyzed three biological replicates in two groups fish homozygous for pycardtpu4 mutation and wild type WT control.	pubmed:39916610	kidney derived neutrophils wt Mm infected rep1	GSM8335402	source name:kidney\|tissue:kidney\|cell type:neutrophils\|genotype:wild type for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB\|infection:M. marinum\|geo loc name:missing\|collection date:missing	kidney derived neutrophils wt Mm infected rep1	Reads were aligned to the reference genome GRz11 grcz11 gca 000002035 4 with HISAT2. Raw expression estimates raw read counts for genes grcz11 gca 000002035 4 were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.	kidney	Adult zebrafish were infected with 69 118 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.	Fish homozygous for pycardtpu4 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.	tissue:kidney\|cell type:neutrophils\|genotype:wild type for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB\|infection:M. marinum	GSM8335402	GSM8335402: kidney derived neutrophils wt Mm infected rep1; Danio rerio; RNA Seq	GSM8335402 r1	GSM8335402	1	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP514613		R5_WT_MM_1.fq.gz R5_WT_MM_2.fq.gz	fastq fastq	6760544400.0	22535148.0	GSM8335402 r1	0:150 1:150	A:1863279045;C:1498858984;G:1519081612;T:1879233731;N:91028	150	150	1863279045	1498858984	1519081612	1879233731	91028	SRX24965352	SRS21668884	SRA1902200	University of Tampere	University of Tampere												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Finland	2024-06-18	Larval	Larval	Kidney	Renal System
34535	34535	SRR32064717	SRX27413530	SRS23843189	SRP558767	PRJNA1213790	RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection	GSE287594	Transcriptome Analysis	Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed six biological replicates in two groups fish homozygous for pycardtpu5 mutation and wild type WT control.	pubmed:39916610	kidney derived neutrophils homozygous Mm infected rep6	GSM8748663	source name:kidney\|tissue:kidney\|cell type:neutrophils\|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected\|geo loc name:missing\|collection date:missing	kidney derived neutrophils homozygous Mm infected rep6	Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.	kidney	Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.	Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.	tissue:kidney\|cell type:neutrophils\|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected	GSM8748663	GSM8748663: kidney derived neutrophils homozygous Mm infected rep6; Danio rerio; RNA Seq	GSM8748663 r1	GSM8748663	1	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP558767		RNA35_H_MM_R_1.fq.gz RNA35_H_MM_R_2.fq.gz	fastq fastq	6950452200.0	23168174.0	GSM8748663 r1	0:150 1:150	A:1920598119;C:1565819640;G:1566891465;T:1896911503;N:231473	150	150	1920598119	1565819640	1566891465	1896911503	231473	SRX27413530	SRS23843189	SRA2056436	University of Tampere	University of Tampere												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Finland	2025-01-21	Larval	Larval	Kidney	Renal System
34536	34536	SRR32064718	SRX27413529	SRS23843188	SRP558767	PRJNA1213790	RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection	GSE287594	Transcriptome Analysis	Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed six biological replicates in two groups fish homozygous for pycardtpu5 mutation and wild type WT control.	pubmed:39916610	kidney derived neutrophils homozygous Mm infected rep5	GSM8748662	source name:kidney\|tissue:kidney\|cell type:neutrophils\|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected\|geo loc name:missing\|collection date:missing	kidney derived neutrophils homozygous Mm infected rep5	Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.	kidney	Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.	Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.	tissue:kidney\|cell type:neutrophils\|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected	GSM8748662	GSM8748662: kidney derived neutrophils homozygous Mm infected rep5; Danio rerio; RNA Seq	GSM8748662 r1	GSM8748662	1	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP558767		RNA31_H_MM_R_1.fq.gz RNA31_H_MM_R_2.fq.gz	fastq fastq	6663708000.0	22212360.0	GSM8748662 r1	0:150 1:150	A:1831236930;C:1510631608;G:1510442962;T:1810728281;N:668219	150	150	1831236930	1510631608	1510442962	1810728281	668219	SRX27413529	SRS23843188	SRA2056436	University of Tampere	University of Tampere												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Finland	2025-01-21	Larval	Larval	Kidney	Renal System
34537	34537	SRR32064719	SRX27413528	SRS23843187	SRP558767	PRJNA1213790	RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection	GSE287594	Transcriptome Analysis	Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed six biological replicates in two groups fish homozygous for pycardtpu5 mutation and wild type WT control.	pubmed:39916610	kidney derived neutrophils homozygous Mm infected rep4	GSM8748661	source name:kidney\|tissue:kidney\|cell type:neutrophils\|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected\|geo loc name:missing\|collection date:missing	kidney derived neutrophils homozygous Mm infected rep4	Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.	kidney	Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.	Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.	tissue:kidney\|cell type:neutrophils\|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected	GSM8748661	GSM8748661: kidney derived neutrophils homozygous Mm infected rep4; Danio rerio; RNA Seq	GSM8748661 r1	GSM8748661	1	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP558767		RNA17_H_MM_R_1.fq.gz RNA17_H_MM_R_2.fq.gz	fastq fastq	6328866900.0	21096223.0	GSM8748661 r1	0:150 1:150	A:1736278764;C:1437925823;G:1439447440;T:1714587759;N:627114	150	150	1736278764	1437925823	1439447440	1714587759	627114	SRX27413528	SRS23843187	SRA2056436	University of Tampere	University of Tampere												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Finland	2025-01-21	Larval	Larval	Kidney	Renal System
34538	34538	SRR32064720	SRX27413527	SRS23843186	SRP558767	PRJNA1213790	RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection	GSE287594	Transcriptome Analysis	Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed six biological replicates in two groups fish homozygous for pycardtpu5 mutation and wild type WT control.	pubmed:39916610	kidney derived neutrophils homozygous Mm infected rep3	GSM8748660	source name:kidney\|tissue:kidney\|cell type:neutrophils\|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected\|geo loc name:missing\|collection date:missing	kidney derived neutrophils homozygous Mm infected rep3	Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.	kidney	Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.	Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.	tissue:kidney\|cell type:neutrophils\|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected	GSM8748660	GSM8748660: kidney derived neutrophils homozygous Mm infected rep3; Danio rerio; RNA Seq	GSM8748660 r1	GSM8748660	1	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP558767		RNA16_H_MM_R_1.fq.gz RNA16_H_MM_R_2.fq.gz	fastq fastq	5994609000.0	19982030.0	GSM8748660 r1	0:150 1:150	A:1647964217;C:1357673528;G:1357262640;T:1631490903;N:217712	150	150	1647964217	1357673528	1357262640	1631490903	217712	SRX27413527	SRS23843186	SRA2056436	University of Tampere	University of Tampere												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Finland	2025-01-21	Larval	Larval	Kidney	Renal System
34539	34539	SRR32064721	SRX27413526	SRS23843185	SRP558767	PRJNA1213790	RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection	GSE287594	Transcriptome Analysis	Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed six biological replicates in two groups fish homozygous for pycardtpu5 mutation and wild type WT control.	pubmed:39916610	kidney derived neutrophils homozygous Mm infected rep2	GSM8748659	source name:kidney\|tissue:kidney\|cell type:neutrophils\|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected\|geo loc name:missing\|collection date:missing	kidney derived neutrophils homozygous Mm infected rep2	Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.	kidney	Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.	Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.	tissue:kidney\|cell type:neutrophils\|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected	GSM8748659	GSM8748659: kidney derived neutrophils homozygous Mm infected rep2; Danio rerio; RNA Seq	GSM8748659 r1	GSM8748659	1	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP558767		RNA15_H_MM_R_1.fq.gz RNA15_H_MM_R_2.fq.gz	fastq fastq	5973435300.0	19911451.0	GSM8748659 r1	0:150 1:150	A:1650140619;C:1346802182;G:1348552488;T:1627259927;N:680084	150	150	1650140619	1346802182	1348552488	1627259927	680084	SRX27413526	SRS23843185	SRA2056436	University of Tampere	University of Tampere												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Finland	2025-01-21	Larval	Larval	Kidney	Renal System
34540	34540	SRR32064722	SRX27413525	SRS23843184	SRP558767	PRJNA1213790	RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection	GSE287594	Transcriptome Analysis	Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed six biological replicates in two groups fish homozygous for pycardtpu5 mutation and wild type WT control.	pubmed:39916610	kidney derived neutrophils homozygous Mm infected rep1	GSM8748658	source name:kidney\|tissue:kidney\|cell type:neutrophils\|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected\|geo loc name:missing\|collection date:missing	kidney derived neutrophils homozygous Mm infected rep1	Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.	kidney	Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.	Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.	tissue:kidney\|cell type:neutrophils\|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected	GSM8748658	GSM8748658: kidney derived neutrophils homozygous Mm infected rep1; Danio rerio; RNA Seq	GSM8748658 r1	GSM8748658	1	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP558767		RNA14_H_MM_R_1.fq.gz RNA14_H_MM_R_2.fq.gz	fastq fastq	6516002400.0	21720008.0	GSM8748658 r1	0:150 1:150	A:1798422932;C:1471942244;G:1470322290;T:1774672386;N:642548	150	150	1798422932	1471942244	1470322290	1774672386	642548	SRX27413525	SRS23843184	SRA2056436	University of Tampere	University of Tampere												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Finland	2025-01-21	Larval	Larval	Kidney	Renal System
34541	34541	SRR32064723	SRX27413524	SRS23843183	SRP558767	PRJNA1213790	RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection	GSE287594	Transcriptome Analysis	Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed six biological replicates in two groups fish homozygous for pycardtpu5 mutation and wild type WT control.	pubmed:39916610	kidney derived neutrophils wt Mm infected rep6	GSM8748657	source name:kidney\|tissue:kidney\|cell type:neutrophils\|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected\|geo loc name:missing\|collection date:missing	kidney derived neutrophils wt Mm infected rep6	Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.	kidney	Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.	Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.	tissue:kidney\|cell type:neutrophils\|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected	GSM8748657	GSM8748657: kidney derived neutrophils wt Mm infected rep6; Danio rerio; RNA Seq	GSM8748657 r1	GSM8748657	1	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP558767		RNA32_W_MM_R_1.fq.gz RNA32_W_MM_R_2.fq.gz	fastq fastq	6440025300.0	21466751.0	GSM8748657 r1	0:150 1:150	A:1785469029;C:1447831778;G:1441059581;T:1765446885;N:218027	150	150	1785469029	1447831778	1441059581	1765446885	218027	SRX27413524	SRS23843183	SRA2056436	University of Tampere	University of Tampere												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Finland	2025-01-21	Larval	Larval	Kidney	Renal System
34542	34542	SRR32064724	SRX27413523	SRS23843182	SRP558767	PRJNA1213790	RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection	GSE287594	Transcriptome Analysis	Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed six biological replicates in two groups fish homozygous for pycardtpu5 mutation and wild type WT control.	pubmed:39916610	kidney derived neutrophils wt Mm infected rep5	GSM8748656	source name:kidney\|tissue:kidney\|cell type:neutrophils\|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected\|geo loc name:missing\|collection date:missing	kidney derived neutrophils wt Mm infected rep5	Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.	kidney	Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.	Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.	tissue:kidney\|cell type:neutrophils\|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected	GSM8748656	GSM8748656: kidney derived neutrophils wt Mm infected rep5; Danio rerio; RNA Seq	GSM8748656 r1	GSM8748656	1	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP558767		RNA29_W_MM_R_1.fq.gz RNA29_W_MM_R_2.fq.gz	fastq fastq	6450517200.0	21501724.0	GSM8748656 r1	0:150 1:150	A:1786241571;C:1451411588;G:1447987838;T:1764221339;N:654864	150	150	1786241571	1451411588	1447987838	1764221339	654864	SRX27413523	SRS23843182	SRA2056436	University of Tampere	University of Tampere												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Finland	2025-01-21	Larval	Larval	Kidney	Renal System
34543	34543	SRR32064725	SRX27413522	SRS23843181	SRP558767	PRJNA1213790	RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection	GSE287594	Transcriptome Analysis	Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed six biological replicates in two groups fish homozygous for pycardtpu5 mutation and wild type WT control.	pubmed:39916610	kidney derived neutrophils wt Mm infected rep4	GSM8748655	source name:kidney\|tissue:kidney\|cell type:neutrophils\|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected\|geo loc name:missing\|collection date:missing	kidney derived neutrophils wt Mm infected rep4	Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.	kidney	Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.	Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.	tissue:kidney\|cell type:neutrophils\|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected	GSM8748655	GSM8748655: kidney derived neutrophils wt Mm infected rep4; Danio rerio; RNA Seq	GSM8748655 r1	GSM8748655	1	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP558767		RNA28_W_MM_R_1.fq.gz RNA28_W_MM_R_2.fq.gz	fastq fastq	6306771900.0	21022573.0	GSM8748655 r1	0:150 1:150	A:1748779929;C:1415200694;G:1412343882;T:1729784544;N:662851	150	150	1748779929	1415200694	1412343882	1729784544	662851	SRX27413522	SRS23843181	SRA2056436	University of Tampere	University of Tampere												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Finland	2025-01-21	Larval	Larval	Kidney	Renal System
34544	34544	SRR32064726	SRX27413521	SRS23843180	SRP558767	PRJNA1213790	RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection	GSE287594	Transcriptome Analysis	Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed six biological replicates in two groups fish homozygous for pycardtpu5 mutation and wild type WT control.	pubmed:39916610	kidney derived neutrophils wt Mm infected rep3	GSM8748654	source name:kidney\|tissue:kidney\|cell type:neutrophils\|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected\|geo loc name:missing\|collection date:missing	kidney derived neutrophils wt Mm infected rep3	Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.	kidney	Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.	Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.	tissue:kidney\|cell type:neutrophils\|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected	GSM8748654	GSM8748654: kidney derived neutrophils wt Mm infected rep3; Danio rerio; RNA Seq	GSM8748654 r1	GSM8748654	1	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP558767		RNA11_W_MM_R_1.fq.gz RNA11_W_MM_R_2.fq.gz	fastq fastq	6880056600.0	22933522.0	GSM8748654 r1	0:150 1:150	A:1907309824;C:1546968275;G:1546306637;T:1879237297;N:234567	150	150	1907309824	1546968275	1546306637	1879237297	234567	SRX27413521	SRS23843180	SRA2056436	University of Tampere	University of Tampere												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Finland	2025-01-21	Larval	Larval	Kidney	Renal System
34545	34545	SRR32064727	SRX27413520	SRS23843179	SRP558767	PRJNA1213790	RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection	GSE287594	Transcriptome Analysis	Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed six biological replicates in two groups fish homozygous for pycardtpu5 mutation and wild type WT control.	pubmed:39916610	kidney derived neutrophils wt Mm infected rep2	GSM8748653	source name:kidney\|tissue:kidney\|cell type:neutrophils\|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected\|geo loc name:missing\|collection date:missing	kidney derived neutrophils wt Mm infected rep2	Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.	kidney	Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.	Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.	tissue:kidney\|cell type:neutrophils\|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected	GSM8748653	GSM8748653: kidney derived neutrophils wt Mm infected rep2; Danio rerio; RNA Seq	GSM8748653 r1	GSM8748653	1	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP558767		RNA10_W_MM_R_1.fq.gz RNA10_W_MM_R_2.fq.gz	fastq fastq	6391782300.0	21305941.0	GSM8748653 r1	0:150 1:150	A:1768453408;C:1440642021;G:1438187733;T:1744118899;N:380239	150	150	1768453408	1440642021	1438187733	1744118899	380239	SRX27413520	SRS23843179	SRA2056436	University of Tampere	University of Tampere												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Finland	2025-01-21	Larval	Larval	Kidney	Renal System
34546	34546	SRR32064728	SRX27413519	SRS23843178	SRP558767	PRJNA1213790	RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection	GSE287594	Transcriptome Analysis	Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed six biological replicates in two groups fish homozygous for pycardtpu5 mutation and wild type WT control.	pubmed:39916610	kidney derived neutrophils wt Mm infected rep1	GSM8748652	source name:kidney\|tissue:kidney\|cell type:neutrophils\|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected\|geo loc name:missing\|collection date:missing	kidney derived neutrophils wt Mm infected rep1	Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.	kidney	Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.	Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.	tissue:kidney\|cell type:neutrophils\|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB\|treatment:M. marinum infected	GSM8748652	GSM8748652: kidney derived neutrophils wt Mm infected rep1; Danio rerio; RNA Seq	GSM8748652 r1	GSM8748652	1	RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing 150 bp read length yielding > 20 million reads per sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP558767		RNA9_W_MM_R_1.fq.gz RNA9_W_MM_R_2.fq.gz	fastq fastq	6637369200.0	22124564.0	GSM8748652 r1	0:150 1:150	A:1824710129;C:1507871608;G:1512676495;T:1791435639;N:675329	150	150	1824710129	1507871608	1512676495	1791435639	675329	SRX27413519	SRS23843178	SRA2056436	University of Tampere	University of Tampere												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Finland	2025-01-21	Larval	Larval	Kidney	Renal System
49049	49049	SRR7633485	SRX4497216	SRS3618216	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2	pubmed:31158233	G2 pod 03	GSM3317057	tissue:zebrafish podocyte\|line:pod:mCherry\|treatment:human APOL1 G2 mRNA	G2 pod 03	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish podocyte	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:pod:mCherry\|treatment:human APOL1 G2 mRNA	GSM3317057	GSM3317057: G2 pod 03; Danio rerio; RNA Seq	GSM3317057		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317057	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S9_trimmed.fastq.gz	fastq	1265733350.0	25073196.0	GSM3317057 r1	0:50.48 1:0	A:351449147;C:285891495;G:278677300;T:349486454;N:228954	50	0	351449147	285891495	278677300	349486454	228954	SRX4497216	SRS3618216	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.88664		0.09978		0.70747		0.46307		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Kidney	Renal System
49050	49050	SRR7633484	SRX4497215	SRS3618215	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2	pubmed:31158233	G2 pod 02	GSM3317056	tissue:zebrafish podocyte\|line:pod:mCherry\|treatment:human APOL1 G2 mRNA	G2 pod 02	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish podocyte	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:pod:mCherry\|treatment:human APOL1 G2 mRNA	GSM3317056	GSM3317056: G2 pod 02; Danio rerio; RNA Seq	GSM3317056		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317056	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S8_trimmed.fastq.gz	fastq	927703036.0	18397661.0	GSM3317056 r1	0:50.43 1:0	A:256098583;C:212027468;G:205646180;T:253765375;N:165430	50	0	256098583	212027468	205646180	253765375	165430	SRX4497215	SRS3618215	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.82269		0.09332		0.70676		0.47673		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Kidney	Renal System
49051	49051	SRR7633483	SRX4497214	SRS3618214	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2	pubmed:31158233	G2 pod 01	GSM3317055	tissue:zebrafish podocyte\|line:pod:mCherry\|treatment:human APOL1 G2 mRNA	G2 pod 01	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish podocyte	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:pod:mCherry\|treatment:human APOL1 G2 mRNA	GSM3317055	GSM3317055: G2 pod 01; Danio rerio; RNA Seq	GSM3317055		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317055	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S7_trimmed.fastq.gz	fastq	1868917850.0	36965227.0	GSM3317055 r1	0:50.56 1:0	A:518334465;C:423085551;G:412301170;T:514857394;N:339270	50	0	518334465	423085551	412301170	514857394	339270	SRX4497214	SRS3618214	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.8967		0.11444		0.66793		0.47524		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Kidney	Renal System
49052	49052	SRR7633482	SRX4497213	SRS3618213	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2	pubmed:31158233	G0 pod 03	GSM3317054	tissue:zebrafish podocyte\|line:pod:mCherry\|treatment:human APOL1 G0 mRNA	G0 pod 03	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish podocyte	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:pod:mCherry\|treatment:human APOL1 G0 mRNA	GSM3317054	GSM3317054: G0 pod 03; Danio rerio; RNA Seq	GSM3317054		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317054	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S6_trimmed.fastq.gz	fastq	1989842108.0	39354652.0	GSM3317054 r1	0:50.56 1:0	A:547820589;C:452831323;G:441782569;T:547047192;N:360435	50	0	547820589	452831323	441782569	547047192	360435	SRX4497213	SRS3618213	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.88797		0.1001		0.67016		0.46755		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Kidney	Renal System
49053	49053	SRR7633481	SRX4497212	SRS3618212	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2	pubmed:31158233	G0 pod 02	GSM3317053	tissue:zebrafish podocyte\|line:pod:mCherry\|treatment:human APOL1 G0 mRNA	G0 pod 02	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish podocyte	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:pod:mCherry\|treatment:human APOL1 G0 mRNA	GSM3317053	GSM3317053: G0 pod 02; Danio rerio; RNA Seq	GSM3317053		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317053	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S5_trimmed.fastq.gz	fastq	1784099065.0	35295758.0	GSM3317053 r1	0:50.55 1:0	A:493338451;C:401706697;G:388876128;T:499853218;N:324571	50	0	493338451	401706697	388876128	499853218	324571	SRX4497212	SRS3618212	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.86757		0.09319		0.6733		0.46511		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Kidney	Renal System
49054	49054	SRR7633480	SRX4497211	SRS3618211	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2	pubmed:31158233	G0 pod 01	GSM3317052	tissue:zebrafish podocyte\|line:pod:mCherry\|treatment:human APOL1 G0 mRNA	G0 pod 01	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish podocyte	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:pod:mCherry\|treatment:human APOL1 G0 mRNA	GSM3317052	GSM3317052: G0 pod 01; Danio rerio; RNA Seq	GSM3317052		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317052	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S4_trimmed.fastq.gz	fastq	1294942611.0	25649695.0	GSM3317052 r1	0:50.49 1:0	A:358939215;C:292943376;G:284204779;T:358621256;N:233985	50	0	358939215	292943376	284204779	358621256	233985	SRX4497211	SRS3618211	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.89677		0.09742		0.66695		0.46036		49		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Kidney	Renal System
49055	49055	SRR7633479	SRX4497210	SRS3618210	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2	pubmed:31158233	control pod 03	GSM3317051	tissue:zebrafish podocyte\|line:pod:mCherry\|treatment:control	control pod 03	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish podocyte	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:pod:mCherry\|treatment:control	GSM3317051	GSM3317051: control pod 03; Danio rerio; RNA Seq	GSM3317051		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317051	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S3_trimmed.fastq.gz	fastq	1864996530.0	36896407.0	GSM3317051 r1	0:50.55 1:0	A:514542102;C:423583183;G:412707586;T:513826127;N:337532	50	0	514542102	423583183	412707586	513826127	337532	SRX4497210	SRS3618210	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.89167		0.10091		0.67773		0.48093		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Kidney	Renal System
49056	49056	SRR7633478	SRX4497209	SRS3618209	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2	pubmed:31158233	control pod 02	GSM3317050	tissue:zebrafish podocyte\|line:pod:mCherry\|treatment:control	control pod 02	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish podocyte	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:pod:mCherry\|treatment:control	GSM3317050	GSM3317050: control pod 02; Danio rerio; RNA Seq	GSM3317050		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317050	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S2_trimmed.fastq.gz	fastq	1405360276.0	27811908.0	GSM3317050 r1	0:50.53 1:0	A:388467227;C:319138771;G:310773160;T:386727396;N:253722	50	0	388467227	319138771	310773160	386727396	253722	SRX4497209	SRS3618209	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.898		0.10269		0.66967		0.45546		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Kidney	Renal System
49057	49057	SRR7633477	SRX4497208	SRS3618208	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2	pubmed:31158233	control pod 01	GSM3317049	tissue:zebrafish podocyte\|line:pod:mCherry\|treatment:control	control pod 01	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish podocyte	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:pod:mCherry\|treatment:control	GSM3317049	GSM3317049: control pod 01; Danio rerio; RNA Seq	GSM3317049		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317049	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S1_trimmed.fastq.gz	fastq	931525657.0	18454172.0	GSM3317049 r1	0:50.48 1:0	A:259125695;C:210068089;G:204402139;T:257763012;N:166722	50	0	259125695	210068089	204402139	257763012	166722	SRX4497208	SRS3618208	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.89072		0.10423		0.67107		0.46057		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Kidney	Renal System
51182	51182	SRR8559985	SRX5361484	SRS4352014	SRP185597	PRJNA521808	Effect of PTBA on acute kidney injury during AKI	GSE126418	Transcriptome Analysis	PTBA has been published to increase renal tubular cell proliferation increased survival and increased renal functional recovery in fish and various models of murine models of acute kidney injury. Immunohistological analyses suggested increased cell proliferation is accompanied by increased epithelial to mesenchymal transition in the RTECs. In order to elucidate pathways responsible for the increased repair response post compound treatment larval zebrafish were given AKI and treated with PTBA analogue UPHD25 or DMSO. Results suggests that epithelial related genes were downregulated while mesenchymal related genes were upregulated with injury and compound treatment. Results further validate our immunohistological finding that our compound increase post AKI repair by increasing EMT in renal tubular cells. Overall design: At 3dpf larval zebrafish are given acute kidney injury with gentamicin microinjection. 2 xxx post injury larvae with AKI are selected and treated with 1uM of PTBA analogue UPHD25 or vehicle control 1% DMSO. The fish were treated with UPHD25 or DMSO for 24 hours. Then pronephric kidneys were collected using DDT collagenase I and manual collection. Total 100 larvae were collected per sample per replicate. Each treatment group was repeated with 3 biological replicates. RNA was collected and sequenced.	pubmed:30890583	AKI UPHD25 Rep3	GSM3598110	source name:zebrafish pr1phros\|tissue:pr1phros\|microinjection:gentamicin\|treatment:1uM UPHD25	AKI UPHD25 Rep3	Reads were aligned using Hisat2 v2.1.0 with the UCSC zebrafish genome version danRer11. Reads for multiple lanes of the same sample were pooled together. Gene level counts were calculated using featureCounts in the R package Rsubread v1.24.2 with the Ensembl GTF file. Genome build: danRer11 Supplementary files format and content: Tab delimited text file with gene level counts for all samples.	zebrafish pronephros	At 2dpi 5dpf injured larvae were incubated with 1uM UPHD25 1%DMSO or control 1% DMSO for 24 hours at 28C	100 larvae were pooled and treated with DTT and Collagenase I to disintegrate tissue. Then they were titurated with p100 to reveal pronephros. GFP+pronephros were dissected and collected. Trizol based RNA isolation was used using RNAeasy Micro Kit QIAGEN TruSeq Stranded mRNA kit was used according to the manufacturer's protocol. Fragmentation was performed for 8 minutes. 15 rounds of PCR amplification provided selective enrichment of DNA with adapters ligated to both ends and was followed by library quantity and quality assessment by fluorometric assay Qubit and Agilent DNA 1000 TapeStation assay respectively. Final libraries were normalized to 10 nM pooled and diluted. Flowcells for the NextSeq 500 were seeded with 1.8 pM denatured library for automated cluster formation and 2 x 75 paired end sequencing approximately 30 40 million reads per sample.	Larvae were incubated in E3 medium until treatment at 3dpf.	genotype transgenic line:TgPT:egfp\|tissue:pr1phros\|microinjection:gentamicin\|treatment:1uM UPHD25	GSM3598110	GSM3598110: AKI UPHD25 Rep3; Danio rerio; RNA Seq	GSM3598110		1	70 100 larvae were pooled and treated with DTT and Collagenase I to disintegrate tissue. Then they were titurated with p100 to reveal pronephros. GFP+pronephros were dissected and collected. Trizol based RNA isolation was used using RNAeasy Micro Kit QIAGEN TruSeq Stranded mRNA kit was used according to the manufacturer's protocol. Fragmentation was performed for 8 minutes. 15 PCR amplification provided selective enrichment of DNA with adapters ligated to both ends and was followed by library quantity and quality assessment by fluorometric assay Qubit and Agilent DNA 1000 TapeStation assay respectively. Final libraries were normalized to 10 nM pooled and diluted. Flowcells for the NextSeq 500 were seeded with 1.8 pM denatured library for automated cluster formation and 2 x 75 paired end sequencing approximately 30 40 million reads per sample. Four samples of the first biological replicates were pooled and sequenced on a single flow cell. Second and third replicates were pooled and ran on 2 flow cells.	GEO Accession:GSM3598110	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP185597		3_AKI_UPHD25_R2_001.fastq.gz 3_AKI_UPHD25_R1_001.fastq.gz	fastq fastq	3306152848.0	21914998.0	GSM3598110 r1	0:75.45 1:75.41	A:879351999;C:770262390;G:771532102;T:884775676;N:230681	75	75	879351999	770262390	771532102	884775676	230681	SRX5361484	SRS4352014	SRA848340	GEO	Hukriede, Developmental Biology, University of Pittsburgh	2	0.95046	0.9524	0.10488	0.10306	0.65281	0.65894	0.48217	0.48269	73	76	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2019-02-11	Larval	Larval	Kidney	Renal System
51183	51183	SRR8559984	SRX5361483	SRS4352013	SRP185597	PRJNA521808	Effect of PTBA on acute kidney injury during AKI	GSE126418	Transcriptome Analysis	PTBA has been published to increase renal tubular cell proliferation increased survival and increased renal functional recovery in fish and various models of murine models of acute kidney injury. Immunohistological analyses suggested increased cell proliferation is accompanied by increased epithelial to mesenchymal transition in the RTECs. In order to elucidate pathways responsible for the increased repair response post compound treatment larval zebrafish were given AKI and treated with PTBA analogue UPHD25 or DMSO. Results suggests that epithelial related genes were downregulated while mesenchymal related genes were upregulated with injury and compound treatment. Results further validate our immunohistological finding that our compound increase post AKI repair by increasing EMT in renal tubular cells. Overall design: At 3dpf larval zebrafish are given acute kidney injury with gentamicin microinjection. 2 xxx post injury larvae with AKI are selected and treated with 1uM of PTBA analogue UPHD25 or vehicle control 1% DMSO. The fish were treated with UPHD25 or DMSO for 24 hours. Then pronephric kidneys were collected using DDT collagenase I and manual collection. Total 100 larvae were collected per sample per replicate. Each treatment group was repeated with 3 biological replicates. RNA was collected and sequenced.	pubmed:30890583	AKI UPHD25 Rep2	GSM3598109	source name:zebrafish pr1phros\|tissue:pr1phros\|microinjection:gentamicin\|treatment:1uM UPHD25	AKI UPHD25 Rep2	Reads were aligned using Hisat2 v2.1.0 with the UCSC zebrafish genome version danRer11. Reads for multiple lanes of the same sample were pooled together. Gene level counts were calculated using featureCounts in the R package Rsubread v1.24.2 with the Ensembl GTF file. Genome build: danRer11 Supplementary files format and content: Tab delimited text file with gene level counts for all samples.	zebrafish pronephros	At 2dpi 5dpf injured larvae were incubated with 1uM UPHD25 1%DMSO or control 1% DMSO for 24 hours at 28C	100 larvae were pooled and treated with DTT and Collagenase I to disintegrate tissue. Then they were titurated with p100 to reveal pronephros. GFP+pronephros were dissected and collected. Trizol based RNA isolation was used using RNAeasy Micro Kit QIAGEN TruSeq Stranded mRNA kit was used according to the manufacturer's protocol. Fragmentation was performed for 8 minutes. 15 rounds of PCR amplification provided selective enrichment of DNA with adapters ligated to both ends and was followed by library quantity and quality assessment by fluorometric assay Qubit and Agilent DNA 1000 TapeStation assay respectively. Final libraries were normalized to 10 nM pooled and diluted. Flowcells for the NextSeq 500 were seeded with 1.8 pM denatured library for automated cluster formation and 2 x 75 paired end sequencing approximately 30 40 million reads per sample.	Larvae were incubated in E3 medium until treatment at 3dpf.	genotype transgenic line:TgPT:egfp\|tissue:pr1phros\|microinjection:gentamicin\|treatment:1uM UPHD25	GSM3598109	GSM3598109: AKI UPHD25 Rep2; Danio rerio; RNA Seq	GSM3598109		1	70 100 larvae were pooled and treated with DTT and Collagenase I to disintegrate tissue. Then they were titurated with p100 to reveal pronephros. GFP+pronephros were dissected and collected. Trizol based RNA isolation was used using RNAeasy Micro Kit QIAGEN TruSeq Stranded mRNA kit was used according to the manufacturer's protocol. Fragmentation was performed for 8 minutes. 15 PCR amplification provided selective enrichment of DNA with adapters ligated to both ends and was followed by library quantity and quality assessment by fluorometric assay Qubit and Agilent DNA 1000 TapeStation assay respectively. Final libraries were normalized to 10 nM pooled and diluted. Flowcells for the NextSeq 500 were seeded with 1.8 pM denatured library for automated cluster formation and 2 x 75 paired end sequencing approximately 30 40 million reads per sample. Four samples of the first biological replicates were pooled and sequenced on a single flow cell. Second and third replicates were pooled and ran on 2 flow cells.	GEO Accession:GSM3598109	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP185597		2_AKI_UPHD25_R2_001.fastq.gz 2_AKI_UPHD25_R1_001.fastq.gz	fastq fastq	2941954752.0	19507003.0	GSM3598109 r1	0:75.43 1:75.39	A:785687409;C:667955893;G:716461151;T:771595436;N:254863	75	75	785687409	667955893	716461151	771595436	254863	SRX5361483	SRS4352013	SRA848340	GEO	Hukriede, Developmental Biology, University of Pittsburgh	2	0.9501	0.94777	0.11457	0.11247	0.68392	0.69814	0.48638	0.49272	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2019-02-11	Larval	Larval	Kidney	Renal System
51184	51184	SRR8559983	SRX5361482	SRS4352012	SRP185597	PRJNA521808	Effect of PTBA on acute kidney injury during AKI	GSE126418	Transcriptome Analysis	PTBA has been published to increase renal tubular cell proliferation increased survival and increased renal functional recovery in fish and various models of murine models of acute kidney injury. Immunohistological analyses suggested increased cell proliferation is accompanied by increased epithelial to mesenchymal transition in the RTECs. In order to elucidate pathways responsible for the increased repair response post compound treatment larval zebrafish were given AKI and treated with PTBA analogue UPHD25 or DMSO. Results suggests that epithelial related genes were downregulated while mesenchymal related genes were upregulated with injury and compound treatment. Results further validate our immunohistological finding that our compound increase post AKI repair by increasing EMT in renal tubular cells. Overall design: At 3dpf larval zebrafish are given acute kidney injury with gentamicin microinjection. 2 xxx post injury larvae with AKI are selected and treated with 1uM of PTBA analogue UPHD25 or vehicle control 1% DMSO. The fish were treated with UPHD25 or DMSO for 24 hours. Then pronephric kidneys were collected using DDT collagenase I and manual collection. Total 100 larvae were collected per sample per replicate. Each treatment group was repeated with 3 biological replicates. RNA was collected and sequenced.	pubmed:30890583	AKI UPHD25 Rep1	GSM3598108	source name:zebrafish pr1phros\|tissue:pr1phros\|microinjection:gentamicin\|treatment:1uM UPHD25	AKI UPHD25 Rep1	Reads were aligned using Hisat2 v2.1.0 with the UCSC zebrafish genome version danRer11. Reads for multiple lanes of the same sample were pooled together. Gene level counts were calculated using featureCounts in the R package Rsubread v1.24.2 with the Ensembl GTF file. Genome build: danRer11 Supplementary files format and content: Tab delimited text file with gene level counts for all samples.	zebrafish pronephros	At 2dpi 5dpf injured larvae were incubated with 1uM UPHD25 1%DMSO or control 1% DMSO for 24 hours at 28C	100 larvae were pooled and treated with DTT and Collagenase I to disintegrate tissue. Then they were titurated with p100 to reveal pronephros. GFP+pronephros were dissected and collected. Trizol based RNA isolation was used using RNAeasy Micro Kit QIAGEN TruSeq Stranded mRNA kit was used according to the manufacturer's protocol. Fragmentation was performed for 8 minutes. 15 rounds of PCR amplification provided selective enrichment of DNA with adapters ligated to both ends and was followed by library quantity and quality assessment by fluorometric assay Qubit and Agilent DNA 1000 TapeStation assay respectively. Final libraries were normalized to 10 nM pooled and diluted. Flowcells for the NextSeq 500 were seeded with 1.8 pM denatured library for automated cluster formation and 2 x 75 paired end sequencing approximately 30 40 million reads per sample.	Larvae were incubated in E3 medium until treatment at 3dpf.	genotype transgenic line:TgPT:egfp\|tissue:pr1phros\|microinjection:gentamicin\|treatment:1uM UPHD25	GSM3598108	GSM3598108: AKI UPHD25 Rep1; Danio rerio; RNA Seq	GSM3598108		1	70 100 larvae were pooled and treated with DTT and Collagenase I to disintegrate tissue. Then they were titurated with p100 to reveal pronephros. GFP+pronephros were dissected and collected. Trizol based RNA isolation was used using RNAeasy Micro Kit QIAGEN TruSeq Stranded mRNA kit was used according to the manufacturer's protocol. Fragmentation was performed for 8 minutes. 15 PCR amplification provided selective enrichment of DNA with adapters ligated to both ends and was followed by library quantity and quality assessment by fluorometric assay Qubit and Agilent DNA 1000 TapeStation assay respectively. Final libraries were normalized to 10 nM pooled and diluted. Flowcells for the NextSeq 500 were seeded with 1.8 pM denatured library for automated cluster formation and 2 x 75 paired end sequencing approximately 30 40 million reads per sample. Four samples of the first biological replicates were pooled and sequenced on a single flow cell. Second and third replicates were pooled and ran on 2 flow cells.	GEO Accession:GSM3598108	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP185597		1_AKI_UPHD25_R1_001.fastq.gz 1_AKI_UPHD25_R2_001.fastq.gz	fastq fastq	6059912984.0	40145674.0	GSM3598108 r1	0:75.50 1:75.45	A:1580876814;C:1444343868;G:1437343041;T:1596089533;N:1259728	75	75	1580876814	1444343868	1437343041	1596089533	1259728	SRX5361482	SRS4352012	SRA848340	GEO	Hukriede, Developmental Biology, University of Pittsburgh	2	0.95682	0.9573	0.09115	0.08901	0.69643	0.70242	0.49657	0.48863	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2019-02-11	Larval	Larval	Kidney	Renal System
51185	51185	SRR8559982	SRX5361481	SRS4352011	SRP185597	PRJNA521808	Effect of PTBA on acute kidney injury during AKI	GSE126418	Transcriptome Analysis	PTBA has been published to increase renal tubular cell proliferation increased survival and increased renal functional recovery in fish and various models of murine models of acute kidney injury. Immunohistological analyses suggested increased cell proliferation is accompanied by increased epithelial to mesenchymal transition in the RTECs. In order to elucidate pathways responsible for the increased repair response post compound treatment larval zebrafish were given AKI and treated with PTBA analogue UPHD25 or DMSO. Results suggests that epithelial related genes were downregulated while mesenchymal related genes were upregulated with injury and compound treatment. Results further validate our immunohistological finding that our compound increase post AKI repair by increasing EMT in renal tubular cells. Overall design: At 3dpf larval zebrafish are given acute kidney injury with gentamicin microinjection. 2 xxx post injury larvae with AKI are selected and treated with 1uM of PTBA analogue UPHD25 or vehicle control 1% DMSO. The fish were treated with UPHD25 or DMSO for 24 hours. Then pronephric kidneys were collected using DDT collagenase I and manual collection. Total 100 larvae were collected per sample per replicate. Each treatment group was repeated with 3 biological replicates. RNA was collected and sequenced.	pubmed:30890583	AKI DMSO Rep3	GSM3598107	source name:zebrafish pr1phros\|tissue:pr1phros\|microinjection:gentamicin\|treatment:1% DMSO	AKI DMSO Rep3	Reads were aligned using Hisat2 v2.1.0 with the UCSC zebrafish genome version danRer11. Reads for multiple lanes of the same sample were pooled together. Gene level counts were calculated using featureCounts in the R package Rsubread v1.24.2 with the Ensembl GTF file. Genome build: danRer11 Supplementary files format and content: Tab delimited text file with gene level counts for all samples.	zebrafish pronephros	At 2dpi 5dpf injured larvae were incubated with 1uM UPHD25 1%DMSO or control 1% DMSO for 24 hours at 28C	100 larvae were pooled and treated with DTT and Collagenase I to disintegrate tissue. Then they were titurated with p100 to reveal pronephros. GFP+pronephros were dissected and collected. Trizol based RNA isolation was used using RNAeasy Micro Kit QIAGEN TruSeq Stranded mRNA kit was used according to the manufacturer's protocol. Fragmentation was performed for 8 minutes. 15 rounds of PCR amplification provided selective enrichment of DNA with adapters ligated to both ends and was followed by library quantity and quality assessment by fluorometric assay Qubit and Agilent DNA 1000 TapeStation assay respectively. Final libraries were normalized to 10 nM pooled and diluted. Flowcells for the NextSeq 500 were seeded with 1.8 pM denatured library for automated cluster formation and 2 x 75 paired end sequencing approximately 30 40 million reads per sample.	Larvae were incubated in E3 medium until treatment at 3dpf.	genotype transgenic line:TgPT:egfp\|tissue:pr1phros\|microinjection:gentamicin\|treatment:1% DMSO	GSM3598107	GSM3598107: AKI DMSO Rep3; Danio rerio; RNA Seq	GSM3598107		1	70 100 larvae were pooled and treated with DTT and Collagenase I to disintegrate tissue. Then they were titurated with p100 to reveal pronephros. GFP+pronephros were dissected and collected. Trizol based RNA isolation was used using RNAeasy Micro Kit QIAGEN TruSeq Stranded mRNA kit was used according to the manufacturer's protocol. Fragmentation was performed for 8 minutes. 15 PCR amplification provided selective enrichment of DNA with adapters ligated to both ends and was followed by library quantity and quality assessment by fluorometric assay Qubit and Agilent DNA 1000 TapeStation assay respectively. Final libraries were normalized to 10 nM pooled and diluted. Flowcells for the NextSeq 500 were seeded with 1.8 pM denatured library for automated cluster formation and 2 x 75 paired end sequencing approximately 30 40 million reads per sample. Four samples of the first biological replicates were pooled and sequenced on a single flow cell. Second and third replicates were pooled and ran on 2 flow cells.	GEO Accession:GSM3598107	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP185597		3_AKI_DMSO_R1_001.fastq.gz 3_AKI_DMSO_R2_001.fastq.gz	fastq fastq	3111109723.0	20604408.0	GSM3598107 r1	0:75.52 1:75.47	A:822122014;C:731386825;G:730530164;T:826925686;N:145034	75	75	822122014	731386825	730530164	826925686	145034	SRX5361481	SRS4352011	SRA848340	GEO	Hukriede, Developmental Biology, University of Pittsburgh	2	0.95508	0.95648	0.09496	0.09287	0.68669	0.69215	0.48663	0.48802	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2019-02-11	Larval	Larval	Kidney	Renal System
51186	51186	SRR8559981	SRX5361480	SRS4352010	SRP185597	PRJNA521808	Effect of PTBA on acute kidney injury during AKI	GSE126418	Transcriptome Analysis	PTBA has been published to increase renal tubular cell proliferation increased survival and increased renal functional recovery in fish and various models of murine models of acute kidney injury. Immunohistological analyses suggested increased cell proliferation is accompanied by increased epithelial to mesenchymal transition in the RTECs. In order to elucidate pathways responsible for the increased repair response post compound treatment larval zebrafish were given AKI and treated with PTBA analogue UPHD25 or DMSO. Results suggests that epithelial related genes were downregulated while mesenchymal related genes were upregulated with injury and compound treatment. Results further validate our immunohistological finding that our compound increase post AKI repair by increasing EMT in renal tubular cells. Overall design: At 3dpf larval zebrafish are given acute kidney injury with gentamicin microinjection. 2 xxx post injury larvae with AKI are selected and treated with 1uM of PTBA analogue UPHD25 or vehicle control 1% DMSO. The fish were treated with UPHD25 or DMSO for 24 hours. Then pronephric kidneys were collected using DDT collagenase I and manual collection. Total 100 larvae were collected per sample per replicate. Each treatment group was repeated with 3 biological replicates. RNA was collected and sequenced.	pubmed:30890583	AKI DMSO Rep2	GSM3598106	source name:zebrafish pr1phros\|tissue:pr1phros\|microinjection:gentamicin\|treatment:1% DMSO	AKI DMSO Rep2	Reads were aligned using Hisat2 v2.1.0 with the UCSC zebrafish genome version danRer11. Reads for multiple lanes of the same sample were pooled together. Gene level counts were calculated using featureCounts in the R package Rsubread v1.24.2 with the Ensembl GTF file. Genome build: danRer11 Supplementary files format and content: Tab delimited text file with gene level counts for all samples.	zebrafish pronephros	At 2dpi 5dpf injured larvae were incubated with 1uM UPHD25 1%DMSO or control 1% DMSO for 24 hours at 28C	100 larvae were pooled and treated with DTT and Collagenase I to disintegrate tissue. Then they were titurated with p100 to reveal pronephros. GFP+pronephros were dissected and collected. Trizol based RNA isolation was used using RNAeasy Micro Kit QIAGEN TruSeq Stranded mRNA kit was used according to the manufacturer's protocol. Fragmentation was performed for 8 minutes. 15 rounds of PCR amplification provided selective enrichment of DNA with adapters ligated to both ends and was followed by library quantity and quality assessment by fluorometric assay Qubit and Agilent DNA 1000 TapeStation assay respectively. Final libraries were normalized to 10 nM pooled and diluted. Flowcells for the NextSeq 500 were seeded with 1.8 pM denatured library for automated cluster formation and 2 x 75 paired end sequencing approximately 30 40 million reads per sample.	Larvae were incubated in E3 medium until treatment at 3dpf.	genotype transgenic line:TgPT:egfp\|tissue:pr1phros\|microinjection:gentamicin\|treatment:1% DMSO	GSM3598106	GSM3598106: AKI DMSO Rep2; Danio rerio; RNA Seq	GSM3598106		1	70 100 larvae were pooled and treated with DTT and Collagenase I to disintegrate tissue. Then they were titurated with p100 to reveal pronephros. GFP+pronephros were dissected and collected. Trizol based RNA isolation was used using RNAeasy Micro Kit QIAGEN TruSeq Stranded mRNA kit was used according to the manufacturer's protocol. Fragmentation was performed for 8 minutes. 15 PCR amplification provided selective enrichment of DNA with adapters ligated to both ends and was followed by library quantity and quality assessment by fluorometric assay Qubit and Agilent DNA 1000 TapeStation assay respectively. Final libraries were normalized to 10 nM pooled and diluted. Flowcells for the NextSeq 500 were seeded with 1.8 pM denatured library for automated cluster formation and 2 x 75 paired end sequencing approximately 30 40 million reads per sample. Four samples of the first biological replicates were pooled and sequenced on a single flow cell. Second and third replicates were pooled and ran on 2 flow cells.	GEO Accession:GSM3598106	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP185597		2_AKI_DMSO_R1_001.fastq.gz 2_AKI_DMSO_R2_001.fastq.gz	fastq fastq	3113907402.0	20663246.0	GSM3598106 r1	0:75.37 1:75.33	A:814534980;C:734388348;G:750932770;T:813688234;N:363070	75	75	814534980	734388348	750932770	813688234	363070	SRX5361480	SRS4352010	SRA848340	GEO	Hukriede, Developmental Biology, University of Pittsburgh	2	0.95423	0.95621	0.09494	0.09343	0.69865	0.70652	0.48602	0.49482	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2019-02-11	Larval	Larval	Kidney	Renal System
51187	51187	SRR8559980	SRX5361479	SRS4352009	SRP185597	PRJNA521808	Effect of PTBA on acute kidney injury during AKI	GSE126418	Transcriptome Analysis	PTBA has been published to increase renal tubular cell proliferation increased survival and increased renal functional recovery in fish and various models of murine models of acute kidney injury. Immunohistological analyses suggested increased cell proliferation is accompanied by increased epithelial to mesenchymal transition in the RTECs. In order to elucidate pathways responsible for the increased repair response post compound treatment larval zebrafish were given AKI and treated with PTBA analogue UPHD25 or DMSO. Results suggests that epithelial related genes were downregulated while mesenchymal related genes were upregulated with injury and compound treatment. Results further validate our immunohistological finding that our compound increase post AKI repair by increasing EMT in renal tubular cells. Overall design: At 3dpf larval zebrafish are given acute kidney injury with gentamicin microinjection. 2 xxx post injury larvae with AKI are selected and treated with 1uM of PTBA analogue UPHD25 or vehicle control 1% DMSO. The fish were treated with UPHD25 or DMSO for 24 hours. Then pronephric kidneys were collected using DDT collagenase I and manual collection. Total 100 larvae were collected per sample per replicate. Each treatment group was repeated with 3 biological replicates. RNA was collected and sequenced.	pubmed:30890583	AKI DMSO Rep1	GSM3598105	source name:zebrafish pr1phros\|tissue:pr1phros\|microinjection:gentamicin\|treatment:1% DMSO	AKI DMSO Rep1	Reads were aligned using Hisat2 v2.1.0 with the UCSC zebrafish genome version danRer11. Reads for multiple lanes of the same sample were pooled together. Gene level counts were calculated using featureCounts in the R package Rsubread v1.24.2 with the Ensembl GTF file. Genome build: danRer11 Supplementary files format and content: Tab delimited text file with gene level counts for all samples.	zebrafish pronephros	At 2dpi 5dpf injured larvae were incubated with 1uM UPHD25 1%DMSO or control 1% DMSO for 24 hours at 28C	100 larvae were pooled and treated with DTT and Collagenase I to disintegrate tissue. Then they were titurated with p100 to reveal pronephros. GFP+pronephros were dissected and collected. Trizol based RNA isolation was used using RNAeasy Micro Kit QIAGEN TruSeq Stranded mRNA kit was used according to the manufacturer's protocol. Fragmentation was performed for 8 minutes. 15 PCR amplification provided selective enrichment of DNA with adapters ligated to both ends and was followed by library quantity and quality assessment by fluorometric assay Qubit and Agilent DNA 1000 TapeStation assay respectively. Final libraries were normalized to 10 nM pooled and diluted. Flowcells for the NextSeq 500 were seeded with 1.8 pM denatured library for automated cluster formation and 2 x 75 paired end sequencing approximately 30 40 million reads per sample.	Larvae were incubated in E3 medium until treatment at 3dpf.	genotype transgenic line:TgPT:egfp\|tissue:pr1phros\|microinjection:gentamicin\|treatment:1% DMSO	GSM3598105	GSM3598105: AKI DMSO Rep1; Danio rerio; RNA Seq	GSM3598105		1	70 100 larvae were pooled and treated with DTT and Collagenase I to disintegrate tissue. Then they were titurated with p100 to reveal pronephros. GFP+pronephros were dissected and collected. Trizol based RNA isolation was used using RNAeasy Micro Kit QIAGEN TruSeq Stranded mRNA kit was used according to the manufacturer's protocol. Fragmentation was performed for 8 minutes. 15 PCR amplification provided selective enrichment of DNA with adapters ligated to both ends and was followed by library quantity and quality assessment by fluorometric assay Qubit and Agilent DNA 1000 TapeStation assay respectively. Final libraries were normalized to 10 nM pooled and diluted. Flowcells for the NextSeq 500 were seeded with 1.8 pM denatured library for automated cluster formation and 2 x 75 paired end sequencing approximately 30 40 million reads per sample. Four samples of the first biological replicates were pooled and sequenced on a single flow cell. Second and third replicates were pooled and ran on 2 flow cells.	GEO Accession:GSM3598105	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP185597		1_AKI_DMSO_R1_001.fastq.gz 1_AKI_DMSO_R2_001.fastq.gz	fastq fastq	7980120725.0	52876593.0	GSM3598105 r1	0:75.49 1:75.43	A:2087481849;C:1906979002;G:1876971548;T:2107071717;N:1616609	75	75	2087481849	1906979002	1876971548	2107071717	1616609	SRX5361479	SRS4352009	SRA848340	GEO	Hukriede, Developmental Biology, University of Pittsburgh	2	0.95866	0.95946	0.08787	0.08682	0.70214	0.70599	0.48955	0.48968	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2019-02-11	Larval	Larval	Kidney	Renal System
60908	60908	SRR12654012	SRX9135234	SRS7377188	SRP282618	PRJNA663897	Identification of enhancer elements that direct long range responses to tissue injury	GSE158079	Other	The goal of this study is to unveal the responses of uninjured tissue to distant tissue injury and the structures required for long range responses to tissue injuries. we profiled responses by the brain and kidney in zebrafish to massive injuries of the heart and identified cebpd transcript induction in both tissue. We also identified and demonstrated that a 1.2kb cebpd downstream element is capable and neccessary for the induction of cebpd in the brain post cardiac injury. Overall design: Brain and kidney RNA seq and ATAC seq profiling post cardiac injury; cebpd+/+ and cebpd / brain RNA seq profiling post cardiac injury	pubmed:35513710	WKM RNAseq uninjured rep2	GSM4790351	source name:Whole kidney marrow\|strain:EK\|tissue:Whole kidney marrow\|genotype:Wild type\|treatment:uninjured	WKM RNAseq uninjured rep2	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	Whole kidney marrow	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction and nuclei isolation.	Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100 000 cells/nuclei were used for library preparation. RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in Buenrostro et al. 2013.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Whole kidney marrow\|genotype:Wild type\|treatment:uninjured	GSM4790351	GSM4790351: WKM RNAseq uninjured rep2; Danio rerio; RNA Seq	GSM4790351		1	Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100 000 cells/nuclei were used for library preparation. RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in Buenrostro et al. 2013.	GEO Accession:GSM4790351	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP282618		WKM.RNAseq.Uninjured.S6_S17_L007_R1_001.fastq.gz	fastq	2128727352.0	41739752.0	GSM4790351 r1	0:51 1:0	A:526003466;C:520045952;G:479756780;T:602686415;N:234739	51	0	526003466	520045952	479756780	602686415	234739	SRX9135234	SRS7377188	SRA1126400	GEO	Poss, Cell Biology, Duke University	1	0.91364		0.16098		0.72101		0.55063		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-09-16	Larval	Larval	Kidney	Renal System
60909	60909	SRR12654011	SRX9135233	SRS7377187	SRP282618	PRJNA663897	Identification of enhancer elements that direct long range responses to tissue injury	GSE158079	Other	The goal of this study is to unveal the responses of uninjured tissue to distant tissue injury and the structures required for long range responses to tissue injuries. we profiled responses by the brain and kidney in zebrafish to massive injuries of the heart and identified cebpd transcript induction in both tissue. We also identified and demonstrated that a 1.2kb cebpd downstream element is capable and neccessary for the induction of cebpd in the brain post cardiac injury. Overall design: Brain and kidney RNA seq and ATAC seq profiling post cardiac injury; cebpd+/+ and cebpd / brain RNA seq profiling post cardiac injury	pubmed:35513710	WKM RNAseq uninjured rep1	GSM4790350	source name:Whole kidney marrow\|strain:EK\|tissue:Whole kidney marrow\|genotype:Wild type\|treatment:uninjured	WKM RNAseq uninjured rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	Whole kidney marrow	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction and nuclei isolation.	Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100 000 cells/nuclei were used for library preparation. RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in Buenrostro et al. 2013.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Whole kidney marrow\|genotype:Wild type\|treatment:uninjured	GSM4790350	GSM4790350: WKM RNAseq uninjured rep1; Danio rerio; RNA Seq	GSM4790350		1	Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100 000 cells/nuclei were used for library preparation. RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in Buenrostro et al. 2013.	GEO Accession:GSM4790350	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP282618		WKM.RNAseq.Uninjured.S4_S16_L007_R1_001.fastq.gz	fastq	2227157658.0	43669758.0	GSM4790350 r1	0:51 1:0	A:537108530;C:560518473;G:511205641;T:618080406;N:244608	51	0	537108530	560518473	511205641	618080406	244608	SRX9135233	SRS7377187	SRA1126400	GEO	Poss, Cell Biology, Duke University	1	0.92052		0.16555		0.72206		0.54742		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-09-16	Larval	Larval	Kidney	Renal System
60910	60910	SRR12654010	SRX9135232	SRS7377186	SRP282618	PRJNA663897	Identification of enhancer elements that direct long range responses to tissue injury	GSE158079	Other	The goal of this study is to unveal the responses of uninjured tissue to distant tissue injury and the structures required for long range responses to tissue injuries. we profiled responses by the brain and kidney in zebrafish to massive injuries of the heart and identified cebpd transcript induction in both tissue. We also identified and demonstrated that a 1.2kb cebpd downstream element is capable and neccessary for the induction of cebpd in the brain post cardiac injury. Overall design: Brain and kidney RNA seq and ATAC seq profiling post cardiac injury; cebpd+/+ and cebpd / brain RNA seq profiling post cardiac injury	pubmed:35513710	WKM RNAseq regeneration rep2	GSM4790349	source name:Whole kidney marrow\|strain:EK\|tissue:Whole kidney marrow\|genotype:Wild type\|treatment:cardiomyocyte ablation	WKM RNAseq regeneration rep2	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	Whole kidney marrow	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction and nuclei isolation.	Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100 000 cells/nuclei were used for library preparation. RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in Buenrostro et al. 2013.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Whole kidney marrow\|genotype:Wild type\|treatment:cardiomyocyte ablation	GSM4790349	GSM4790349: WKM RNAseq regeneration rep2; Danio rerio; RNA Seq	GSM4790349		1	Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100 000 cells/nuclei were used for library preparation. RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in Buenrostro et al. 2013.	GEO Accession:GSM4790349	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP282618		WKM.RNAseq.Injured.S3_S15_L007_R1_001.fastq.gz	fastq	2221210599.0	43553149.0	GSM4790349 r1	0:51 1:0	A:550217634;C:538023788;G:499202852;T:633520371;N:245954	51	0	550217634	538023788	499202852	633520371	245954	SRX9135232	SRS7377186	SRA1126400	GEO	Poss, Cell Biology, Duke University	1	0.91459		0.14893		0.7152		0.53335		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-09-16	Larval	Larval	Kidney	Renal System
60911	60911	SRR12654009	SRX9135231	SRS7377185	SRP282618	PRJNA663897	Identification of enhancer elements that direct long range responses to tissue injury	GSE158079	Other	The goal of this study is to unveal the responses of uninjured tissue to distant tissue injury and the structures required for long range responses to tissue injuries. we profiled responses by the brain and kidney in zebrafish to massive injuries of the heart and identified cebpd transcript induction in both tissue. We also identified and demonstrated that a 1.2kb cebpd downstream element is capable and neccessary for the induction of cebpd in the brain post cardiac injury. Overall design: Brain and kidney RNA seq and ATAC seq profiling post cardiac injury; cebpd+/+ and cebpd / brain RNA seq profiling post cardiac injury	pubmed:35513710	WKM RNAseq regeneration rep1	GSM4790348	source name:Whole kidney marrow\|strain:EK\|tissue:Whole kidney marrow\|genotype:Wild type\|treatment:cardiomyocyte ablation	WKM RNAseq regeneration rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	Whole kidney marrow	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction and nuclei isolation.	Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100 000 cells/nuclei were used for library preparation. RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in Buenrostro et al. 2013.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Whole kidney marrow\|genotype:Wild type\|treatment:cardiomyocyte ablation	GSM4790348	GSM4790348: WKM RNAseq regeneration rep1; Danio rerio; RNA Seq	GSM4790348		1	Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100 000 cells/nuclei were used for library preparation. RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in Buenrostro et al. 2013.	GEO Accession:GSM4790348	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP282618		WKM.RNAseq.Injured.S1_S14_L007_R1_001.fastq.gz	fastq	1732396917.0	33968567.0	GSM4790348 r1	0:51 1:0	A:421512333;C:432906390;G:394818884;T:482970998;N:188312	51	0	421512333	432906390	394818884	482970998	188312	SRX9135231	SRS7377185	SRA1126400	GEO	Poss, Cell Biology, Duke University	1	0.91203		0.15222		0.71486		0.54145		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-09-16	Larval	Larval	Kidney	Renal System
67666	67666	SRR17259778	SRX13438135	SRS11337557	SRP351293	PRJNA788929	CXCR4 CXCL12 axis promotes the efficient T cell reconstitution by the HSPCs immigration	GSE190921	Transcriptome Analysis	T cells are essentially involved in safeguarding homeostasis through fighting against the pathogens and malignant cells. T cell immunodeficiency especially their perturbation in the severe infection irradiation chemotherapy and thymic atrophy in ageing is detrimental. Therefore strategies that enhance T cell reconstitution provide considerable benefit and warrant intensive investigation. Here we constructed a T cells ablation model in Tgcoro1a:DenNTR zebrafish via administrating a proper volume of metronidazole MTZ. T cells completely recovered at 6.5 days post treatment dpt. The nascent regenerated T cells were mainly derived from the immigration of hematopoietic stem/progenitor cells HSPCs in the kidney the functional homologue of BM. cxcr4b but not ccr9 nor ccr7 was drastically unregulated in the responsive HSPCs. Functional interference of CXCR4 via both genetic and chemical assays yielded limited influence in T lymphopoiesis but notably delayed T cells regeneration by a destroyed HSPCs migration. In contrast hematopoietic providing cxcr4b in Tg:coro1a:cxcr4b accelerates thymus replenishment of HSPCs. Correspondingly Cxcl12b the ligand of Cxcr4 exhibited impressive increment presentation in the thymic epithelial cells of injured animals. Interfering or overacting Cxcl12b in either cxcl12b / mutants or Tghsp70:cxcl12b recapitulated the similarly compromised or promoted T cells recovery as that seen in Cxcr4b scenario. Therefore CXCR4 CXCL12 axis plays a crucial role in promoting thymocyte reconstitution but did not influence T cell development. Our study discloses a special role of CXCR4 CXCL12 signaling in promoting T cells recovery and provides a promising target to mitigate T cell immunodeficiency. Overall design: 6 Smart seq data of kidney hematopoietic cells in DMSO and MTZ treated zebrafish	pubmed:35483564	MTZ treated zebrafish larval kiney hematopoietic cells rep3	GSM5734069	source name:kidney hematopoietic cells\|genotype:WT\|tissue:kidney\|age:3.5 dpt/9 dpf	MTZ treated zebrafish larval kiney hematopoietic cells rep3	Illumina NovaSeq 6000 software used for basecalling. Raw reads used FASTP for quality control to filter low quality data. Then the clean reads were aligned to the GRCz119 genome assembly using HISAT2 Genome build: GRCz11	kidney hematopoietic cells		The cells in the 3.5 dpt kidney of DMSO or MTZ groups were labeled by red color via irradiating Tgcoro1a:DenNTR transgenic larvae by a 405 nm laser in an LSM880 confocal microscope for 30 seconds. post photoconversion approximately eighty zebrafish larvae were collected mixed dissected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was re suspended in PBS followed by cell sorting using flow cytometry Moflo XDP Beckman. A cDNA library was generated from fifty red Dendra2+ cells by using the Smart seq2 protocol.		genotype:WT\|tissue:kidney\|age:3.5 dpt/9 dpf	GSM5734069	GSM5734069: MTZ treated zebrafish larval kiney hematopoietic cells rep3; Danio rerio; RNA Seq	GSM5734069		1	The cells in the 3.5 dpt kidney of DMSO or MTZ groups were labeled by red color via irradiating Tgcoro1a:DenNTR transgenic larvae by a 405 nm laser in an LSM880 confocal microscope for 30 seconds. post photoconversion approximately eighty zebrafish larvae were collected mixed dissected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was re suspended in PBS followed by cell sorting using flow cytometry Moflo XDP Beckman. A cDNA library was generated from fifty red Dendra2+ cells by using the Smart seq2 protocol.	GEO Accession:GSM5734069	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351293	loader:fastq load.py	MTZ_3_1.fq.gz MTZ_3_2.fq.gz	fastq fastq	13305900900.0	44353003.0	GSM5734069 r1	0:150 1:150	A:3765273957;C:2874608177;G:2915027688;T:3750920667;N:70411	150	150	3765273957	2874608177	2915027688	3750920667	70411	SRX13438135	SRS11337557	SRA1345009	GEO	Lili laboratory, southwest university	2	0.9308	0.93244	0.14771	0.14887	0.79924	0.79845	0.47006	0.47211	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2021-12-14	Larval	Larval	Kidney	Renal System
67667	67667	SRR17259777	SRX13438134	SRS11337556	SRP351293	PRJNA788929	CXCR4 CXCL12 axis promotes the efficient T cell reconstitution by the HSPCs immigration	GSE190921	Transcriptome Analysis	T cells are essentially involved in safeguarding homeostasis through fighting against the pathogens and malignant cells. T cell immunodeficiency especially their perturbation in the severe infection irradiation chemotherapy and thymic atrophy in ageing is detrimental. Therefore strategies that enhance T cell reconstitution provide considerable benefit and warrant intensive investigation. Here we constructed a T cells ablation model in Tgcoro1a:DenNTR zebrafish via administrating a proper volume of metronidazole MTZ. T cells completely recovered at 6.5 days post treatment dpt. The nascent regenerated T cells were mainly derived from the immigration of hematopoietic stem/progenitor cells HSPCs in the kidney the functional homologue of BM. cxcr4b but not ccr9 nor ccr7 was drastically unregulated in the responsive HSPCs. Functional interference of CXCR4 via both genetic and chemical assays yielded limited influence in T lymphopoiesis but notably delayed T cells regeneration by a destroyed HSPCs migration. In contrast hematopoietic providing cxcr4b in Tg:coro1a:cxcr4b accelerates thymus replenishment of HSPCs. Correspondingly Cxcl12b the ligand of Cxcr4 exhibited impressive increment presentation in the thymic epithelial cells of injured animals. Interfering or overacting Cxcl12b in either cxcl12b / mutants or Tghsp70:cxcl12b recapitulated the similarly compromised or promoted T cells recovery as that seen in Cxcr4b scenario. Therefore CXCR4 CXCL12 axis plays a crucial role in promoting thymocyte reconstitution but did not influence T cell development. Our study discloses a special role of CXCR4 CXCL12 signaling in promoting T cells recovery and provides a promising target to mitigate T cell immunodeficiency. Overall design: 6 Smart seq data of kidney hematopoietic cells in DMSO and MTZ treated zebrafish	pubmed:35483564	MTZ treated zebrafish larval kiney hematopoietic cells rep2	GSM5734068	source name:kidney hematopoietic cells\|genotype:WT\|tissue:kidney\|age:3.5 dpt/9 dpf	MTZ treated zebrafish larval kiney hematopoietic cells rep2	Illumina NovaSeq 6000 software used for basecalling. Raw reads used FASTP for quality control to filter low quality data. Then the clean reads were aligned to the GRCz119 genome assembly using HISAT2 Genome build: GRCz11	kidney hematopoietic cells		The cells in the 3.5 dpt kidney of DMSO or MTZ groups were labeled by red color via irradiating Tgcoro1a:DenNTR transgenic larvae by a 405 nm laser in an LSM880 confocal microscope for 30 seconds. post photoconversion approximately eighty zebrafish larvae were collected mixed dissected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was re suspended in PBS followed by cell sorting using flow cytometry Moflo XDP Beckman. A cDNA library was generated from fifty red Dendra2+ cells by using the Smart seq2 protocol.		genotype:WT\|tissue:kidney\|age:3.5 dpt/9 dpf	GSM5734068	GSM5734068: MTZ treated zebrafish larval kiney hematopoietic cells rep2; Danio rerio; RNA Seq	GSM5734068		1	The cells in the 3.5 dpt kidney of DMSO or MTZ groups were labeled by red color via irradiating Tgcoro1a:DenNTR transgenic larvae by a 405 nm laser in an LSM880 confocal microscope for 30 seconds. post photoconversion approximately eighty zebrafish larvae were collected mixed dissected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was re suspended in PBS followed by cell sorting using flow cytometry Moflo XDP Beckman. A cDNA library was generated from fifty red Dendra2+ cells by using the Smart seq2 protocol.	GEO Accession:GSM5734068	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351293	loader:fastq load.py	MTZ_2_1.fq.gz MTZ_2_2.fq.gz	fastq fastq	11346292500.0	37820975.0	GSM5734068 r1	0:150 1:150	A:3231427552;C:2430960232;G:2466455686;T:3217389193;N:59837	150	150	3231427552	2430960232	2466455686	3217389193	59837	SRX13438134	SRS11337556	SRA1345009	GEO	Lili laboratory, southwest university	2	0.90152	0.90146	0.14685	0.14727	0.82351	0.82325	0.45812	0.44937	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2021-12-14	Larval	Larval	Kidney	Renal System
67668	67668	SRR17259776	SRX13438133	SRS11337555	SRP351293	PRJNA788929	CXCR4 CXCL12 axis promotes the efficient T cell reconstitution by the HSPCs immigration	GSE190921	Transcriptome Analysis	T cells are essentially involved in safeguarding homeostasis through fighting against the pathogens and malignant cells. T cell immunodeficiency especially their perturbation in the severe infection irradiation chemotherapy and thymic atrophy in ageing is detrimental. Therefore strategies that enhance T cell reconstitution provide considerable benefit and warrant intensive investigation. Here we constructed a T cells ablation model in Tgcoro1a:DenNTR zebrafish via administrating a proper volume of metronidazole MTZ. T cells completely recovered at 6.5 days post treatment dpt. The nascent regenerated T cells were mainly derived from the immigration of hematopoietic stem/progenitor cells HSPCs in the kidney the functional homologue of BM. cxcr4b but not ccr9 nor ccr7 was drastically unregulated in the responsive HSPCs. Functional interference of CXCR4 via both genetic and chemical assays yielded limited influence in T lymphopoiesis but notably delayed T cells regeneration by a destroyed HSPCs migration. In contrast hematopoietic providing cxcr4b in Tg:coro1a:cxcr4b accelerates thymus replenishment of HSPCs. Correspondingly Cxcl12b the ligand of Cxcr4 exhibited impressive increment presentation in the thymic epithelial cells of injured animals. Interfering or overacting Cxcl12b in either cxcl12b / mutants or Tghsp70:cxcl12b recapitulated the similarly compromised or promoted T cells recovery as that seen in Cxcr4b scenario. Therefore CXCR4 CXCL12 axis plays a crucial role in promoting thymocyte reconstitution but did not influence T cell development. Our study discloses a special role of CXCR4 CXCL12 signaling in promoting T cells recovery and provides a promising target to mitigate T cell immunodeficiency. Overall design: 6 Smart seq data of kidney hematopoietic cells in DMSO and MTZ treated zebrafish	pubmed:35483564	MTZ treated zebrafish larval kiney hematopoietic cells rep1	GSM5734067	source name:kidney hematopoietic cells\|genotype:WT\|tissue:kidney\|age:3.5 dpt/9 dpf	MTZ treated zebrafish larval kiney hematopoietic cells rep1	Illumina NovaSeq 6000 software used for basecalling. Raw reads used FASTP for quality control to filter low quality data. Then the clean reads were aligned to the GRCz119 genome assembly using HISAT2 Genome build: GRCz11	kidney hematopoietic cells		The cells in the 3.5 dpt kidney of DMSO or MTZ groups were labeled by red color via irradiating Tgcoro1a:DenNTR transgenic larvae by a 405 nm laser in an LSM880 confocal microscope for 30 seconds. post photoconversion approximately eighty zebrafish larvae were collected mixed dissected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was re suspended in PBS followed by cell sorting using flow cytometry Moflo XDP Beckman. A cDNA library was generated from fifty red Dendra2+ cells by using the Smart seq2 protocol.		genotype:WT\|tissue:kidney\|age:3.5 dpt/9 dpf	GSM5734067	GSM5734067: MTZ treated zebrafish larval kiney hematopoietic cells rep1; Danio rerio; RNA Seq	GSM5734067		1	The cells in the 3.5 dpt kidney of DMSO or MTZ groups were labeled by red color via irradiating Tgcoro1a:DenNTR transgenic larvae by a 405 nm laser in an LSM880 confocal microscope for 30 seconds. post photoconversion approximately eighty zebrafish larvae were collected mixed dissected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was re suspended in PBS followed by cell sorting using flow cytometry Moflo XDP Beckman. A cDNA library was generated from fifty red Dendra2+ cells by using the Smart seq2 protocol.	GEO Accession:GSM5734067	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351293	loader:fastq load.py	MTZ_1_1.fq.gz MTZ_1_2.fq.gz	fastq fastq	11932352400.0	39774508.0	GSM5734067 r1	0:150 1:150	A:3365811963;C:2585455457;G:2645069810;T:3335951861;N:63309	150	150	3365811963	2585455457	2645069810	3335951861	63309	SRX13438133	SRS11337555	SRA1345009	GEO	Lili laboratory, southwest university	2	0.92022	0.92145	0.12712	0.12767	0.80977	0.80943	0.46384	0.47092	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2021-12-14	Larval	Larval	Kidney	Renal System
67669	67669	SRR17259775	SRX13438132	SRS11337553	SRP351293	PRJNA788929	CXCR4 CXCL12 axis promotes the efficient T cell reconstitution by the HSPCs immigration	GSE190921	Transcriptome Analysis	T cells are essentially involved in safeguarding homeostasis through fighting against the pathogens and malignant cells. T cell immunodeficiency especially their perturbation in the severe infection irradiation chemotherapy and thymic atrophy in ageing is detrimental. Therefore strategies that enhance T cell reconstitution provide considerable benefit and warrant intensive investigation. Here we constructed a T cells ablation model in Tgcoro1a:DenNTR zebrafish via administrating a proper volume of metronidazole MTZ. T cells completely recovered at 6.5 days post treatment dpt. The nascent regenerated T cells were mainly derived from the immigration of hematopoietic stem/progenitor cells HSPCs in the kidney the functional homologue of BM. cxcr4b but not ccr9 nor ccr7 was drastically unregulated in the responsive HSPCs. Functional interference of CXCR4 via both genetic and chemical assays yielded limited influence in T lymphopoiesis but notably delayed T cells regeneration by a destroyed HSPCs migration. In contrast hematopoietic providing cxcr4b in Tg:coro1a:cxcr4b accelerates thymus replenishment of HSPCs. Correspondingly Cxcl12b the ligand of Cxcr4 exhibited impressive increment presentation in the thymic epithelial cells of injured animals. Interfering or overacting Cxcl12b in either cxcl12b / mutants or Tghsp70:cxcl12b recapitulated the similarly compromised or promoted T cells recovery as that seen in Cxcr4b scenario. Therefore CXCR4 CXCL12 axis plays a crucial role in promoting thymocyte reconstitution but did not influence T cell development. Our study discloses a special role of CXCR4 CXCL12 signaling in promoting T cells recovery and provides a promising target to mitigate T cell immunodeficiency. Overall design: 6 Smart seq data of kidney hematopoietic cells in DMSO and MTZ treated zebrafish	pubmed:35483564	DMSO treated zebrafish larval kiney hematopoietic cells rep3	GSM5734066	source name:kidney hematopoietic cells\|genotype:WT\|tissue:kidney\|age:3.5 dpt/9 dpf	DMSO treated zebrafish larval kiney hematopoietic cells rep3	Illumina NovaSeq 6000 software used for basecalling. Raw reads used FASTP for quality control to filter low quality data. Then the clean reads were aligned to the GRCz119 genome assembly using HISAT2 Genome build: GRCz11	kidney hematopoietic cells		The cells in the 3.5 dpt kidney of DMSO or MTZ groups were labeled by red color via irradiating Tgcoro1a:DenNTR transgenic larvae by a 405 nm laser in an LSM880 confocal microscope for 30 seconds. post photoconversion approximately eighty zebrafish larvae were collected mixed dissected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was re suspended in PBS followed by cell sorting using flow cytometry Moflo XDP Beckman. A cDNA library was generated from fifty red Dendra2+ cells by using the Smart seq2 protocol.		genotype:WT\|tissue:kidney\|age:3.5 dpt/9 dpf	GSM5734066	GSM5734066: DMSO treated zebrafish larval kiney hematopoietic cells rep3; Danio rerio; RNA Seq	GSM5734066		1	The cells in the 3.5 dpt kidney of DMSO or MTZ groups were labeled by red color via irradiating Tgcoro1a:DenNTR transgenic larvae by a 405 nm laser in an LSM880 confocal microscope for 30 seconds. post photoconversion approximately eighty zebrafish larvae were collected mixed dissected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was re suspended in PBS followed by cell sorting using flow cytometry Moflo XDP Beckman. A cDNA library was generated from fifty red Dendra2+ cells by using the Smart seq2 protocol.	GEO Accession:GSM5734066	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351293	loader:fastq load.py	DMSO-3_1.fq.gz DMSO-3_2.fq.gz	fastq fastq	11408306700.0	38027689.0	GSM5734066 r1	0:150 1:150	A:3247281964;C:2443184752;G:2483245163;T:3234534644;N:60177	150	150	3247281964	2443184752	2483245163	3234534644	60177	SRX13438132	SRS11337553	SRA1345009	GEO	Lili laboratory, southwest university	2	0.85938	0.85997	0.14372	0.14405	0.81406	0.8145	0.54289	0.54626	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2021-12-14	Larval	Larval	Kidney	Renal System
67670	67670	SRR17259774	SRX13438131	SRS11337554	SRP351293	PRJNA788929	CXCR4 CXCL12 axis promotes the efficient T cell reconstitution by the HSPCs immigration	GSE190921	Transcriptome Analysis	T cells are essentially involved in safeguarding homeostasis through fighting against the pathogens and malignant cells. T cell immunodeficiency especially their perturbation in the severe infection irradiation chemotherapy and thymic atrophy in ageing is detrimental. Therefore strategies that enhance T cell reconstitution provide considerable benefit and warrant intensive investigation. Here we constructed a T cells ablation model in Tgcoro1a:DenNTR zebrafish via administrating a proper volume of metronidazole MTZ. T cells completely recovered at 6.5 days post treatment dpt. The nascent regenerated T cells were mainly derived from the immigration of hematopoietic stem/progenitor cells HSPCs in the kidney the functional homologue of BM. cxcr4b but not ccr9 nor ccr7 was drastically unregulated in the responsive HSPCs. Functional interference of CXCR4 via both genetic and chemical assays yielded limited influence in T lymphopoiesis but notably delayed T cells regeneration by a destroyed HSPCs migration. In contrast hematopoietic providing cxcr4b in Tg:coro1a:cxcr4b accelerates thymus replenishment of HSPCs. Correspondingly Cxcl12b the ligand of Cxcr4 exhibited impressive increment presentation in the thymic epithelial cells of injured animals. Interfering or overacting Cxcl12b in either cxcl12b / mutants or Tghsp70:cxcl12b recapitulated the similarly compromised or promoted T cells recovery as that seen in Cxcr4b scenario. Therefore CXCR4 CXCL12 axis plays a crucial role in promoting thymocyte reconstitution but did not influence T cell development. Our study discloses a special role of CXCR4 CXCL12 signaling in promoting T cells recovery and provides a promising target to mitigate T cell immunodeficiency. Overall design: 6 Smart seq data of kidney hematopoietic cells in DMSO and MTZ treated zebrafish	pubmed:35483564	DMSO treated zebrafish larval kiney hematopoietic cells rep2	GSM5734065	source name:kidney hematopoietic cells\|genotype:WT\|tissue:kidney\|age:3.5 dpt/9 dpf	DMSO treated zebrafish larval kiney hematopoietic cells rep2	Illumina NovaSeq 6000 software used for basecalling. Raw reads used FASTP for quality control to filter low quality data. Then the clean reads were aligned to the GRCz119 genome assembly using HISAT2 Genome build: GRCz11	kidney hematopoietic cells		The cells in the 3.5 dpt kidney of DMSO or MTZ groups were labeled by red color via irradiating Tgcoro1a:DenNTR transgenic larvae by a 405 nm laser in an LSM880 confocal microscope for 30 seconds. post photoconversion approximately eighty zebrafish larvae were collected mixed dissected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was re suspended in PBS followed by cell sorting using flow cytometry Moflo XDP Beckman. A cDNA library was generated from fifty red Dendra2+ cells by using the Smart seq2 protocol.		genotype:WT\|tissue:kidney\|age:3.5 dpt/9 dpf	GSM5734065	GSM5734065: DMSO treated zebrafish larval kiney hematopoietic cells rep2; Danio rerio; RNA Seq	GSM5734065		1	The cells in the 3.5 dpt kidney of DMSO or MTZ groups were labeled by red color via irradiating Tgcoro1a:DenNTR transgenic larvae by a 405 nm laser in an LSM880 confocal microscope for 30 seconds. post photoconversion approximately eighty zebrafish larvae were collected mixed dissected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was re suspended in PBS followed by cell sorting using flow cytometry Moflo XDP Beckman. A cDNA library was generated from fifty red Dendra2+ cells by using the Smart seq2 protocol.	GEO Accession:GSM5734065	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351293	loader:fastq load.py	DMSO-2_1.fq.gz DMSO-2_2.fq.gz	fastq fastq	11556992700.0	38523309.0	GSM5734065 r1	0:150 1:150	A:3286230684;C:2481190727;G:2527388699;T:3262121371;N:61219	150	150	3286230684	2481190727	2527388699	3262121371	61219	SRX13438131	SRS11337554	SRA1345009	GEO	Lili laboratory, southwest university	2	0.89912	0.8983	0.14258	0.14322	0.81341	0.81408	0.5562	0.55202	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2021-12-14	Larval	Larval	Kidney	Renal System
67671	67671	SRR17259773	SRX13438130	SRS11337552	SRP351293	PRJNA788929	CXCR4 CXCL12 axis promotes the efficient T cell reconstitution by the HSPCs immigration	GSE190921	Transcriptome Analysis	T cells are essentially involved in safeguarding homeostasis through fighting against the pathogens and malignant cells. T cell immunodeficiency especially their perturbation in the severe infection irradiation chemotherapy and thymic atrophy in ageing is detrimental. Therefore strategies that enhance T cell reconstitution provide considerable benefit and warrant intensive investigation. Here we constructed a T cells ablation model in Tgcoro1a:DenNTR zebrafish via administrating a proper volume of metronidazole MTZ. T cells completely recovered at 6.5 days post treatment dpt. The nascent regenerated T cells were mainly derived from the immigration of hematopoietic stem/progenitor cells HSPCs in the kidney the functional homologue of BM. cxcr4b but not ccr9 nor ccr7 was drastically unregulated in the responsive HSPCs. Functional interference of CXCR4 via both genetic and chemical assays yielded limited influence in T lymphopoiesis but notably delayed T cells regeneration by a destroyed HSPCs migration. In contrast hematopoietic providing cxcr4b in Tg:coro1a:cxcr4b accelerates thymus replenishment of HSPCs. Correspondingly Cxcl12b the ligand of Cxcr4 exhibited impressive increment presentation in the thymic epithelial cells of injured animals. Interfering or overacting Cxcl12b in either cxcl12b / mutants or Tghsp70:cxcl12b recapitulated the similarly compromised or promoted T cells recovery as that seen in Cxcr4b scenario. Therefore CXCR4 CXCL12 axis plays a crucial role in promoting thymocyte reconstitution but did not influence T cell development. Our study discloses a special role of CXCR4 CXCL12 signaling in promoting T cells recovery and provides a promising target to mitigate T cell immunodeficiency. Overall design: 6 Smart seq data of kidney hematopoietic cells in DMSO and MTZ treated zebrafish	pubmed:35483564	DMSO treated zebrafish larval kiney hematopoietic cells rep1	GSM5734064	source name:kidney hematopoietic cells\|genotype:WT\|tissue:kidney\|age:3.5 dpt/9 dpf	DMSO treated zebrafish larval kiney hematopoietic cells rep1	Illumina NovaSeq 6000 software used for basecalling. Raw reads used FASTP for quality control to filter low quality data. Then the clean reads were aligned to the GRCz119 genome assembly using HISAT2 Genome build: GRCz11	kidney hematopoietic cells		The cells in the 3.5 dpt kidney of DMSO or MTZ groups were labeled by red color via irradiating Tgcoro1a:DenNTR transgenic larvae by a 405 nm laser in an LSM880 confocal microscope for 30 seconds. post photoconversion approximately eighty zebrafish larvae were collected mixed dissected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was re suspended in PBS followed by cell sorting using flow cytometry Moflo XDP Beckman. A cDNA library was generated from fifty red Dendra2+ cells by using the Smart seq2 protocol.		genotype:WT\|tissue:kidney\|age:3.5 dpt/9 dpf	GSM5734064	GSM5734064: DMSO treated zebrafish larval kiney hematopoietic cells rep1; Danio rerio; RNA Seq	GSM5734064		1	The cells in the 3.5 dpt kidney of DMSO or MTZ groups were labeled by red color via irradiating Tgcoro1a:DenNTR transgenic larvae by a 405 nm laser in an LSM880 confocal microscope for 30 seconds. post photoconversion approximately eighty zebrafish larvae were collected mixed dissected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was re suspended in PBS followed by cell sorting using flow cytometry Moflo XDP Beckman. A cDNA library was generated from fifty red Dendra2+ cells by using the Smart seq2 protocol.	GEO Accession:GSM5734064	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP351293	loader:fastq load.py	DMSO-1_1.fq.gz DMSO-1_2.fq.gz	fastq fastq	11201034000.0	37336780.0	GSM5734064 r1	0:150 1:150	A:3116600998;C:2476477366;G:2517609773;T:3090286042;N:59821	150	150	3116600998	2476477366	2517609773	3090286042	59821	SRX13438130	SRS11337552	SRA1345009	GEO	Lili laboratory, southwest university	2	0.79346	0.79439	0.12785	0.12859	0.81917	0.81962	0.53832	0.5416	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2021-12-14	Larval	Larval	Kidney	Renal System
68121	68121	SRR17606004	SRX13774802	SRS11654800	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	CEN Homo Kidney RNAseq rep3	GSM5815265	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:CEN homozygous knockout\|treatment:cardiomyocyte ablation	CEN Homo Kidney RNAseq rep3	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:CEN homozygous knockout\|treatment:cardiomyocyte ablation	GSM5815265	GSM5815265: CEN Homo Kidney RNAseq rep3; Danio rerio; RNA Seq	GSM5815265 r1	GSM5815265	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915		CENHOMO3_2.fq.gz CENHOMO3_1.fq.gz	fastq fastq	7215517200.0	72155172.0	GSM5815265 r1	0:100 1:100	A:1927134950;C:1661322135;G:1683841967;T:1943218148;N:0	100	100	1927134950	1661322135	1683841967	1943218148	0	SRX13774802	SRS11654800	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.94062		0.07183		0.72596		0.55426		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68122	68122	SRR17606005	SRX13774801	SRS11654799	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	CEN Homo Kidney RNAseq rep2	GSM5815264	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:CEN homozygous knockout\|treatment:cardiomyocyte ablation	CEN Homo Kidney RNAseq rep2	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:CEN homozygous knockout\|treatment:cardiomyocyte ablation	GSM5815264	GSM5815264: CEN Homo Kidney RNAseq rep2; Danio rerio; RNA Seq	GSM5815264 r1	GSM5815264	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915		CENHOMO2_2.fq.gz CENHOMO2_1.fq.gz	fastq fastq	7207596800.0	72075968.0	GSM5815264 r1	0:100 1:100	A:1913835378;C:1670319627;G:1686651138;T:1936790657;N:0	100	100	1913835378	1670319627	1686651138	1936790657	0	SRX13774801	SRS11654799	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.94306		0.06924		0.72376		0.56145		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68123	68123	SRR17606006	SRX13774800	SRS11654798	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	CEN Homo Kidney RNAseq rep1	GSM5815263	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:CEN homozygous knockout\|treatment:cardiomyocyte ablation	CEN Homo Kidney RNAseq rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:CEN homozygous knockout\|treatment:cardiomyocyte ablation	GSM5815263	GSM5815263: CEN Homo Kidney RNAseq rep1; Danio rerio; RNA Seq	GSM5815263 r1	GSM5815263	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915		CENHOMO1_1.fq.gz CENHOMO1_2.fq.gz	fastq fastq	7204062600.0	72040626.0	GSM5815263 r1	0:100 1:100	A:1902216192;C:1680493255;G:1696367176;T:1924985977;N:0	100	100	1902216192	1680493255	1696367176	1924985977	0	SRX13774800	SRS11654798	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.9408		0.06772		0.71545		0.53936		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68124	68124	SRR17606007	SRX13774799	SRS11654797	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	CEN WT Kidney RNAseq rep3	GSM5815262	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	CEN WT Kidney RNAseq rep3	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	GSM5815262	GSM5815262: CEN WT Kidney RNAseq rep3; Danio rerio; RNA Seq	GSM5815262 r1	GSM5815262	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915		CENWT3_2.fq.gz CENWT3_1.fq.gz	fastq fastq	7205589000.0	72055890.0	GSM5815262 r1	0:100 1:100	A:1892937448;C:1690826558;G:1711136694;T:1910688300;N:0	100	100	1892937448	1690826558	1711136694	1910688300	0	SRX13774799	SRS11654797	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.94358		0.06548		0.72336		0.54655		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68125	68125	SRR17606008	SRX13774798	SRS11654796	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	CEN WT Kidney RNAseq rep2	GSM5815261	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	CEN WT Kidney RNAseq rep2	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	GSM5815261	GSM5815261: CEN WT Kidney RNAseq rep2; Danio rerio; RNA Seq	GSM5815261 r1	GSM5815261	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915		CENWT2_1.fq.gz CENWT2_2.fq.gz	fastq fastq	7219678800.0	72196788.0	GSM5815261 r1	0:100 1:100	A:1908750065;C:1680876268;G:1700533938;T:1929518529;N:0	100	100	1908750065	1680876268	1700533938	1929518529	0	SRX13774798	SRS11654796	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.94561		0.06821		0.71792		0.54803		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68126	68126	SRR17606009	SRX13774797	SRS11654795	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	CEN WT Kidney RNAseq rep1	GSM5815260	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	CEN WT Kidney RNAseq rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	GSM5815260	GSM5815260: CEN WT Kidney RNAseq rep1; Danio rerio; RNA Seq	GSM5815260 r1	GSM5815260	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915		CENWT1_1.fq.gz CENWT1_2.fq.gz	fastq fastq	7213577400.0	72135774.0	GSM5815260 r1	0:100 1:100	A:1899760333;C:1688268609;G:1705140400;T:1920408058;N:0	100	100	1899760333	1688268609	1705140400	1920408058	0	SRX13774797	SRS11654795	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.94364		0.06593		0.71796		0.55315		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68127	68127	SRR17606010	SRX13774796	SRS11654794	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	cebpd Homo Kidney RNAseq rep3	GSM5815259	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:cebpd homozygous knockout\|treatment:cardiomyocyte ablation	cebpd Homo Kidney RNAseq rep3	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:cebpd homozygous knockout\|treatment:cardiomyocyte ablation	GSM5815259	GSM5815259: cebpd Homo Kidney RNAseq rep3; Danio rerio; RNA Seq	GSM5815259 r1	GSM5815259	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915		cebpdHomo3_1.fq.gz cebpdHomo3_2.fq.gz	fastq fastq	7279069400.0	72790694.0	GSM5815259 r1	0:100 1:100	A:1930406096;C:1690658505;G:1705808112;T:1952196687;N:0	100	100	1930406096	1690658505	1705808112	1952196687	0	SRX13774796	SRS11654794	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.94225		0.05895		0.74353		0.55835		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68128	68128	SRR17606011	SRX13774795	SRS11654793	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	cebpd Homo Kidney RNAseq rep2	GSM5815258	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:cebpd homozygous knockout\|treatment:cardiomyocyte ablation	cebpd Homo Kidney RNAseq rep2	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:cebpd homozygous knockout\|treatment:cardiomyocyte ablation	GSM5815258	GSM5815258: cebpd Homo Kidney RNAseq rep2; Danio rerio; RNA Seq	GSM5815258 r1	GSM5815258	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915		cebpdHomo2_2.fq.gz cebpdHomo2_1.fq.gz	fastq fastq	7264240800.0	72642408.0	GSM5815258 r1	0:100 1:100	A:1907893057;C:1703728991;G:1717658793;T:1934959959;N:0	100	100	1907893057	1703728991	1717658793	1934959959	0	SRX13774795	SRS11654793	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.94566		0.06391		0.72417		0.5235		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68129	68129	SRR17606012	SRX13774794	SRS11654791	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	cebpd Homo Kidney RNAseq rep1	GSM5815257	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:cebpd homozygous knockout\|treatment:cardiomyocyte ablation	cebpd Homo Kidney RNAseq rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:cebpd homozygous knockout\|treatment:cardiomyocyte ablation	GSM5815257	GSM5815257: cebpd Homo Kidney RNAseq rep1; Danio rerio; RNA Seq	GSM5815257 r1	GSM5815257	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915		cebpdHomo1_2.fq.gz cebpdHomo1_1.fq.gz	fastq fastq	7192873200.0	71928732.0	GSM5815257 r1	0:100 1:100	A:1905599298;C:1665589905;G:1707980534;T:1913703463;N:0	100	100	1905599298	1665589905	1707980534	1913703463	0	SRX13774794	SRS11654791	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.92744		0.062		0.72393		0.55384		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68130	68130	SRR17606013	SRX13774793	SRS11654792	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	cebpd WT Kidney RNAseq rep3	GSM5815256	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	cebpd WT Kidney RNAseq rep3	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	GSM5815256	GSM5815256: cebpd WT Kidney RNAseq rep3; Danio rerio; RNA Seq	GSM5815256 r1	GSM5815256	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915		cebpdWT3_1.fq.gz cebpdWT3_2.fq.gz	fastq fastq	7280350400.0	72803504.0	GSM5815256 r1	0:100 1:100	A:1925119485;C:1698344141;G:1714885029;T:1942001745;N:0	100	100	1925119485	1698344141	1714885029	1942001745	0	SRX13774793	SRS11654792	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.94212		0.05877		0.73446		0.54431		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68131	68131	SRR17606014	SRX13774792	SRS11654802	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	cebpd WT Kidney RNAseq rep2	GSM5815255	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	cebpd WT Kidney RNAseq rep2	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	GSM5815255	GSM5815255: cebpd WT Kidney RNAseq rep2; Danio rerio; RNA Seq	GSM5815255 r1	GSM5815255	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915		cebpdWT2_1.fq.gz cebpdWT2_2.fq.gz	fastq fastq	7264980400.0	72649804.0	GSM5815255 r1	0:100 1:100	A:1953740321;C:1658035501;G:1681062257;T:1972142321;N:0	100	100	1953740321	1658035501	1681062257	1972142321	0	SRX13774792	SRS11654802	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.93531		0.06698		0.73499		0.56385		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68132	68132	SRR17606015	SRX13774791	SRS11654790	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	cebpd WT Kidney RNAseq rep1	GSM5815254	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	cebpd WT Kidney RNAseq rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	GSM5815254	GSM5815254: cebpd WT Kidney RNAseq rep1; Danio rerio; RNA Seq	GSM5815254 r1	GSM5815254	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915		cebpdWT1_1.fq.gz cebpdWT1_2.fq.gz	fastq fastq	7256843800.0	72568438.0	GSM5815254 r1	0:100 1:100	A:1920544243;C:1687420610;G:1707252526;T:1941626421;N:0	100	100	1920544243	1687420610	1707252526	1941626421	0	SRX13774791	SRS11654790	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.94388		0.06494		0.7265		0.54419		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
69454	69454	SRR21377195	SRX17382862	SRS14941934	SRP369366	PRJNA825466	The transcriptome profiling analysis of intestines and kidneys in conventionally raised CV and germ free GF wild type zebrafish embryos	GSE200577	Transcriptome Analysis	To investigate how the zebrafish embryos respond to the absence of the microbiota the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32 948 cDNAs of the zebrafish genome assembly were annotated post reads mapping for further analysis. For the 5 dpf intestinal tissue samples 948 genes 4% of the total number of genes were differentially expressed 371 genes were up regulated and 577 genes were down regulated in the GF group . For the 7 dpf kidney tissue samples 697 genes 3% of the total number of genes were differentially expressed 341 genes were up regulated and 356 genes were down regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos both in intestines at 5 dpf and in kidneys at 7 dpf. To investigate how the transcriptome changes in the chd8 / zebrafish embryos the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. Overall design: Intestinal mRNA profiles of conventionally raisedCV and germ freeGF embryos at 5 dpf and renal the location of their hematopoietic tissue mRNA profiles of CV and GF embryos at 7 dpf. Analysis of mRNA profiles of intestines at 5 dpf and renal the location of their hematopoietic tissue at 7 dpf in chd8 / embryos and comparing the data with those from the wildtype embryos.		7d chd8 / zebrafish rep3	GSM6532689	source name:kidney\|strain:AB\|tissue:kidney\|age:7 dpf /	7d chd8 / zebrafish rep3	Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim galore version 0.6.7 for subsequent analysis with parameters phred33 q 20 length 15 stringency 3 fastqc max n 3 The processed datas have been mapped to Danio rerio.GRCz11 whole genome using STAR version 2.7.9a then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts T 6 t exon g gene id Assembly: GRCz11 Supplementary files format and content: Table with raw gene counts for every gene and every sample	kidney	40 chd8 / zebrafish embryos at 5 dpf were collected and anesthetized in 0.4% 4g/L tricane. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo and samples were storaged at 4℃ for more than 24h. The intestines were removed and collected by tweezers under the microscope and the isolated tissue was then transfered into Trizol. About 70 chd8 / zebrafish embryos at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane. Then the media were replaced with RNAlater RNA Solution and samples were storaged at 4℃ for more than 24h. Their kidneys were removed by tweezers under the microscope. Then the tissues were immersed in Trizol and the RNA of them were extracted as previously described for intestine tissues.	Intestines and kidneys were removed immerse the tissues in Trizol reagent immediately flash frozen in 80℃ and RNA was harvested following the manual of the Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	The parent adult zebrafish are placed in pair mating tanks with dividers separating males and females the postnoon or evening prior to mating Day 1. At the start of the light cycle the following morning day x the parents were transferred to new clean pair mating tanks with fish feeding circulation system water and allowed to mate for no more than 1 hour. Fertilized eggs were transfered into petri dishes less than 100 embryos per dish with embryo media. Then all of the embryos are incubated at 28.5℃ until the 5 dpf or 7 dpf. Embryo media:1L ddH2O with 10 ml stock solution A 1 mL stock solution B 10 mL stock solution C 10 mL stock solution D and 10 mL stock solution E adjust pH to 7.2 with 1 M HCl.A: 250 mL RO H2O 20 g NaCl 1 g KCl;B: 100 mL RO H2O 0.358 g Na2HPO4 anhydrous 0.6 g KH2PO4 monobasic;C: 250 mL RO H2O 4.68 g CaCl2 dihydrate;D: 250 mL RO H2O 6.15 g MgSO4·7H2O;E: 250 mL RO H2O 8.75 g NaHCO3. System water:purified water with sea salt and NaHCO3，conductivity 450 500 μs/cm，pH 7.0±0.2.	strain:AB\|tissue:kidney\|age:7 dpf /	GSM6532689	GSM6532689: 7d chd8 / zebrafish rep3; Danio rerio; RNA Seq	GSM6532689 r1	GSM6532689	1	Intestines and kidneys were removed immerse the tissues in Trizol reagent immediately flash frozen in 80℃ and RNA was harvested following the manual of the Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP369366		7d_chd8_3.fq.gz	fastq	5703645600.0	19012152.0	GSM6532689 r1	0:150 1:150	A:1472893141;C:1378744688;G:1384835454;T:1466499737;N:672580	150	150	1472893141	1378744688	1384835454	1466499737	672580	SRX17382862	SRS14941934			Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University	2	0.96656	0.96614	0.06713	0.06541	0.71451	0.71713	0.47578	0.47388	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-08-31	Larval	Larval	Kidney	Renal System
69455	69455	SRR21377196	SRX17382861	SRS14941973	SRP369366	PRJNA825466	The transcriptome profiling analysis of intestines and kidneys in conventionally raised CV and germ free GF wild type zebrafish embryos	GSE200577	Transcriptome Analysis	To investigate how the zebrafish embryos respond to the absence of the microbiota the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32 948 cDNAs of the zebrafish genome assembly were annotated post reads mapping for further analysis. For the 5 dpf intestinal tissue samples 948 genes 4% of the total number of genes were differentially expressed 371 genes were up regulated and 577 genes were down regulated in the GF group . For the 7 dpf kidney tissue samples 697 genes 3% of the total number of genes were differentially expressed 341 genes were up regulated and 356 genes were down regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos both in intestines at 5 dpf and in kidneys at 7 dpf. To investigate how the transcriptome changes in the chd8 / zebrafish embryos the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. Overall design: Intestinal mRNA profiles of conventionally raisedCV and germ freeGF embryos at 5 dpf and renal the location of their hematopoietic tissue mRNA profiles of CV and GF embryos at 7 dpf. Analysis of mRNA profiles of intestines at 5 dpf and renal the location of their hematopoietic tissue at 7 dpf in chd8 / embryos and comparing the data with those from the wildtype embryos.		7d chd8 / zebrafish rep2	GSM6532688	source name:kidney\|strain:AB\|tissue:kidney\|age:7 dpf /	7d chd8 / zebrafish rep2	Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim galore version 0.6.7 for subsequent analysis with parameters phred33 q 20 length 15 stringency 3 fastqc max n 3 The processed datas have been mapped to Danio rerio.GRCz11 whole genome using STAR version 2.7.9a then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts T 6 t exon g gene id Assembly: GRCz11 Supplementary files format and content: Table with raw gene counts for every gene and every sample	kidney	40 chd8 / zebrafish embryos at 5 dpf were collected and anesthetized in 0.4% 4g/L tricane. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo and samples were storaged at 4℃ for more than 24h. The intestines were removed and collected by tweezers under the microscope and the isolated tissue was then transfered into Trizol. About 70 chd8 / zebrafish embryos at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane. Then the media were replaced with RNAlater RNA Solution and samples were storaged at 4℃ for more than 24h. Their kidneys were removed by tweezers under the microscope. Then the tissues were immersed in Trizol and the RNA of them were extracted as previously described for intestine tissues.	Intestines and kidneys were removed immerse the tissues in Trizol reagent immediately flash frozen in 80℃ and RNA was harvested following the manual of the Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	The parent adult zebrafish are placed in pair mating tanks with dividers separating males and females the postnoon or evening prior to mating Day 1. At the start of the light cycle the following morning day x the parents were transferred to new clean pair mating tanks with fish feeding circulation system water and allowed to mate for no more than 1 hour. Fertilized eggs were transfered into petri dishes less than 100 embryos per dish with embryo media. Then all of the embryos are incubated at 28.5℃ until the 5 dpf or 7 dpf. Embryo media:1L ddH2O with 10 ml stock solution A 1 mL stock solution B 10 mL stock solution C 10 mL stock solution D and 10 mL stock solution E adjust pH to 7.2 with 1 M HCl.A: 250 mL RO H2O 20 g NaCl 1 g KCl;B: 100 mL RO H2O 0.358 g Na2HPO4 anhydrous 0.6 g KH2PO4 monobasic;C: 250 mL RO H2O 4.68 g CaCl2 dihydrate;D: 250 mL RO H2O 6.15 g MgSO4·7H2O;E: 250 mL RO H2O 8.75 g NaHCO3. System water:purified water with sea salt and NaHCO3，conductivity 450 500 μs/cm，pH 7.0±0.2.	strain:AB\|tissue:kidney\|age:7 dpf /	GSM6532688	GSM6532688: 7d chd8 / zebrafish rep2; Danio rerio; RNA Seq	GSM6532688 r1	GSM6532688	1	Intestines and kidneys were removed immerse the tissues in Trizol reagent immediately flash frozen in 80℃ and RNA was harvested following the manual of the Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP369366		7d_chd8_2.fq.gz	fastq	5791321500.0	19304405.0	GSM6532688 r1	0:150 1:150	A:1504780584;C:1391586880;G:1405013206;T:1489820370;N:120460	150	150	1504780584	1391586880	1405013206	1489820370	120460	SRX17382861	SRS14941973			Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University	2	0.95947	0.95202	0.07494	0.07307	0.71074	0.71163	0.45745	0.44001	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-08-31	Larval	Larval	Kidney	Renal System
69456	69456	SRR21377197	SRX17382860	SRS14941972	SRP369366	PRJNA825466	The transcriptome profiling analysis of intestines and kidneys in conventionally raised CV and germ free GF wild type zebrafish embryos	GSE200577	Transcriptome Analysis	To investigate how the zebrafish embryos respond to the absence of the microbiota the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32 948 cDNAs of the zebrafish genome assembly were annotated post reads mapping for further analysis. For the 5 dpf intestinal tissue samples 948 genes 4% of the total number of genes were differentially expressed 371 genes were up regulated and 577 genes were down regulated in the GF group . For the 7 dpf kidney tissue samples 697 genes 3% of the total number of genes were differentially expressed 341 genes were up regulated and 356 genes were down regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos both in intestines at 5 dpf and in kidneys at 7 dpf. To investigate how the transcriptome changes in the chd8 / zebrafish embryos the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. Overall design: Intestinal mRNA profiles of conventionally raisedCV and germ freeGF embryos at 5 dpf and renal the location of their hematopoietic tissue mRNA profiles of CV and GF embryos at 7 dpf. Analysis of mRNA profiles of intestines at 5 dpf and renal the location of their hematopoietic tissue at 7 dpf in chd8 / embryos and comparing the data with those from the wildtype embryos.		7d chd8 / zebrafish rep1	GSM6532687	source name:kidney\|strain:AB\|tissue:kidney\|age:7 dpf /	7d chd8 / zebrafish rep1	Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim galore version 0.6.7 for subsequent analysis with parameters phred33 q 20 length 15 stringency 3 fastqc max n 3 The processed datas have been mapped to Danio rerio.GRCz11 whole genome using STAR version 2.7.9a then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts T 6 t exon g gene id Assembly: GRCz11 Supplementary files format and content: Table with raw gene counts for every gene and every sample	kidney	40 chd8 / zebrafish embryos at 5 dpf were collected and anesthetized in 0.4% 4g/L tricane. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo and samples were storaged at 4℃ for more than 24h. The intestines were removed and collected by tweezers under the microscope and the isolated tissue was then transfered into Trizol. About 70 chd8 / zebrafish embryos at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane. Then the media were replaced with RNAlater RNA Solution and samples were storaged at 4℃ for more than 24h. Their kidneys were removed by tweezers under the microscope. Then the tissues were immersed in Trizol and the RNA of them were extracted as previously described for intestine tissues.	Intestines and kidneys were removed immerse the tissues in Trizol reagent immediately flash frozen in 80℃ and RNA was harvested following the manual of the Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	The parent adult zebrafish are placed in pair mating tanks with dividers separating males and females the postnoon or evening prior to mating Day 1. At the start of the light cycle the following morning day x the parents were transferred to new clean pair mating tanks with fish feeding circulation system water and allowed to mate for no more than 1 hour. Fertilized eggs were transfered into petri dishes less than 100 embryos per dish with embryo media. Then all of the embryos are incubated at 28.5℃ until the 5 dpf or 7 dpf. Embryo media:1L ddH2O with 10 ml stock solution A 1 mL stock solution B 10 mL stock solution C 10 mL stock solution D and 10 mL stock solution E adjust pH to 7.2 with 1 M HCl.A: 250 mL RO H2O 20 g NaCl 1 g KCl;B: 100 mL RO H2O 0.358 g Na2HPO4 anhydrous 0.6 g KH2PO4 monobasic;C: 250 mL RO H2O 4.68 g CaCl2 dihydrate;D: 250 mL RO H2O 6.15 g MgSO4·7H2O;E: 250 mL RO H2O 8.75 g NaHCO3. System water:purified water with sea salt and NaHCO3，conductivity 450 500 μs/cm，pH 7.0±0.2.	strain:AB\|tissue:kidney\|age:7 dpf /	GSM6532687	GSM6532687: 7d chd8 / zebrafish rep1; Danio rerio; RNA Seq	GSM6532687 r1	GSM6532687	1	Intestines and kidneys were removed immerse the tissues in Trizol reagent immediately flash frozen in 80℃ and RNA was harvested following the manual of the Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP369366		7d_chd8_1.fq.gz	fastq	5644382100.0	18814607.0	GSM6532687 r1	0:150 1:150	A:1422529122;C:1396709260;G:1413922498;T:1411168964;N:52256	150	150	1422529122	1396709260	1413922498	1411168964	52256	SRX17382860	SRS14941972			Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University	2	0.97204	0.96429	0.07483	0.07187	0.72064	0.72275	0.51419	0.5078	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-08-31	Larval	Larval	Kidney	Renal System
69460	69460	SRR18710063	SRX14810879	SRS12567670	SRP369366	PRJNA825466	The transcriptome profiling analysis of intestines and kidneys in conventionally raised CV and germ free GF wild type zebrafish embryos	GSE200577	Transcriptome Analysis	To investigate how the zebrafish embryos respond to the absence of the microbiota the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32 948 cDNAs of the zebrafish genome assembly were annotated post reads mapping for further analysis. For the 5 dpf intestinal tissue samples 948 genes 4% of the total number of genes were differentially expressed 371 genes were up regulated and 577 genes were down regulated in the GF group . For the 7 dpf kidney tissue samples 697 genes 3% of the total number of genes were differentially expressed 341 genes were up regulated and 356 genes were down regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos both in intestines at 5 dpf and in kidneys at 7 dpf. To investigate how the transcriptome changes in the chd8 / zebrafish embryos the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. Overall design: Intestinal mRNA profiles of conventionally raisedCV and germ freeGF embryos at 5 dpf and renal the location of their hematopoietic tissue mRNA profiles of CV and GF embryos at 7 dpf. Analysis of mRNA profiles of intestines at 5 dpf and renal the location of their hematopoietic tissue at 7 dpf in chd8 / embryos and comparing the data with those from the wildtype embryos.		7d GF zebrafish rep3	GSM6038014	source name:kidney\|strain:AB\|tissue:kidney\|age:7 dpf free	7d GF zebrafish rep3	Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim galore version 0.6.7 for subsequent analysis with parameters phred33 q 20 length 15 stringency 3 fastqc max n 3 The processed datas have been mapped to Danio rerio.GRCz11 whole genome using STAR version 2.7.9a then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts T 6 t exon g gene id Assembly: GRCz11 Supplementary files format and content: Table with raw gene counts for every gene and every sample	kidney	30 CV and GF zebrafish at 5 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo and samples were storaged at 4℃ for more than 24h.Their intestines were collected by tweezers under the microscope and the isolated intestines was then transfered into Trizol.50 CV and GF zebrafish at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Their kidneys were collected as previously described as intestines.	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	The parent adult zebrafish are placed in pair mating tanks with dividers separating males and females the postnoon or evening prior to mating Day 1. At the start of the light cycle the following morning day x the parents were transferred to new clean pair mating tanks with autoclaved system water and allowed to mate for no more than 60 min. Fertilized eggs were seperated into two groupsCV group and GF group.The CV embryos were transfered to dishes with embryo media and incubated at 28.5℃. The GF embryos subsequently washed three times with the sterile embryo media SEM and transferred to a petri dish with the filter sterilized embryo medium containing antibiotics ABEM. Healthy embryos were sorted into fresh ABEM per 2 hours less than 200 per dish and incubated for 6 h at 28.5℃. The GF zebrafish embryos were then generated as previously described Pham Kanther et al. 2008. Briefly embryos were then washed at room temperature with 0.1% polyvinylpyrrolidone for 90s followed with three times rinsing with the SEM at room temperature. post soaking in 0.003% sodium hypochlorite for 16 min at room temperature these embryos were then washed for three times with the SEM. Finally the GF embryos were transferred into plastic cell culture flasks with SEM and incubated at 28.5℃.	strain:AB\|tissue:kidney\|age:7 dpf free	GSM6038014	GSM6038014: 7d GF zebrafish rep3; Danio rerio; RNA Seq	GSM6038014 r1	GSM6038014	1	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP369366		7d_GF_3.fq.gz	fastq	5277204300.0	17590681.0	GSM6038014 r1	0:150 1:150	A:1366859942;C:1272510413;G:1282815853;T:1354917079;N:101013	150	150	1366859942	1272510413	1282815853	1354917079	101013	SRX14810879	SRS12567670			Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University	2	0.97097	0.96817	0.06893	0.06764	0.71603	0.71514	0.46915	0.46548	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-04-11	Larval	Larval	Kidney	Renal System
69461	69461	SRR18710064	SRX14810878	SRS12567669	SRP369366	PRJNA825466	The transcriptome profiling analysis of intestines and kidneys in conventionally raised CV and germ free GF wild type zebrafish embryos	GSE200577	Transcriptome Analysis	To investigate how the zebrafish embryos respond to the absence of the microbiota the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32 948 cDNAs of the zebrafish genome assembly were annotated post reads mapping for further analysis. For the 5 dpf intestinal tissue samples 948 genes 4% of the total number of genes were differentially expressed 371 genes were up regulated and 577 genes were down regulated in the GF group . For the 7 dpf kidney tissue samples 697 genes 3% of the total number of genes were differentially expressed 341 genes were up regulated and 356 genes were down regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos both in intestines at 5 dpf and in kidneys at 7 dpf. To investigate how the transcriptome changes in the chd8 / zebrafish embryos the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. Overall design: Intestinal mRNA profiles of conventionally raisedCV and germ freeGF embryos at 5 dpf and renal the location of their hematopoietic tissue mRNA profiles of CV and GF embryos at 7 dpf. Analysis of mRNA profiles of intestines at 5 dpf and renal the location of their hematopoietic tissue at 7 dpf in chd8 / embryos and comparing the data with those from the wildtype embryos.		7d GF zebrafish rep2	GSM6038013	source name:kidney\|strain:AB\|tissue:kidney\|age:7 dpf free	7d GF zebrafish rep2	Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim galore version 0.6.7 for subsequent analysis with parameters phred33 q 20 length 15 stringency 3 fastqc max n 3 The processed datas have been mapped to Danio rerio.GRCz11 whole genome using STAR version 2.7.9a then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts T 6 t exon g gene id Assembly: GRCz11 Supplementary files format and content: Table with raw gene counts for every gene and every sample	kidney	30 CV and GF zebrafish at 5 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo and samples were storaged at 4℃ for more than 24h.Their intestines were collected by tweezers under the microscope and the isolated intestines was then transfered into Trizol.50 CV and GF zebrafish at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Their kidneys were collected as previously described as intestines.	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	The parent adult zebrafish are placed in pair mating tanks with dividers separating males and females the postnoon or evening prior to mating Day 1. At the start of the light cycle the following morning day x the parents were transferred to new clean pair mating tanks with autoclaved system water and allowed to mate for no more than 60 min. Fertilized eggs were seperated into two groupsCV group and GF group.The CV embryos were transfered to dishes with embryo media and incubated at 28.5℃. The GF embryos subsequently washed three times with the sterile embryo media SEM and transferred to a petri dish with the filter sterilized embryo medium containing antibiotics ABEM. Healthy embryos were sorted into fresh ABEM per 2 hours less than 200 per dish and incubated for 6 h at 28.5℃. The GF zebrafish embryos were then generated as previously described Pham Kanther et al. 2008. Briefly embryos were then washed at room temperature with 0.1% polyvinylpyrrolidone for 90s followed with three times rinsing with the SEM at room temperature. post soaking in 0.003% sodium hypochlorite for 16 min at room temperature these embryos were then washed for three times with the SEM. Finally the GF embryos were transferred into plastic cell culture flasks with SEM and incubated at 28.5℃.	strain:AB\|tissue:kidney\|age:7 dpf free	GSM6038013	GSM6038013: 7d GF zebrafish rep2; Danio rerio; RNA Seq	GSM6038013 r1	GSM6038013	1	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP369366		7d_GF_2.fq.gz	fastq	5438226900.0	18127423.0	GSM6038013 r1	0:150 1:150	A:1415418105;C:1302388066;G:1315056110;T:1404800640;N:563979	150	150	1415418105	1302388066	1315056110	1404800640	563979	SRX14810878	SRS12567669			Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University	2	0.95347	0.95229	0.07185	0.06896	0.70674	0.70784	0.45432	0.45007	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-04-11	Larval	Larval	Kidney	Renal System
69462	69462	SRR18710065	SRX14810877	SRS12567668	SRP369366	PRJNA825466	The transcriptome profiling analysis of intestines and kidneys in conventionally raised CV and germ free GF wild type zebrafish embryos	GSE200577	Transcriptome Analysis	To investigate how the zebrafish embryos respond to the absence of the microbiota the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32 948 cDNAs of the zebrafish genome assembly were annotated post reads mapping for further analysis. For the 5 dpf intestinal tissue samples 948 genes 4% of the total number of genes were differentially expressed 371 genes were up regulated and 577 genes were down regulated in the GF group . For the 7 dpf kidney tissue samples 697 genes 3% of the total number of genes were differentially expressed 341 genes were up regulated and 356 genes were down regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos both in intestines at 5 dpf and in kidneys at 7 dpf. To investigate how the transcriptome changes in the chd8 / zebrafish embryos the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. Overall design: Intestinal mRNA profiles of conventionally raisedCV and germ freeGF embryos at 5 dpf and renal the location of their hematopoietic tissue mRNA profiles of CV and GF embryos at 7 dpf. Analysis of mRNA profiles of intestines at 5 dpf and renal the location of their hematopoietic tissue at 7 dpf in chd8 / embryos and comparing the data with those from the wildtype embryos.		7d GF zebrafish rep1	GSM6038012	source name:kidney\|strain:AB\|tissue:kidney\|age:7 dpf free	7d GF zebrafish rep1	Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim galore version 0.6.7 for subsequent analysis with parameters phred33 q 20 length 15 stringency 3 fastqc max n 3 The processed datas have been mapped to Danio rerio.GRCz11 whole genome using STAR version 2.7.9a then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts T 6 t exon g gene id Assembly: GRCz11 Supplementary files format and content: Table with raw gene counts for every gene and every sample	kidney	30 CV and GF zebrafish at 5 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo and samples were storaged at 4℃ for more than 24h.Their intestines were collected by tweezers under the microscope and the isolated intestines was then transfered into Trizol.50 CV and GF zebrafish at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Their kidneys were collected as previously described as intestines.	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	The parent adult zebrafish are placed in pair mating tanks with dividers separating males and females the postnoon or evening prior to mating Day 1. At the start of the light cycle the following morning day x the parents were transferred to new clean pair mating tanks with autoclaved system water and allowed to mate for no more than 60 min. Fertilized eggs were seperated into two groupsCV group and GF group.The CV embryos were transfered to dishes with embryo media and incubated at 28.5℃. The GF embryos subsequently washed three times with the sterile embryo media SEM and transferred to a petri dish with the filter sterilized embryo medium containing antibiotics ABEM. Healthy embryos were sorted into fresh ABEM per 2 hours less than 200 per dish and incubated for 6 h at 28.5℃. The GF zebrafish embryos were then generated as previously described Pham Kanther et al. 2008. Briefly embryos were then washed at room temperature with 0.1% polyvinylpyrrolidone for 90s followed with three times rinsing with the SEM at room temperature. post soaking in 0.003% sodium hypochlorite for 16 min at room temperature these embryos were then washed for three times with the SEM. Finally the GF embryos were transferred into plastic cell culture flasks with SEM and incubated at 28.5℃.	strain:AB\|tissue:kidney\|age:7 dpf free	GSM6038012	GSM6038012: 7d GF zebrafish rep1; Danio rerio; RNA Seq	GSM6038012 r1	GSM6038012	1	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP369366	loader:fastq load.py\|options: concatPairFiles	7d_GF_1.fq.gz	fastq	5155842300.0	17186141.0	GSM6038012 r1	0:150 1:150	A:1336194101;C:1239856396;G:1253784751;T:1325279831;N:727221	150	150	1336194101	1239856396	1253784751	1325279831	727221	SRX14810877	SRS12567668			Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University	2	0.95926	0.95555	0.07118	0.06919	0.70001	0.70116	0.43654	0.43125	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-04-11	Larval	Larval	Kidney	Renal System
69463	69463	SRR18710066	SRX14810876	SRS12567667	SRP369366	PRJNA825466	The transcriptome profiling analysis of intestines and kidneys in conventionally raised CV and germ free GF wild type zebrafish embryos	GSE200577	Transcriptome Analysis	To investigate how the zebrafish embryos respond to the absence of the microbiota the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32 948 cDNAs of the zebrafish genome assembly were annotated post reads mapping for further analysis. For the 5 dpf intestinal tissue samples 948 genes 4% of the total number of genes were differentially expressed 371 genes were up regulated and 577 genes were down regulated in the GF group . For the 7 dpf kidney tissue samples 697 genes 3% of the total number of genes were differentially expressed 341 genes were up regulated and 356 genes were down regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos both in intestines at 5 dpf and in kidneys at 7 dpf. To investigate how the transcriptome changes in the chd8 / zebrafish embryos the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. Overall design: Intestinal mRNA profiles of conventionally raisedCV and germ freeGF embryos at 5 dpf and renal the location of their hematopoietic tissue mRNA profiles of CV and GF embryos at 7 dpf. Analysis of mRNA profiles of intestines at 5 dpf and renal the location of their hematopoietic tissue at 7 dpf in chd8 / embryos and comparing the data with those from the wildtype embryos.		7d CV zebrafish rep3	GSM6038011	source name:kidney\|strain:AB\|tissue:kidney\|age:7 dpf type	7d CV zebrafish rep3	Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim galore version 0.6.7 for subsequent analysis with parameters phred33 q 20 length 15 stringency 3 fastqc max n 3 The processed datas have been mapped to Danio rerio.GRCz11 whole genome using STAR version 2.7.9a then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts T 6 t exon g gene id Assembly: GRCz11 Supplementary files format and content: Table with raw gene counts for every gene and every sample	kidney	30 CV and GF zebrafish at 5 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo and samples were storaged at 4℃ for more than 24h.Their intestines were collected by tweezers under the microscope and the isolated intestines was then transfered into Trizol.50 CV and GF zebrafish at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Their kidneys were collected as previously described as intestines.	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	The parent adult zebrafish are placed in pair mating tanks with dividers separating males and females the postnoon or evening prior to mating Day 1. At the start of the light cycle the following morning day x the parents were transferred to new clean pair mating tanks with autoclaved system water and allowed to mate for no more than 60 min. Fertilized eggs were seperated into two groupsCV group and GF group.The CV embryos were transfered to dishes with embryo media and incubated at 28.5℃. The GF embryos subsequently washed three times with the sterile embryo media SEM and transferred to a petri dish with the filter sterilized embryo medium containing antibiotics ABEM. Healthy embryos were sorted into fresh ABEM per 2 hours less than 200 per dish and incubated for 6 h at 28.5℃. The GF zebrafish embryos were then generated as previously described Pham Kanther et al. 2008. Briefly embryos were then washed at room temperature with 0.1% polyvinylpyrrolidone for 90s followed with three times rinsing with the SEM at room temperature. post soaking in 0.003% sodium hypochlorite for 16 min at room temperature these embryos were then washed for three times with the SEM. Finally the GF embryos were transferred into plastic cell culture flasks with SEM and incubated at 28.5℃.	strain:AB\|tissue:kidney\|age:7 dpf type	GSM6038011	GSM6038011: 7d CV zebrafish rep3; Danio rerio; RNA Seq	GSM6038011 r1	GSM6038011	1	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP369366	loader:fastq load.py\|options: concatPairFiles	7d_CV_3.fq.gz	fastq	5141724000.0	17139080.0	GSM6038011 r1	0:150 1:150	A:1326004313;C:1239710760;G:1254841650;T:1320440570;N:726707	150	150	1326004313	1239710760	1254841650	1320440570	726707	SRX14810876	SRS12567667			Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University	2	0.95248	0.95498	0.06745	0.06581	0.70078	0.70214	0.46456	0.46536	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-04-11	Larval	Larval	Kidney	Renal System
69464	69464	SRR18710067	SRX14810875	SRS12567666	SRP369366	PRJNA825466	The transcriptome profiling analysis of intestines and kidneys in conventionally raised CV and germ free GF wild type zebrafish embryos	GSE200577	Transcriptome Analysis	To investigate how the zebrafish embryos respond to the absence of the microbiota the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32 948 cDNAs of the zebrafish genome assembly were annotated post reads mapping for further analysis. For the 5 dpf intestinal tissue samples 948 genes 4% of the total number of genes were differentially expressed 371 genes were up regulated and 577 genes were down regulated in the GF group . For the 7 dpf kidney tissue samples 697 genes 3% of the total number of genes were differentially expressed 341 genes were up regulated and 356 genes were down regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos both in intestines at 5 dpf and in kidneys at 7 dpf. To investigate how the transcriptome changes in the chd8 / zebrafish embryos the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. Overall design: Intestinal mRNA profiles of conventionally raisedCV and germ freeGF embryos at 5 dpf and renal the location of their hematopoietic tissue mRNA profiles of CV and GF embryos at 7 dpf. Analysis of mRNA profiles of intestines at 5 dpf and renal the location of their hematopoietic tissue at 7 dpf in chd8 / embryos and comparing the data with those from the wildtype embryos.		7d CV zebrafish rep2	GSM6038010	source name:kidney\|strain:AB\|tissue:kidney\|age:7 dpf type	7d CV zebrafish rep2	Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim galore version 0.6.7 for subsequent analysis with parameters phred33 q 20 length 15 stringency 3 fastqc max n 3 The processed datas have been mapped to Danio rerio.GRCz11 whole genome using STAR version 2.7.9a then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts T 6 t exon g gene id Assembly: GRCz11 Supplementary files format and content: Table with raw gene counts for every gene and every sample	kidney	30 CV and GF zebrafish at 5 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo and samples were storaged at 4℃ for more than 24h.Their intestines were collected by tweezers under the microscope and the isolated intestines was then transfered into Trizol.50 CV and GF zebrafish at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Their kidneys were collected as previously described as intestines.	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	The parent adult zebrafish are placed in pair mating tanks with dividers separating males and females the postnoon or evening prior to mating Day 1. At the start of the light cycle the following morning day x the parents were transferred to new clean pair mating tanks with autoclaved system water and allowed to mate for no more than 60 min. Fertilized eggs were seperated into two groupsCV group and GF group.The CV embryos were transfered to dishes with embryo media and incubated at 28.5℃. The GF embryos subsequently washed three times with the sterile embryo media SEM and transferred to a petri dish with the filter sterilized embryo medium containing antibiotics ABEM. Healthy embryos were sorted into fresh ABEM per 2 hours less than 200 per dish and incubated for 6 h at 28.5℃. The GF zebrafish embryos were then generated as previously described Pham Kanther et al. 2008. Briefly embryos were then washed at room temperature with 0.1% polyvinylpyrrolidone for 90s followed with three times rinsing with the SEM at room temperature. post soaking in 0.003% sodium hypochlorite for 16 min at room temperature these embryos were then washed for three times with the SEM. Finally the GF embryos were transferred into plastic cell culture flasks with SEM and incubated at 28.5℃.	strain:AB\|tissue:kidney\|age:7 dpf type	GSM6038010	GSM6038010: 7d CV zebrafish rep2; Danio rerio; RNA Seq	GSM6038010 r1	GSM6038010	1	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP369366		7d_CV_2.fq.gz	fastq	5661243900.0	18870813.0	GSM6038010 r1	0:150 1:150	A:1461910631;C:1369500371;G:1376299382;T:1453491360;N:42156	150	150	1461910631	1369500371	1376299382	1453491360	42156	SRX14810875	SRS12567666			Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University	2	0.96148	0.95899	0.06956	0.06718	0.7165	0.71683	0.46433	0.44486	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-04-11	Larval	Larval	Kidney	Renal System
69465	69465	SRR18710068	SRX14810874	SRS12567665	SRP369366	PRJNA825466	The transcriptome profiling analysis of intestines and kidneys in conventionally raised CV and germ free GF wild type zebrafish embryos	GSE200577	Transcriptome Analysis	To investigate how the zebrafish embryos respond to the absence of the microbiota the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32 948 cDNAs of the zebrafish genome assembly were annotated post reads mapping for further analysis. For the 5 dpf intestinal tissue samples 948 genes 4% of the total number of genes were differentially expressed 371 genes were up regulated and 577 genes were down regulated in the GF group . For the 7 dpf kidney tissue samples 697 genes 3% of the total number of genes were differentially expressed 341 genes were up regulated and 356 genes were down regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos both in intestines at 5 dpf and in kidneys at 7 dpf. To investigate how the transcriptome changes in the chd8 / zebrafish embryos the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. Overall design: Intestinal mRNA profiles of conventionally raisedCV and germ freeGF embryos at 5 dpf and renal the location of their hematopoietic tissue mRNA profiles of CV and GF embryos at 7 dpf. Analysis of mRNA profiles of intestines at 5 dpf and renal the location of their hematopoietic tissue at 7 dpf in chd8 / embryos and comparing the data with those from the wildtype embryos.		7d CV zebrafish rep1	GSM6038009	source name:kidney\|strain:AB\|tissue:kidney\|age:7 dpf type	7d CV zebrafish rep1	Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim galore version 0.6.7 for subsequent analysis with parameters phred33 q 20 length 15 stringency 3 fastqc max n 3 The processed datas have been mapped to Danio rerio.GRCz11 whole genome using STAR version 2.7.9a then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts T 6 t exon g gene id Assembly: GRCz11 Supplementary files format and content: Table with raw gene counts for every gene and every sample	kidney	30 CV and GF zebrafish at 5 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo and samples were storaged at 4℃ for more than 24h.Their intestines were collected by tweezers under the microscope and the isolated intestines was then transfered into Trizol.50 CV and GF zebrafish at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Their kidneys were collected as previously described as intestines.	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	The parent adult zebrafish are placed in pair mating tanks with dividers separating males and females the postnoon or evening prior to mating Day 1. At the start of the light cycle the following morning day x the parents were transferred to new clean pair mating tanks with autoclaved system water and allowed to mate for no more than 60 min. Fertilized eggs were seperated into two groupsCV group and GF group.The CV embryos were transfered to dishes with embryo media and incubated at 28.5℃. The GF embryos subsequently washed three times with the sterile embryo media SEM and transferred to a petri dish with the filter sterilized embryo medium containing antibiotics ABEM. Healthy embryos were sorted into fresh ABEM per 2 hours less than 200 per dish and incubated for 6 h at 28.5℃. The GF zebrafish embryos were then generated as previously described Pham Kanther et al. 2008. Briefly embryos were then washed at room temperature with 0.1% polyvinylpyrrolidone for 90s followed with three times rinsing with the SEM at room temperature. post soaking in 0.003% sodium hypochlorite for 16 min at room temperature these embryos were then washed for three times with the SEM. Finally the GF embryos were transferred into plastic cell culture flasks with SEM and incubated at 28.5℃.	strain:AB\|tissue:kidney\|age:7 dpf type	GSM6038009	GSM6038009: 7d CV zebrafish rep1; Danio rerio; RNA Seq	GSM6038009 r1	GSM6038009	1	Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP369366		7d_CV_1.fq.gz	fastq	5645537400.0	18818458.0	GSM6038009 r1	0:150 1:150	A:1445455143;C:1370729088;G:1387744819;T:1440941365;N:666985	150	150	1445455143	1370729088	1387744819	1440941365	666985	SRX14810874	SRS12567665			Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University	2	0.95837	0.95913	0.06057	0.05807	0.72267	0.7236	0.4382	0.44735	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-04-11	Larval	Larval	Kidney	Renal 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");;